General Info¶
The contacts to reach me can be found at this page.
Timetable and lecture rooms¶
Due to the current situation regarding the Covid-19 pandemic, Practicals will take place ONLINE this year. They will be held on Mondays from 14:30 to 16:30 and on Wednesdays from 11:30 to 13:30.
Practicals will use the Zoom platform (https://zoom.us/) and the link for the connection will be published on the practical page available in this site a few minutes before the start of the session.
This first part of the course will tentatively run from Wednesday, September 23rd, 2020 to Monday, November 2nd, 2020.
Moodle¶
In the moodle page of the course you can find announcements and videos of the lectures. It can be found here.
Zoom links¶
The zoom links for the practicals can be found in the Announcements section of the moodle web page.
Slides¶
Slides of the practicals will be available on the top part of each practical page.
Acknowledgements¶
I would like to thank Dr. David Leoni for all his help and for sharing Jupman with me. I would also like to thank Dr. Stefano Teso for allowing us to use some of his material of a previous course.
Practical 1¶
The aim of this practical is to set up a working Python3.x development environment and will start familiarizing a bit with Python.
Setting up the environment¶
We will need to install several pieces of software to get a working programming environment suitable for this practical. In this section we will install everything that we are going to need in the next few weeks.
Python3 is available for Windows, Linux and Mac, therefore you can run it on your preferred platform.
Note:
Altough for this course you will be fine with any operating system, my advice, if you are interested in pursuing a bioinformatics career, is to get familiar with Linux.
The following section explains how to install Linux on a windows machine. This is for your reference, you can read the following instructions before the next practical and try to instally Linux if you want to test it out.
Linux on windows¶
If your computer has Windows installed but you want to learn Linux you have several options to get it to run Linux:
This video tutorial (only in Italian) shows you how to set up a usb stick to run Linux from it: https://youtu.be/8_SK8iEMyJk
You can install a virtualization software like vmware player and download the .iso image of a linux distribution like ubuntu. and install/run it from vmware player. For more information you can look at this tutorial. Another option is to install virtual box.
Here you can find some VDI images that you can load in virtual box or in vmware player with several different operating systems including Linux distributions like Ubuntu, Debian, Centos, Fedora, etc. Please refer to this guide (for information on vmware please click on VM IMAGES –> VMware IMAGES in the menu of the page).
A dual boot system¶
You can also install Linux and Windows on the same machine and every time you boot your system up you can decide on which one of the two operating systems you want to use. Unlike the case described above in which Linux runs within Windows, in this case to switch from one operating system to the other you will always have to reboot the machine.
The installation of a dual boot system is easy, in principle, but there are a few things that you have to be careful on, like creating a partition of the hard disk on which you want to install Linux. If you make a mistake here you might end up losing Windows for example. My advice is to read carefully one of the following (or other guides) before attempting this:
Our toolbox¶
If you decide to work on Windows or Mac, you can safely skip the following information and go straight to the section “Installing Python3 in Windows/Mac”. Note that, regardless your operating system, a useful source of information on how to install python can be found here.
Installing Python3 in Linux¶
The Python interpreter. In this course we will use python version 3.x. A lot of information on python can be found on the python web page. Open a terminal and try typing in:
python3
if you get an error like “python3 command not found” you need to install it, while if you get something like this (note that the version might be different):
you are already sorted, just press Ctrl-D to exit.
Installation on a debian-like linux distribution (e.g. Ubuntu) can be done by typing the following commands on a terminal:
sudo apt-get update
sudo apt-get install python3
While if you are using Fedora you can use:
sudo dnf install python3
Install now the package manager pip, which is a very convenient tool to install python packages, with the following command (on Fedora, the command above should have already installed it):
sudo apt-get install python3-pipNote:
If pip is already installed in your system you will get a message like: python3-pip is already the newest version (3.x.y)
Finally, install the Integrated Development Environment (IDE) that we will be using. This is called Visual Studio Code and is available for all platforms. You can read about it here. Downloads for all platforms can be found here. On a debian-like distribution go to the folder where you downloaded the .deb package and type:
sudo dpkg -i code*.debWhile if you are using Fedora you can use:
sudo dnf install code*.rpm
Installing Python3 in Windows/Mac¶
Two options are available, please read them both CAREFULLY and then pick the one you are more comfortable with.
OPTION 1:¶
The python interpreter. In this course we will use python version 3.x. A lot of information on python can be found on the python web page. Installers for Windows and Mac can be downloaded from this page. Click on Download Python 3.8.x. PLEASE REFRAIN FROM DOUBLE-CLICKING ON THE INSTALLER LIKE THERE IS NO TOMORROW AND READ BELOW FIRST.
Attention! Important note
When executing the installer, please remember to tick the flag “Add Python 3.8.x to PATH” and then click on Install now (see picture below noting that the current version might differ from the picture).
OPTION 2 (easier):¶
Additional Information:
It is also possible to install python through the Anaconda package manager. You can install Visual Studio Code together with Anaconda(the Anaconda installer will ask if you want it, just say yes!).
Anaconda is available here
Upon launching the installer you should be prompted something like:
at the next step flag the correct items as in the figure below (i.e. Flag Register Anaconda as my Default Python 3.x):
When installation is complete, start anaconda through the Anaconda Navigator in the windows menu. When the navigator starts, you should see a screen similar to:
from which you can install Visual Studio Code as IDE (by clicking on Install).
For more information please have a look here.
The console¶
To access the console on Linux just open a terminal and type:
python3
while in Windows you have to look for “Python” and run “Python 3.x”. The console should look like this:
Now we are all set to start interacting with the Python interpreter. In the console, type the following instructions (i.e. the first line and then press ENTER):
[1]:
5 + 3
[1]:
8
All as expected. The “In [1]” line is the input, while the “Out [1]” reports the output of the interpreter. Let’s challenge python with some other operations:
[2]:
12 / 5
[2]:
2.4
[3]:
1/133
[3]:
0.007518796992481203
[4]:
2**1000
[4]:
10715086071862673209484250490600018105614048117055336074437503883703510511249361224931983788156958581275946729175531468251871452856923140435984577574698574803934567774824230985421074605062371141877954182153046474983581941267398767559165543946077062914571196477686542167660429831652624386837205668069376
And some assignments:
[5]:
a = 10
b = 7
s = a + b
d = a / b
print("sum is:",s, " division is:",d)
sum is: 17 division is: 1.4285714285714286
In the first four lines, values have been assigned to variables through the = operator. In the last line, the print function is used to display the output. For the time being, we will skip all the details and just notice that the print function somehow managed to get text and variables in input and coherently merged them in an output text. Although quite useful in some occasions, the console is quite limited therefore you can close it for now. To exit press Ctrl-D or type exit() and press ENTER.
Visual Studio Code¶
Once you open the IDE Visual Studio Code you will see the welcome screen:
You can find useful information on this tool here. Please spend some time having a look at that page. Once you are done with it you can close this window pressing on the “x”.
Attention! Important note
The following procedure is quite important and you will need to remember it to do the exams on the PCs of the lab.
The first thing to do is to set the python interpreter to use. Click on View –> Command Palette and type “Python” in the text search space. Select Python: Select Workspace Interpreter as shown in the picture below.
Finally, select the python version you want to use (e.g. Python3.x).
Now you can click on Open Folder to create a new folder to place all the scripts you are going to create. You can call it something like “exercises”. Next you can create a new file, example1.py (as you might have guessed the .py extension stands for python).
Visual Studio Code will understand that you are writing Python code and will help you writing valid syntax in your scripts.
Warning:
If you get the following error message:
click on Install Pylint which is a useful tool to help your coding experience.
Add the following text to your example1.py file.
[6]:
"""
This is the first example of Python script.
"""
a = 10 # variable a
b = 33 # variable b
c = a / b # variable c holds the ratio
# Let's print the result to screen.
print("a:", a, " b:", b, " a/b=", c)
a: 10 b: 33 a/b= 0.30303030303030304
A couple of things worth nothing: the first three lines opened and closed by “”” are some text describing the content of the script. Moreover, comments are proceeded by the hash key (#) and they are just ignored by the python interpreter.
Note
Good Pythonic code follows some syntactic rules on how to write things, naming conventions etc. The IDE will help you writing pythonic code even though we will not enforce this too much in this course. If you are interested in getting more details on this, you can have a look at the PEP8 Python Style Guide (Python Enanchement Proposals - index 8).
Warning
Please remember to comment your code, as it helps readability and will make your life easier when you have to modify or just understand the code you wrote some time in the past.
Please notice that Visual Studio Code will help you writing your Python scripts. For example, when you start writing the print line it will complete the code for you (if the Pylint extension mentioned above is installed), suggesting the functions that match the letters typed in. This useful feature is called code completion and, alongside suggesting possible matches, it also visualizes a description of the function and parameters it needs. Here is an example:
Save the file (Ctrl+S as shortcut). It is convenient to ask the IDE to highlight potential syntactic problems found in the code. You can toggle this function on/off by clicking on View –> Problems. The Problems panel should look like this
Visual Studio Code is warning us that the variable names a,b,c at lines 4,5,6 do not follow Python naming conventions for constants (do you understand why? Check here to find the answer). This warning is because they have been defined at the top level (there is no structure to our script yet) and therefore are interpreted as constants. The naming convention for constants states that they should be in capital letters. To amend the code, you can just replace all the names with the corresponding capitalized name (i.e. A,B,C). If you do that, and you save the file again (Ctrl+S), you will see all these problems disappearing as well as the green underlining of the variable names. If your code does not have an empty line before the end, you might get another warning “Final new line missing”.
Info
Note that these were just warnings and the interpreter in this case will happily and correctly execute the code anyway, but it is always good practice to understand what the warnings are telling us before deciding to ignore them!
Had we by mistake mispelled the print function name (something that should not happen with the code completion tool that suggests functions names!) writing printt (note the double t), upon saving the file, the IDE would have underlined in red the function name and flagged it up as a problem.
This is because the builtin function printt does not exist and the python interpreter does not know what to do when it reads it. Note that printt is actually underlined in red, meaning that there is an error which will cause the interpreter to stop the execution with a failure. Please remember ALL ERRORS MUST BE FIXED before running any piece of code.
Now it is time to execute the code. By right-clicking in the code panel and selecting Run Python File in Terminal (see picture below) you can execute the code you have just written.
Upon clicking on Run Python File in Terminal a terminal panel should pop up in the lower section of the coding panel and the result shown above should be reported.
Saving script files like the example1.py above is also handy because they can be invoked several times (later on we will learn how to get inputs from the command line to make them more useful…). To do so, you just need to call the python intepreter passing the script file as parameter. From the folder containing the example1.py script:
python3 example1.py
will in fact return:
a: 10 b: 33 a/b= 0.30303030303030304
Info: syntactic vs semantic errors
Before ending this section, let me add another note on errors. The IDE will diligently point you out syntactic warnings and errors (i.e. errors/warnings concerning the structure of the written code like name of functions, number and type of parameters, etc.) but it will not detect semantic or runtime errors (i.e. connected to the meaning of your code or to the value of your variables). These sort of errors will most probably make your code crash or may result in unexpected results/behaviours. In the next section we will introduce the debugger, which is a useful tool to help detecting these errors.
Before getting into that, consider the following lines of code (do not focus on the import line, this is only to load the mathematics module and use its method sqrt to compute the square root of its parameter):
[7]:
"""
Runtime error example, compute square root of numbers
"""
import math
A = 16
B = math.sqrt(A)
C = 5*B
print("A:", A, " B:", B, " C:", C)
D = math.sqrt(A-C) # whoops, A-C is now -4!!!
print(D)
A: 16 B: 4.0 C: 20.0
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-7-5d4ed1b10924> in <module>
9 print("A:", A, " B:", B, " C:", C)
10
---> 11 D = math.sqrt(A-C) # whoops, A-C is now -4!!!
12 print(D)
ValueError: math domain error
If you add that code to a python file (e.g. sqrt_example.py), you save it and you try to execute it, you should get an error message as reported above. You can see that the interpreter has happily printed off the vaule of A,B and C but then stumbled into an error at line 9 (math domain error) when trying to compute \(\sqrt{A-C} = \sqrt{-4}\), because the sqrt method of the math module cannot be applied to negative values (i.e. it works in the domain of real numbers).
Please take some time to familiarize with Visual Studio Code (creating files, saving files etc.) as in the next practicals we will take this ability for granted.
The debugger¶
Another important feature of advanced Integrated Development Environments (IDEs) is their debugging capabilities. Visual Studio Code comes with a debugging tool that can help you trace the execution of your code and understand where possible errors hide.
Write the following code on a new file (let’s call it integer_sum.py) and execute it to get the result.
[1]:
""" integer_sum.py is a script to
compute the sum of the first 1200 integers. """
S = 0
for i in range(0, 1201):
S = S + i
print("The sum of the first 1200 integers is: ", S)
The sum of the first 1200 integers is: 720600
Without getting into too many details, the code you just wrote starts initializing a variable S to zero, and then loops from 0 to 1200 assigning each time the value to a variable i, accumulating the sum of S + i in the variable S.
A final thing to notice is indentation.
Info
In Python it is important to indent the code properly as this provides the right scope for variables (e.g. see that the line S = S + 1 starts more to the right than the previous and following line – this is because it is inside the for loop). You do not have to worry about this for the time being, we will get to this in a later practical…
How does this code work? How does the value of S and i change as the code is executed? These are questions that can be answered by the debugger.
To start the debugger, click on Debug –> Start Debugging (shortcut F5). The following small panel should pop up:
We will use it shortly, but before that, let’s focus on what we want to track. On the left hand side of the main panel, a Watch panel appeared. This is where we need to add the things we want to monitor as the execution of the program goes. With respect to the code written above, we are interested in keeping an eye on the variables S, i and also of the expression S+i (that will give us the value of S of the next iteration). Add these three expressions in the watch panel (click on + to add new expressions). The watch panel should look like this:
do not worry about the message “name X is not defined”, this is normal as no execution has taken place yet and the interpreter still does not know the value of these expressions.
The final thing before starting to debug is to set some breakpoints, places where the execution will stop so that we can check the value of the watched expressions. This can be done by hovering with the mouse on the left of the line number. A small reddish dot should appear, place the mouse over the correct line (e.g. the line corresponding to S = S + 1 and click to add the breakpoint (a red dot should appear once you click).
Now we are ready to start debugging the code. Click on the green triangle on the small debug panel and you will see that the yellow arrow moved to the breakpoint and that the watch panel updated the value of all our expressions.
The value of all expressions is zero because the debugger stopped before executing the code specified at the breakpoint line (recall that S is initialized to 0 and that i will range from 0 to 1200). If you click again on the green arrow, execution will continue until the next breakpoint (we are in a for loop, so this will be again the same line - trust me for the time being).
Now i has been increased to 1, S is still 0 (remember that the execution stopped before executing the code at the breakpoint) and therefore S + i is now 1. Click one more time on the green arrow and values should update accordingly (i.e. S to 1, i to 2 and S + i to 3), another round of execution should update S to 3, i to 3 and S + i to 6. Got how this works? Variable i is increased by one each time, while S increases by i. You can go on for a few more iterations and see if this makes any sense to you, once you are done with debugging you can stop the execution by pressing the red square on the small debug panel.
Note
The debugger is very useful to understand what your program does. Please spend some time to understand how this works as being able to run the debugger properly is a good help to identify and solve semantic errors of your code.
Other editors are available, if you already have your favourite one you can stick to it. Some examples are:
Jupyter Notebook. Note: we might use it later on in the course.
A quick Jupyter primer (just for your information, skip if not interested)¶
Jupyter allows to write notebooks organized in cells (these can be saved in files with .ipynb extension). Notebooks contain both the code, some text describing the code and the output of the code execution, they are quite useful to produce some quick reports on data analysis. where there is both code, output of running that code and text. The code by default is Python, but can also support other languages like R). The text is formatted using the **Markdown language** - see cheatsheet for its details. Jupyter is becoming the de-facto standard for writing technical documentation.
Installation¶
To install it (if you have not installed python with Anaconda otherwise you should have it already):
python3 -m pip install jupyter
you can find more information here
Upon successful installation, you can run it with:
jupyter-notebook
This should fire up a browser on a page where you can start creating your notebooks or modifying existing ones. To create a new notebook you simply click on New:
and then you can start adding cells (i.e. containers of code and text). The type of each cell is specified by selecting the cell and selecting the right type in the dropdown list:
Cells can be executed by clicking on the Run button. This will get the code to execute (and output to be written) and text to be processed to provide the final page layout. To go back to the edit mode, just double click on an executed cell.
Please take some more time to familiarize with Visual Studio Code (creating files, saving files, interacting with the debugger etc.) as in the next practicals we will take this ability for granted. Once you are done you can move on and do the following exercises.
Exercises¶
The size of the Sars-Cov-2 genome is 29,811 base pairs. 8,903 of these bases are adenines. Write some python code to compute the percentage of the genome that is an adenine and print it.
Show/Hide Solution
Compute the area of a triangle having base 120 units (B) and height 33 (H). Assign the result to a variable named area and print it.
Show/Hide Solution
Compute the area of a square having side (S) equal to 145 units. Assign the result to a variable named area and print it.
Show/Hide Solution
Modify the program at point 2. to acquire the side S from the user at runtime. Hint: use the input function (details here) and remember to convert the acquired value into an int.
Show/Hide Solution
If you have not done so already, put the two previous scripts in two separate files (e.g. triangle_area.py and square_area.py and execute them from the terminal).
Write a small script (trapezoid.py) that computes the area of a trapezoid having major base (MB) equal to 30 units, minor base (mb) equal to 12 and height (H) equal to 17. Print the resulting area. Try executing the script from inside Visual Studio Code and from the terminal.
Show/Hide Solution
Rewrite the example of the sum of the first 1200 integers by using the following equation: \(\sum\limits_{i=1}^n i = \frac{n (n+1)}{2}\).
Show/Hide Solution
Modify the program at point 6. to make it acquire the number of integers to sum N from the user at runtime.
Show/Hide Solution
Write a small script to compute the length of the hypotenuse (c) of a right triangle having sides a=133 and b=72 units (see picture below). Hint: remember the Pythagorean theorem and use math.sqrt).
Show/Hide Solution
Rewrite the trapezoid script making it compute the area of the trapezoid starting from the major base (MB), minor base (mb) and height (H) taken in input. (Hint: use the input function and remember to convert the acquired value into an int).
Show/Hide Solution
Write a script that reads the side of an hexagon in input and computes its perimeter and area printing them to the screen. Hint: \(Area = \frac{3*\sqrt{3}*side^{2}}{2}\)
Show/Hide Solution
Practical 2¶
In this practical we will start interacting more with Python, practicing on how to handle data, functions and methods. We will see several built-in data types and then dive deeper into the data type string.
Modules¶
Python modules are simply text files having the extension .py (e.g. exercise.py). When you were writing the code in the IDE in the previous practical, you were in fact implementing a module.
As said in the previous practical, once you implemented and saved the code of the module, you can execute it by typing
python3 exercise1.py
(which in Windows might be python exercise1.py, just make sure you are using python 3.x) or, in Visual Studio Code, by right clicking on the code panel and selecting Run Python File in Terminal.
A Module A can be loaded from another module B so that B can use the functions defined in A. Remember when we used the sqrt function? It is defined in the module math. To import it and use it we indeed wrote something like:
[1]:
import math
A = math.sqrt(4)
print(A)
2.0
Note
When importing modules we do not need to specify the extension “.py” of the file.
Objects¶
Python understands very well objects, and in fact everything is an object in Python.
Objects have properties (characteristic features) and methods (things they can do). For example, an object car could be defined to have the properties model, make, color, number of doors, position etc., and the methods steer right, steer left, accelerate, break, stop, change gear, repaint,… whose application might affect the state of the object.
According to Python’s official documentation:
“Objects are Python’s abstraction for data. All data in a Python program is represented by objects or by relations between objects.”
All you need to know for now is that in Python objects have an identifier (ID) (i.e. their name), a type (numbers, text, collections,…) and a value (the actual data represented by the objects). Once an object has been created the identifier and the type never change, while its value can either change (mutable objects) or stay constant (immutable objects).
Python provides the following built-in data types:
We will stick with the simplest ones for now, but later on we will dive deeper into all of them.
Variables¶
Variables are just references to objects, in other words they are the name given to an object. Variables can be assigned to objects by using the assignment operator =.
The instruction
[2]:
sides = 4
might represent the number of sides of a square. What happens when we execute it in Python? An object is created, it is given an identifier, its type is set to “int” (an integer number), its value to 4 and a name sides is placed in the current namespace to point to that object, so that after that instruction we can access that object through its name. The type of an object can be accessed with the function type() and the identifier with the function id():
[3]:
sides = 4
print( type(sides) )
print( id(sides) )
<class 'int'>
10914592
Consider now the following code:
[4]:
sides = 4 #a square
print ("value:", sides, " type:", type(sides), " id:", id(sides))
sides = 5 #a pentagon
print ("value:", sides, " type:", type(sides), " id:", id(sides))
value: 4 type: <class 'int'> id: 10914592
value: 5 type: <class 'int'> id: 10914624
The value of the variable sides has been changed from 4 to 5, but as stated in the table above, the type int is immutable. Luckily, this did not prevent us to change the value of sides from 4 to 5. What happened behind the scenes when we executed the instruction sides = 5 is that a new object has been created of type int (5 is still an integer) and it has been made accessible with the same name sides, but since it is a different object (i.e. the integer 5). As a poof of this,
check that the that the identifier printed above is actually different.
Note: You do not have to really worry about what happens behind the scenes, as the Python interpreter will take care of these aspects for you, but it is nice to know what it does.
You can even change the type of a variable during execution but that is normally a bad idea as it makes understanding the code more complicated and leaves more room for errors.
Python allows you to do (but, please, REFRAIN FROM DOING SO!):
[5]:
sides = 4 #a square
print ("value:", sides, " type:", type(sides), " id:", id(sides))
sides = "four" #the sides in text format
print ("value:", sides, " type:", type(sides), " id:", id(sides))
value: 4 type: <class 'int'> id: 10914592
value: four type: <class 'str'> id: 140640184741312
IMPORTANT NOTE: You can choose the name that you like for your variables (I advise to pick something reminding their meaning), but you need to adhere to some simple rules.
Names can only contain upper/lower case digits (
A-Z,a-z), numbers (0-9) or underscores_;Names cannot start with a number;
Names cannot be equal to reserved keywords:
Numeric types¶
We already mentioned that numbers are immutable objects. Python provides different numeric types: integers, booleans, reals (floats) and even complex numbers and fractions (but we will not get into those).
Integers¶
Their range of values is limited only by the memory available. As we have already seen, python provides also a set of standard operators to work with numbers:
[6]:
a = 7
b = 4
print(a + b) # 11
print(a - b) # 3
print(a // b) # integer division: 1
print(a * b) # 28
print(a ** b) # power: 2401
print(a / b) # division 1.75
print(type(a / b))
11
3
1
28
2401
1.75
<class 'float'>
Note that in the latter case the result is no more an integer, but a float (we will get to that later).
Booleans¶
These objects are used for the boolean algebra. Truth values are represented with the keywords True and False in Python. A boolean object can only have value True or False. We can convert booleans into integers with the builtin function int. Any integer can be converted into a boolean (and vice-versa) with:
[7]:
a = bool(1)
b = bool(0)
c = bool(72)
d = bool(-5)
t = int(True)
f = int(False)
print("a: ", a, " b: ", b, " c: ", c, " d: ", d , " t: ", t, " f: ", f)
a: True b: False c: True d: True t: 1 f: 0
any integer is evaluated to true, except 0. Note that, the truth values True and False respectively behave like the integers 1 and 0.
We can operate on boolean values with the boolean operators and, or, not. Recall boolean algebra for their use:
[8]:
T = True
F = False
print ("T: ", T, " F:", F)
print ("T and F: ", T and F) #False
print ("T and T: ", T and T) #True
print ("F and F: ", F and F) #False
print ("not T: ", not T) # False
print ("not F: ", not F) # True
print ("T or F: ", T or F) # True
print ("T or T: ", T or T) # True
print ("F or F: ", F or F) # False
T: True F: False
T and F: False
T and T: True
F and F: False
not T: False
not F: True
T or F: True
T or T: True
F or F: False
Numeric comparators are operators that return a boolean value. Here are some examples:
Example: Given a variable a = 10 and a variable b = 77, let’s swap their values (i.e. at the end a will be equal to 77 and b to 10). Let’s also check the values at the beginning and at the end.
[9]:
a = 10
b = 77
print("a: ", a, " b:", b)
print("is a equal to 10?", a == 10)
print("is b equal to 77?", b == 77)
TMP = b #we need to store the value of b safely
b = a #ok, the old value of b is gone... is it?
a = TMP #a gets the old value of b... :-)
print("a: ", a, " b:", b)
print("is a equal to 10?", a == 10)
print("is a equal to 77?", a == 77)
print("is b equal to 10?", b == 10)
print("is b equal to 77?", b == 77)
a: 10 b: 77
is a equal to 10? True
is b equal to 77? True
a: 77 b: 10
is a equal to 10? False
is a equal to 77? True
is b equal to 10? True
is b equal to 77? False
Real numbers¶
Python stores real numbers (floating point numbers) in 64 bits of information divided in sign, exponent and mantissa.
Example: Let’s calculate the area of the center circle of a football pitch (radius = 9.15m) recalling that \(area= \Pi*R^2\):
[10]:
R = 9.15
Pi = 3.141592653589793
Area = Pi*(R**2)
print (Area)
263.02199094017146
Note that the builtin math module of python contains the definition of \(\Pi\), therefore we could rewrite the code above as:
[11]:
import math
R = 9.15
Pi = math.pi
Area = Pi*(R**2)
print (Area)
263.02199094017146
Note that the parenthesis around the R**2 are not necessary as the operator ** has the precedence, but I personally think it helps readability.
Here is a reminder of the precedence of operators:
Example: Let’s compute the GC content of a DNA sequence 33 base pairs long, having 12 As, 9 Ts, 5 Cs and 7Gs. The GC content can be expressed by the formula: \(gc = \frac{G+C}{A+T+C+G}\) where A,T,C,G represent the number of nucleotides of each kind. What is the AT content? Is the GC content higher than the AT content?
[12]:
A = 12
T = 9
C = 5
G = 7
gc = (G+C)/(A+T+C+G)
print("The GC content is: ", gc)
at = 1 - gc
print("The AT content is: ", at)
print (gc > at)
The GC content is: 0.36363636363636365
The AT content is: 0.6363636363636364
False
Strings¶
Strings are immutable objects (note the actual type is str) used by python to handle text data. Strings are sequences of unicode code points that can represent characters, but also formatting information (e.g. ‘\n’ for new line). Unlike other programming languages, python does not have the data type character, which is represented as a string of length 1.
There are several ways to define a string:
[13]:
S = "my first string, in double quotes"
S1 = 'my second string, in single quotes'
S2 = '''my third string is
in triple quotes
therefore it can span several lines'''
S3 = """my fourth string, in triple double-quotes
can also span
several lines"""
print(S, '\n') #let's add a new line at the end of the string with \n
print(S1,'\n')
print(S2, '\n')
print(S3, '\n')
my first string, in double quotes
my second string, in single quotes
my third string is
in triple quotes
therefore it can span several lines
my fourth string, in triple double-quotes
can also span
several lines
To put special characters like ‘,” and so on you need to “escape them” (i.e. write them following a back-slash).
Example: Let’s print a string containing a quote and double quote (i.e. ‘ and “).
[14]:
myString = "This is how I \'quote\' and \"double quote\" things in strings"
print(myString)
This is how I 'quote' and "double quote" things in strings
Strings can be converted to and from numbers with the functions str(), int() or float().
Example: Let’s define a string myString with the value “47001” and convert it into an int. Try adding one and print the result.
[15]:
my_string = "47001"
print(my_string, " has type ", type(my_string))
my_int = int(my_string)
print(my_int, " has type ", type(my_int))
my_int = my_int + 1 #adds one
my_string = my_string + "1" #cannot add 1 (we need to use a string).
#This will append 1 at the end of the string
print(my_int)
print(my_string)
47001 has type <class 'str'>
47001 has type <class 'int'>
47002
470011
Be careful though that if the string cannot be converted into an integer, then you get an error
[16]:
my_wrong_number = "13a"
N = int(my_wrong_number)
print(N)
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-16-bcfe98c1ea66> in <module>
1 my_wrong_number = "13a"
2
----> 3 N = int(my_wrong_number)
4
5 print(N)
ValueError: invalid literal for int() with base 10: '13a'
Python defines some operators to work with strings. Recall the slides shown during the lecture:
Example A tandem repeat is a short sequence of DNA that is repeated several times in a row. Let’s create a string representing the tandem repeat of the motif “ATTCG” repeated 5 times. What is the length of the whole repetitive region? Is the motif “TCGAT” (m1) present in the region? The motif “TCCT” (m2)? Let’s give an orientation to the tandem repeat by adding the string “5’-” (5’ end) on the left and “-3’” (3’ end) to the right.
[17]:
motif = "ATTCG"
tandem_repeat = motif * 5
print(motif)
print(tandem_repeat, " has length", len(tandem_repeat))
m1 = "TCGAT"
m2 = "TCCT"
print("Is ", m1, " in ", tandem_repeat, " ? ", m1 in tandem_repeat )
print("Is ", m2, " in ", tandem_repeat, " ? ", m2 in tandem_repeat )
oriented_tr = "5\'-" + tandem_repeat + "-3\'"
print(oriented_tr)
ATTCG
ATTCGATTCGATTCGATTCGATTCG has length 25
Is TCGAT in ATTCGATTCGATTCGATTCGATTCG ? True
Is TCCT in ATTCGATTCGATTCGATTCGATTCG ? False
5'-ATTCGATTCGATTCGATTCGATTCG-3'
We can access strings at specific positions (indexing) or get a substring starting from a position S to a position E. The only thing to remember is that numbering starts from 0. Thei-th character of a string can be accessed as str[i-1]. Substrings can be accessed as str[S:E], optionally a third parameter can be specified to set the step (i.e. str[S:E:STEP]).
Important note. Remember that when you do str[S:E], S is inclusive, while E is exclusive (see S[0:6] below).
Let’s see these aspects in action with an example:
[18]:
S = "Luther College"
print(S) #print the whole string
print(S == S[:]) #a fancy way of making a copy of the original string
print(S[0]) #first character
print(S[3]) #fourth character
print(S[-1]) #last character
print(S[0:6]) #first six characters
print(S[-7:]) #final seven characters
print(S[0:len(S):2]) #every other character starting from the first
print(S[1:len(S):2]) #every other character starting from the second
Luther College
True
L
h
e
Luther
College
Lte olg
uhrClee
Methods for the str object¶
The object str has some methods that can be applied to it (remember methods are things you can do on objects). Recall from the lecture that the main methods are:
IMPORTANT NOTE: Since Strings are immutable, every operation that changes the string actually produces a new str object having the modified string as value.
Moreover, since strings are immutable we cannot directly change them with an assignment operator.
Example: Since the genetic code is degenerate, there are many codons encoding for the same aminoacid. Consider Proline, it can be encoded by the following codons: CCU, CCA,CCG, CCC. Let’s create a string proline and assign it to its possible codons one after the other.
[19]:
"""
Wrong solution. We cannot directly replace the value of a string
"""
proline = "CCU"
print("Proline can be encoded by: ", proline)
proline[2]="A"
print(".. or by: ", proline)
Proline can be encoded by: CCU
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-19-9750dcfa1cbd> in <module>
5 proline = "CCU"
6 print("Proline can be encoded by: ", proline)
----> 7 proline[2]="A"
8 print(".. or by: ", proline)
9
TypeError: 'str' object does not support item assignment
[20]:
"""
Correct solution. Using str.replace
"""
proline = "CCU"
print("Proline can be encoded by: ", proline)
proline = proline.replace("U","A")
print(".. or by: ", proline)
proline = proline.replace("A","G")
print(".. or by: ", proline)
proline = proline.replace("G","C")
print(".. or by: ", proline)
Proline can be encoded by: CCU
.. or by: CCA
.. or by: CCG
.. or by: CCC
[21]:
"""
Another correct solution. Using string slicing and catenation.
"""
proline = "CCU"
print("Proline can be encoded by: ", proline)
proline = proline[:-1]+"A" #equal to proline[0:-1] or proline[0:2]
print(".. or by: ", proline)
proline = proline[:-1]+"G"
print(".. or by: ", proline)
proline = proline[:-1]+"C"
print(".. or by: ", proline)
Proline can be encoded by: CCU
.. or by: CCA
.. or by: CCG
.. or by: CCC
Example: Given the DNA sequence S = ” aTATGCCCATatcgctAAATTGCTGCCATTACA “. Print its length (removing any blank spaces at either sides), the number of adenines, cytosines, guanines and thymines present. Is the sequence “ATCG” present in S? Print how many times the substring “TGCC” appears in S and all the corresponding indexes.
[22]:
S = " aTATGCCCATatcgctAAATTGCTGCCATTACA "
print(S)
S = S.strip(" ")
print(S)
print(len(S))
tmp_s = S.upper() #for simplicity to count only 4 different nucleotides
print("A count: ", tmp_s.count("A"))
print("C count: ", tmp_s.count("C"))
print("T count: ", tmp_s.count("T"))
print("G count: ", tmp_s.count("G"))
print("Is ATCG in ", tmp_s, "? ", tmp_s.find("ATCG") != -1) #or tmp_s.count("ATCG") > 0
print("TGCC is present ", tmp_s.count("TGCC"), " times in ", tmp_s)
print("TGCC is present at pos ", tmp_s.find("TGCC"))
print("TGCC is present at pos ", tmp_s.rfind("TGCC")) #or tmp_S.find("TGCC",4)
aTATGCCCATatcgctAAATTGCTGCCATTACA
aTATGCCCATatcgctAAATTGCTGCCATTACA
33
A count: 10
C count: 9
T count: 10
G count: 4
Is ATCG in ATATGCCCATATCGCTAAATTGCTGCCATTACA ? True
TGCC is present 2 times in ATATGCCCATATCGCTAAATTGCTGCCATTACA
TGCC is present at pos 3
TGCC is present at pos 23
Exercises¶
Given the following string on two lines:
text = """Nobody said it was easy
No one ever said it would be this hard"""
write some python code that a)prints the whole string; b) prints the first and last character; c) prints the first 10 characters; d) prints from the 19th character to the 31st; e) prints the string all in capital letters.
Show/Hide Solution
An exon of a gene starts from position 12030 on a genome and ends at position 12174. Does an A/T SNP present at position 12111 affect this exon (i.e. is it inside the exon)? And what about a SNP present at position 12188? Hint: create a suitable boolean expression to check if the positions are within the interval of the exon.
Show/Hide Solution
SNP FB_AFFY_0000024 of the Apple 480K SNP chip has 5’ flanking region (i.e. the forward probe) CATTATTTTCACTTGGGTCGAGGCCAGATTCCATC and 3’ flanking region (i.e. the reverse probe) GGATTGCCCGAAATCAGAGAAAAGTCG. The SNP is a G/A transversion. Answer the following questions:
What is the length of the 5’ flanking region? And that of the 3’ flanking region?
The IUPAC code of the G/A transversion is R. What is the sequence of the whole region using the “[G/A]” notation for the SNP (hint: concatenate it in a new string called region) and the iupac notation R (region_iupac)?
Retrive and print only the SNP from region and iupac_region
Show/Hide Solution
Compute the melting temperature \(T_m\) of the primer with sequence “TTAGCACACGTGAGCCAATGGAGCAAACGGGTAATT”. The melting temperature \(T_m\) (in degrees Celtius) can be computed as: \(T_m = 64.9 + 41(GC - 16.4)/N\), where \(GC\) is the total number of G and C in the primer and \(N\) is its length.
Show/Hide Solution
The spike protein of the Sars-CoV-2 virus has the following aminoacidic sequence:
S = """ MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFS NVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIV NNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLE GKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQT LLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETK CTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISN CVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIAD YNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPC NGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVN FNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITP GTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSY ECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTI SVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQE VFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDC LGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAM QMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALN TLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA SANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPA ICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP LQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDL QELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDD SEPVLKGVKLHYT """
Write a little python script to answer the following questions: 1) What are the first 10 and the last 10 aminoacids? 2) How many aminoacids does it have (beware of new lines)? 3) How many Tyrosines (T) does it contain? 4) How many Triptophanes (W)? 5) How many Valines (V) followed by at least one Lysine (K)?
Show/Hide Solution
Convert the following extract of the PalB2 gene into mRNA (i.e. replace thymine with uracile):
seq ="""CTGTCTCCCTCACTGTATGTAAATTGCATCTAGAATAGCA
TCTGGAGCACTAATTGACACATAGTGGGTATCAATTATTA
TTCCAGGTACTAGAGATACCTGGACCATTAACGGATAAAT
AGAAGATTCATTTGTTGAGTGACTGAGGATGGCAGTTCCT
GCTACCTTCAAGGATCTGGATGATGGGGAGAAACAGAGAA
CATAGTGTGAGAATACTGTGGTAAGGAAAGTACAGAGGAC
TGGTAGAGTGTCTAACCTAGATTTGGAGAAGGACCTAGAA
GTCTATCCCAGGGAAATAAAAATCTAAGCTAAGGTTTGAG
GAATCAGTAGGAATTGGCAAAGGAAGGACATGTTCCAGAT
GATAGGAACAGGTTATGCAAAGATCCTGAAATGGTCAGAG
CTTGGTGCTTTTTGAGAACCAAAAGTAGATTGTTATGGAC
CAGTGCTACTCCCTGCCTCTTGCCAAGGGACCCCGCCAAG
CACTGCATCCCTTCCCTCTGACTCCACCTTTCCACTTGCC
CAGTATTGTTGGTGT"""
and print the number of uracils present and the total length of the sequence (remember to remove newlines).
Considering the genetic code and all the possible open reading frames, answer the following questions:
How many stop codons are present in the sequence?
How many Glycines (Gly)?
Is Tryptophane (Trp) present?
What is the position of the leftmost Trp? Print the codon to double check correctness (hint: slicing).
What is the position of the rightmost Trp? Print the codon to double check correctness (hint: slicing).
Show/Hide Solution
Consider the following Illumina HiSeq 4000 read:
read = """AATGATACGGCGACCACCGAGATCTACACGCCTCCCTCGCGC
CATCAGAGAGTCTGGGTCTCAGGTACCGCAGTTGTATCTTGCGCGACTATA
ATCCACGGCTCTTATTCTAGCGTGCGCGTACGGCGGTGGGCGTCGTTACGCTATATT"""
and try to answer the following questions:
1. How long is the read (beware of newlines)?
2. What is the GC content of the read (remember $gc = \frac{G+C}{A+T+C+G}$)?
3. A Nextera adapter is "AATGATACGGCGACCACCGAGATCTACACGCCTCCCTCGCGCCATCAG".
Is it present in the read? How long is it?
4. Remove the Nextera adapter from the read and recompute the GC content.
Has GC content increased after adapter trimmming?
Show/Hide Solution
Given geneA starting at position 1000 and ending at position 3400, and geneB starting at position 3700 and ending at position 6000. Randomly select a position (pos) from 1 to 5202 and check the following: a. is pos in geneA? b. is pos in geneB? c. is pos in between the two genes? d. is pos within one of the two genes? e. is pos outside both genes? f. is pos within 100 bases before the start of geneA? To pick a random number you can import the random module and use the random.randint(start,end) function:
import randompos = random.randint(1,6000)
Show/Hide Solution
The DNA-binding domain of the Tumor Suppressor Protein TP53 can be represented by the string:
chain_a = """SSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKM
FCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVV
RRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFR
HSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILT
IITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKG
EPHHELPPGSTKRALPNNT"""
Answer the following questions:
1. How many lines is the sequence written on?
2. How long is the sequence (remove newlines)?
3. Create a new sequence with all new lines removed
4. How many cysteines "C" and histidines "H" are there in the sequence?
5. Does the chain contain the sub-sequence "NLRVEYLDDRN"? Where?
6. Extract the first line of the sequence (Hint: use find and string slicing).
Show/Hide Solution
Calculate the zeros of the equation \(ax^2-b = 0\) where a = 10 and b = 1. Hint: use math.sqrt or ** 0.5. Finally check that substituting the obtained value of x in the equation gives zero.
Show/Hide Solution
Practical 3¶
In this practical we will work with lists and tuples.
Lists¶
Python lists are ordered collections of (homogeneous) objects, but they can hold also non-homogeneous data. List are mutable objects. Elements of the collection are specified within two square brackets [] and are comma separated.
We can use the function print to print the content of lists. Some examples of list definitions follow:
[1]:
my_first_list = [1,2,3]
print("first:" , my_first_list)
my_second_list = [1,2,3,1,3] #elements can appear several times
print("second: ", my_second_list)
fruits = ["apple", "pear", "peach", "strawberry", "cherry"] #elements can be strings
print("fruits:", fruits)
an_empty_list = []
print("empty:" , an_empty_list)
another_empty_list = list()
print("another empty:", another_empty_list)
a_list_containing_other_lists = [[1,2], [3,4,5,6]] #elements can be other lists
print("list of lists:", a_list_containing_other_lists)
my_final_example = [my_first_list, a_list_containing_other_lists]
print("a list of lists of lists:", my_final_example)
first: [1, 2, 3]
second: [1, 2, 3, 1, 3]
fruits: ['apple', 'pear', 'peach', 'strawberry', 'cherry']
empty: []
another empty: []
list of lists: [[1, 2], [3, 4, 5, 6]]
a list of lists of lists: [[1, 2, 3], [[1, 2], [3, 4, 5, 6]]]
Operators for lists¶
Python provides several operators to handle lists. The following operators behave like on strings (remember that, as in strings, the first position is 0!):
While this in operator requires that the whole tested obj is present in the list
and
can also change the corresponding value of the list (lists are mutable objects).
Let’s see some examples.
[2]:
A = [1, 2, 3 ]
B = [1, 2, 3, 1, 2]
print("A is a ", type(A))
print(A, " has length: ", len(A))
print("A[0]: ", A[0], " A[1]:", A[1], " A[-1]:", A[-1])
print(B, " has length: ", len(B))
print("Is A equal to B?", A == B)
C = A + [1, 2]
print(C)
print("Is C equal to B?", B == C) #same content
print("Is C the same object as B?", B is C) #different objects
D = [1, 2, 3]*8
print(D)
E = D[12:18] #slicing
print(E)
print("Is A*2 equal to E?", A*2 == E)
A is a <class 'list'>
[1, 2, 3] has length: 3
A[0]: 1 A[1]: 2 A[-1]: 3
[1, 2, 3, 1, 2] has length: 5
Is A equal to B? False
[1, 2, 3, 1, 2]
Is C equal to B? True
Is C the same object as B? False
[1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3]
[1, 2, 3, 1, 2, 3]
Is A*2 equal to E? True
[3]:
A = [1, 2, 3, 4, 5, 6]
B = [1, 3, 5]
print("A:", A)
print("B:", B)
print("Is B in A?", B in A)
print("A\'s ID:", id(A))
A[5] = [1,3,5] #we can add elements
print(A)
print("A\'s ID:", id(A)) #same as before! why?
print("A has length:", len(A))
print("Is now B in A?", B in A)
A: [1, 2, 3, 4, 5, 6]
B: [1, 3, 5]
Is B in A? False
A's ID: 139779855942920
[1, 2, 3, 4, 5, [1, 3, 5]]
A's ID: 139779855942920
A has length: 6
Is now B in A? True
Note: When indexing, do not exceed the list boundaries (or you will be prompted a list index out of range error).
Consider the following example:
[4]:
A = [1, 2, 3, 4, 5, 6]
print("A has length:", len(A))
print("First element:", A[0])
print("7th-element: ", A[6])
A has length: 6
First element: 1
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
<ipython-input-4-699e5f04cae0> in <module>
3
4 print("First element:", A[0])
----> 5 print("7th-element: ", A[6])
IndexError: list index out of range
It is actually fine to exceed boundaries with slicing instead:
[5]:
A = [1, 2, 3, 4, 5, 6]
print("A has length:", len(A))
print("First element:", A[0])
print("last element: ", A[-1])
print("3rd to 10th: ", A[2:10])
print("8th to 11th:", A[7:11])
A has length: 6
First element: 1
last element: 6
3rd to 10th: [3, 4, 5, 6]
8th to 11th: []
Example: Consider the matrix \(M = \begin{bmatrix}1 & 2 & 3\\ 1 & 2 & 1\\ 1 & 1 & 3\end{bmatrix}\) and the vector \(v=[10, 5, 10]^T\). What is the matrix-vector product \(M*v\)?
\[\begin{split}\begin{bmatrix}1 & 2 & 3\\ 1 & 2 & 1\\ 1 & 1 & 3\end{bmatrix}*[10,5,10]^T = [50, 30, 45]^T\end{split}\]
[6]:
M = [[1, 2, 3], [1, 2, 1], [1, 1, 3]]
v = [10, 5, 10]
prod = [0, 0 ,0] #at the beginning the product is the null vector
prod[0]=M[0][0]*v[0] + M[0][1]*v[1] + M[0][2]*v[2]
prod[1]=M[1][0]*v[0] + M[1][1]*v[1] + M[1][2]*v[2]
prod[2]=M[2][0]*v[0] + M[2][1]*v[1] + M[2][2]*v[2]
print("M: ", M)
print("v: ", v)
print("M*v: ", prod)
M: [[1, 2, 3], [1, 2, 1], [1, 1, 3]]
v: [10, 5, 10]
M*v: [50, 30, 45]
Methods of the class list¶
The class list has some methods that can be used to operate on it. Recall from the lecture the following methods:
Note: Lists are mutable objects and therefore virtually all the previous methods (except count) do not have an output value, but they modify the list.
Some usage examples follow:
[7]:
#A numeric list
A = [1, 2, 3]
print(A)
print("A has id:", id(A))
A.append(72) #appends one and only one object
print(A)
print("A has id:", id(A))
A.extend([1, 5, 124, 99]) #adds all these objects, one after the other.
print(A)
A.reverse() #NOTE: NO RETURN VALUE!!!
print(A)
A.sort()
print(A)
print("Min value: ", A[0]) # In this simple case, could have used min(A)
print("Max value: ", A[-1]) #In this simple case, could have used max(A)
print("Number 1 appears:", A.count(1), " times")
print("While number 837: ", A.count(837))
print("\nDone with numbers, let's go strings...\n")
#A string list
fruits = ["apple", "banana", "pineapple", "cherry","pear", "almond", "orange"]
#Let's get a reverse lexicographic order:
print(fruits)
fruits.sort()
fruits.reverse() # equivalent to: fruits.sort(reverse=True)
print(fruits)
fruits.remove("banana")
print(fruits)
fruits.insert(5, "wild apple") #put wild apple after apple.
print(fruits)
print("\nSorted fruits:")
fruits.sort() # does not return anything. Modifies list!
print(fruits)
[1, 2, 3]
A has id: 139779846805128
[1, 2, 3, 72]
A has id: 139779846805128
[1, 2, 3, 72, 1, 5, 124, 99]
[99, 124, 5, 1, 72, 3, 2, 1]
[1, 1, 2, 3, 5, 72, 99, 124]
Min value: 1
Max value: 124
Number 1 appears: 2 times
While number 837: 0
Done with numbers, let's go strings...
['apple', 'banana', 'pineapple', 'cherry', 'pear', 'almond', 'orange']
['pineapple', 'pear', 'orange', 'cherry', 'banana', 'apple', 'almond']
['pineapple', 'pear', 'orange', 'cherry', 'apple', 'almond']
['pineapple', 'pear', 'orange', 'cherry', 'apple', 'wild apple', 'almond']
Sorted fruits:
['almond', 'apple', 'cherry', 'orange', 'pear', 'pineapple', 'wild apple']
An important thing to remember that we mentioned already a couple of times is that lists are mutable objects and therefore virtually all the previous methods (except count) do not have an output value:
[8]:
A = ["A", "B", "C"]
print("A:", A)
A_new = A.append("D")
print("A:", A)
print("A_new:", A_new)
#A_new is None. We cannot apply methods to it...
print(A_new is None)
print("A_new has " , A_new.count("D"), " Ds")
A: ['A', 'B', 'C']
A: ['A', 'B', 'C', 'D']
A_new: None
True
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
<ipython-input-8-114913bce16b> in <module>
11 #A_new is None. We cannot apply methods to it...
12 print(A_new is None)
---> 13 print("A_new has " , A_new.count("D"), " Ds")
AttributeError: 'NoneType' object has no attribute 'count'
Some things to remember
append and extend work quite differently:
[ ]:
A = [1, 2, 3]
A.extend([4, 5])
print(A)
B = [1, 2, 3]
B.append([4,5])
print(B)
To remove an object it must exist:
[ ]:
A = [1,2,3, [[4],[5,6]], 8]
print(A)
A.remove(2)
print(A)
A.remove([[4],[5,6]])
print(A)
A.remove(7)
To sort a list, its elements must be sortable (i.e. homogeneous)!
[9]:
A = [4,3, 1,7, 2]
print("A:", A)
A.sort()
print("A sorted:", A)
A.append("banana")
print("A:", A)
A.sort()
print("A:", A)
A: [4, 3, 1, 7, 2]
A sorted: [1, 2, 3, 4, 7]
A: [1, 2, 3, 4, 7, 'banana']
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-9-b37960bcb6f2> in <module>
5 A.append("banana")
6 print("A:", A)
----> 7 A.sort()
8 print("A:", A)
TypeError: '<' not supported between instances of 'str' and 'int'
Important to remember:
Lists are mutable objects and this has some consequences! Since lists are mutable objects, they hold references to objects rather than objects.
Take a look at the following examples:
[10]:
l1 = [1, 2]
l2 = [4, 3]
LL = [l1, l2]
print("l1:", l1)
print("l2:",l2)
print("LL:", LL)
l1.append(7)
print("\nAppending 7 to l1...")
print("l1:", l1)
print("LL now: ", LL)
LL[0][1] = -1
print("\nSetting LL[0][1]=-1...")
print("LL now:" , LL)
print("l1 now", l1)
#but the list can point also to a different object,
#without affecting the original list.
LL[0] = 100
print("\nSetting LL[0] = 100")
print("LL now:", LL)
print("l1 now", l1)
l1: [1, 2]
l2: [4, 3]
LL: [[1, 2], [4, 3]]
Appending 7 to l1...
l1: [1, 2, 7]
LL now: [[1, 2, 7], [4, 3]]
Setting LL[0][1]=-1...
LL now: [[1, -1, 7], [4, 3]]
l1 now [1, -1, 7]
Setting LL[0] = 100
LL now: [100, [4, 3]]
l1 now [1, -1, 7]
Making copies
There are several ways to copy a list into another. Let’s see the difference between = and [:]. Note what happens when lists get complicated.
[11]:
A = ["hi", "there"]
B = A
print("A:", A)
print("B:", B)
A.extend(["from", "python"])
print("A now: ", A)
print("B now: ", B)
print("\n---- copy example -------")
#Let's make a distinct copy of A.
C = A[:] #all the elements of A have been copied in C
print("C:", C)
A[3] = "java"
print("A now:", A)
print("C now:", C)
print("\n---- be careful though -------")
#Watch out though that this is a shallow copy...
D = [A, A]
E = D[:]
print("D:", D)
print("E:", E)
D[0][0] = "hello"
print("\nD now:", D)
print("E now:", E)
print("A now:", A)
A: ['hi', 'there']
B: ['hi', 'there']
A now: ['hi', 'there', 'from', 'python']
B now: ['hi', 'there', 'from', 'python']
---- copy example -------
C: ['hi', 'there', 'from', 'python']
A now: ['hi', 'there', 'from', 'java']
C now: ['hi', 'there', 'from', 'python']
---- be careful though -------
D: [['hi', 'there', 'from', 'java'], ['hi', 'there', 'from', 'java']]
E: [['hi', 'there', 'from', 'java'], ['hi', 'there', 'from', 'java']]
D now: [['hello', 'there', 'from', 'java'], ['hello', 'there', 'from', 'java']]
E now: [['hello', 'there', 'from', 'java'], ['hello', 'there', 'from', 'java']]
A now: ['hello', 'there', 'from', 'java']
Equality and identity
Two different operators exist to check the equality of two lists (==) and the identity of two lists (is).
[12]:
A = [1, 2, 3]
B = A
C = [1, 2, 3]
print("Is A equal to B?", A == B)
print("Is A actually B?", A is B)
print("Is A equal to C?", A == C)
print("Is A actually C?", A is C)
#in fact:
print("\nA's id:", id(A))
print("B's id:", id(B))
print("C's id:", id(C))
#just to confirm that:
A.append(4)
B.append(5)
print("\nA now: ", A)
print("B now: ", B)
print("C now:", C)
Is A equal to B? True
Is A actually B? True
Is A equal to C? True
Is A actually C? False
A's id: 139779847198600
B's id: 139779847198600
C's id: 139779847159368
A now: [1, 2, 3, 4, 5]
B now: [1, 2, 3, 4, 5]
C now: [1, 2, 3]
From strings to lists, the split method¶
Strings have a method split that can literally split the string at specific characters.
Example
Recall the protein seen in the previous practical:
chain_a = """SSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKM
FCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVV
RRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFR
HSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILT
IITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKG
EPHHELPPGSTKRALPNNT"""
how can we split it into several lines?
[13]:
chain_a = """SSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKM
FCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVV
RRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFR
HSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILT
IITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKG
EPHHELPPGSTKRALPNNT"""
lines = chain_a.split('\n')
print("Original sequence:")
print( chain_a, "\n") #some spacing to keep things clear
print("line by line:")
# write the following and you will appreciate loops! :-)
print("1st line:" ,lines[0])
print("2nd line:" ,lines[1])
print("3rd line:" ,lines[2])
print("4th line:" ,lines[3])
print("5th line:" ,lines[4])
print("6th line:" ,lines[5])
print("\nSplit the 1st line in correspondence of FRL:\n",lines[0].split("FRL"))
Original sequence:
SSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKM
FCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVV
RRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFR
HSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILT
IITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKG
EPHHELPPGSTKRALPNNT
line by line:
1st line: SSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKM
2nd line: FCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVV
3rd line: RRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFR
4th line: HSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILT
5th line: IITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKG
6th line: EPHHELPPGSTKRALPNNT
Split the 1st line in correspondence of FRL:
['SSSVPSQKTYQGSYG', 'GFLHSGTAKSVTCTYSPALNKM']
Note that in the last instruction, the substring FRL is disappeared (as happened to the newline).
And back to strings with the join method¶
Given a list, one can join the elements of the list together into a string by using the join method of the class string. The syntax is the following: str.join(list) which joins together all the elements in the list in a string separating them with the string str.
Example Given the list [‘Sept’, ‘30th’, ‘2020’, ‘11:30’], let’s combine all its elements in a string joining the elements with a dash (“-“) and print them. Let’s finally join them with a tab (“\t”) and print them.
[14]:
vals = ['Sept', '30th', '2020', '11:30']
print(vals)
myStr = "-".join(vals)
print("\n" + myStr)
myStr = "\t".join(vals)
print("\n" + myStr)
['Sept', '30th', '2020', '11:30']
Sept-30th-2020-11:30
Sept 30th 2020 11:30
Tuples¶
Tuples are the immutable version of lists (i.e. it is not possible to change their content without actually changing the object). They are sequential collections of objects, and elements of tuples are assumed to be in a particular order. They can hold heterogeneous information. They are defined with the brackets (). Some examples:
[15]:
first_tuple = (1,2,3)
print(first_tuple)
second_tuple = (1,) #this contains one element only, but we need the comma!
var = (1) #This is not a tuple!!!
print(second_tuple, " type:", type(second_tuple))
print(var, " type:", type(var))
empty_tuple = () #fairly useless
print(empty_tuple, "\n")
third_tuple = ("January", 1 ,2007) #heterogeneous info
print(third_tuple)
days = (third_tuple,("February",2,1998), ("March",2,1978),("June",12,1978))
print(days, "\n")
#Remember tuples are immutable objects...
print("Days has id: ", id(days))
days = ("Mon","Tue","Wed","Thu","Fri","Sat","Sun")
#...hence reassignment creates a new object
print("Days now has id: ", id(days))
(1, 2, 3)
(1,) type: <class 'tuple'>
1 type: <class 'int'>
()
('January', 1, 2007)
(('January', 1, 2007), ('February', 2, 1998), ('March', 2, 1978), ('June', 12, 1978))
Days has id: 139779908702520
Days now has id: 139779855774080
The following operators work on tuples and they behave exactly as on lists:
[16]:
practical1 = ("Wednesday", "23/09/2020")
practical2 = ("Monday", "28/09/2020")
practical3 = ("Wednesday", "30/09/2020")
#A tuple containing 3 tuples
lectures = (practical1, practical2, practical3)
#One tuple only
mergedLectures = practical1 + practical2 + practical3
print("The first three lectures:\n", lectures, "\n")
print("mergedLectures:\n", mergedLectures)
#This returns the whole tuple
print("1st lecture was on: ", lectures[0], "\n")
#2 elements from the same tuple
print("1st lecture was on ", mergedLectures[0], ", ", mergedLectures[1], "\n")
# Return type is tuple!
print("3rd lecture was on: ", lectures[2])
#2 elements from the same tuple returned in tuple
print("3rd lecture was on ", mergedLectures[4:], "\n")
The first three lectures:
(('Wednesday', '23/09/2020'), ('Monday', '28/09/2020'), ('Wednesday', '30/09/2020'))
mergedLectures:
('Wednesday', '23/09/2020', 'Monday', '28/09/2020', 'Wednesday', '30/09/2020')
1st lecture was on: ('Wednesday', '23/09/2020')
1st lecture was on Wednesday , 23/09/2020
3rd lecture was on: ('Wednesday', '30/09/2020')
3rd lecture was on ('Wednesday', '30/09/2020')
The following methods are available for tuples:
[17]:
practical1 = ("Wednesday", "23/09/2020")
practical2 = ("Monday", "28/09/2020")
practical3 = ("Wednesday", "30/09/2020")
mergedLectures = practical1 + practical2 + practical3 #One tuple only
print(mergedLectures.count("Wednesday"), " lectures were on Wednesday")
print(mergedLectures.count("Monday"), " lecture was on Monday")
print(mergedLectures.count("Friday"), " lectures was on Friday")
print("Index:", practical2.index("Monday"))
#You cannot look for an element that does not exist
print("Index:", practical2.index("Wednesday"))
2 lectures were on Wednesday
1 lecture was on Monday
0 lectures was on Friday
Index: 0
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-17-f06c6edd5ecf> in <module>
11 print("Index:", practical2.index("Monday"))
12 #You cannot look for an element that does not exist
---> 13 print("Index:", practical2.index("Wednesday"))
14
ValueError: tuple.index(x): x not in tuple
Exercises¶
Given the following text string:
"""this is a text
string on
several lines that does not say anything."""
print it; b) print how many lines, words and characters it contains. Finally, c)sort the words alphabetically and print the first and the last in lexicographic order.
Show/Hide Solution
The variant calling format (VCF) is a format to represent structural variants of genomes (i.e. SNPs, insertions, deletions) . Each line of this format represents a variant, every piece of information within a line is separated by a tab (\t in python). The first 5 fields of this format report the chromosome (chr), the position (pos), the name of the variant (name), the reference allele (REF) and the alternative allele (ALT). Assuming to have a variable VCF defined containing the following three lines (representing three SNPs):
VCF = """MDC000001.124\\t7112\\tFB_AFFY_0000024\\tG\\tA
MDC000002.328\\t941\\tFB_AFFY_0000144\\tC\\tT
MDC000004.272\\t2015\\tFB_AFFY_0000222\\tG\\tA"""
1. Store these three variants as a list of lists, where each one of the fields is kept separate
(e.g. the list should be similar to:
[[chr1,pos1,name1,ref1,alt1], [chr2, pos2, name2, ref2, alt2], ...] where all the elements
are as specified in the string VCF (note that "..." means that the list is not complete).
2. Print each variant changing its format in: "name|chr|pos|REF/ALT".
Show/Hide Solution
Given the list L = [“walnut”, “eggplant”, “lemon”, “lime”, “date”, “onion”, “nectarine”, “endive” ]:
1. Create another list (called newList) containing the first letter of each element of L (e.g newList =["w", "e", ...]). 2. Add a space to newList at position 4 and append an exclamation mark (!) at the end. 3. Print the list. 4. Print the content of the list joining all the elements with an empty space (i.e. use the method join: "".join(newList) )
Show/Hide Solution
Fastq is a standard format for storing sequences and quality information. More information on the format can be found here. This format can be used to store sequencing information coming from the sequencer. Each entry represents a read (i.e. a sequence) and carries four different pieces of information. A sample entry is the following:
entry = """@HWI-ST1296:75:C3F7CACXX:1:1101:19142:14904
CCAACAACTTTGACGCTAAGGATAGCTCCATGGCAGCATATCTGGCACAA
+
FHIIJIJJGIJJJJJIHHHFFFFFEE:;CIDDDDDDDDDDDDEDDDDDDB"""
where:
the first line is the read identifier starts with a “@” and carries several types of information regarding the instrument used for sequencing (the reported example is an illumina read - if you are interested, you can find more info on the format of the ID here.
(ii). the second information is the sequence of the read (note that it can span several lines, not in our simple example though);
a “+” sign to mark the end of the sequence information (optionally the read identifier can be repeated);
the phred quality score of the read encoded as a text string. It must contain the same number of elements that are in the sequence. To decode each character into a the corresponding phred score, one needs to convert it into the unicode integer representation of it - 33. For example, the conversion of a character “I” in python can be done using the ord built in function in the following way: ord(“I”) - 33 = 40. Finally the phred score can be converted into probability of the base to be wrong with the following formula: \(P = 10^{-Q/10}\), where \(Q\) is the phred quality score.
Given the entry above:
1. Check that the ID starts with a @
2. Store the sequence as a list where each element is one single base
(e.g. sequence =['T', 'A',...])
3. Store the quality as a list where each element is one single quality character
(e.g. qualChar = ['C', 'C', ...])
4. Check that the length of the sequence and quality are the same
5. Count how many times the sequence "TCCA" appears in the read
6. Retrieve the sub-list containing the quality values corresponding to the "TCCA" string
7. Convert each value in the list at point 6 in the corresponding probability of the base
being wrong
Show/Hide Solution
Given the list L = [10, 60, 72, 118, 11, 71, 56, 89, 120, 175] find the min, max and median value (hint: sort it and extract the right values). Create a list with only the elements at even indexes (i.e. [10, 72, 11, ..], note that the “..” means that the list is not complete) and re-compute min, max and median values. Finally, re-do the same for the elements located at odd indexes (i.e. [60, 118,..]).
Show/Hide Solution
Given the string pets = “siamese cat,dog,songbird,guinea pig,rabbit,hampster” convert it into a list. Create then a tuple of tuples where each tuple has two information: the name of the pet and the length of the name. E.g. ((“dog”,3), ( “hampster”,8)). Print the tuple.
Show/Hide Solution
Given the string S=”apple|pear|apple|cherry|pear|apple|pear|pear|cherry|pear|strawberry”. Store the elements separated by the “|” in a list.
How many elements does the list have?
Knowing that the list created at the previous point has only four distinct elements (i.e. “apple”,”pear”,”cherry” and “strawberry”), create another list where each element is a tuple containing the name of the fruit and its multiplicity (that is how many times it appears in the original list). Ex. list_of_tuples = [(“apple”, 3), (“pear”, “5”),…]
Print the content of each tuple in a separate line (ex. first line: apple is present 3 times)
Show/Hide Solution
Define three tuples representing points in the 3D space: A = (10,20,30), B = (1,72, 100) and C = (4, 9, 20).
Compute the Euclidean distance between A and B (let’s call it AB), A and C (AC), B and C (BC) and print them. Remember that the distance \(d\) between two points \(X_1 = (x_1,y_1,z_1)\) and \(X_2 = (x_2,y_2,z_2)\) is \(d = \sqrt{(x_2-x_1)^2 + (y_2 - y_1)^2 + (z_2-z_1)^2}\). Hint: remember to import math to use the sqrt method.
Create a point D multiplying every element of C by 10. (Hint: do not use C*10, as this will repeat C 10 times). And compute the distance AD, BD, CD.
Answer to the following questions (writing a suitable boolean expression and printing the result):
Is A closer to B than to C?
Is A closer to C than to B or to D?
Is B closer to A than to C to D?
Show/Hide Solution
Given the matrix \(M =\begin{bmatrix}1 & 2 & 3\\ 4 & 5 & 6\\ 7 & 8 & 9\end{bmatrix}\) compute \(M^2 = \begin{bmatrix}1 & 2 & 3\\ 4 & 5 & 6\\ 7 & 8 & 9\end{bmatrix} \times \begin{bmatrix}1 & 2 & 3\\ 4 & 5 & 6\\ 7 & 8 & 9\end{bmatrix} = \begin{bmatrix}30 & 36 & 42\\ 66 & 81 & 96\\ 102 & 126 & 150\end{bmatrix}\)
Show/Hide Solution
Practical 4¶
In this practical we will work with conditionals (branching) and loops.
Execution flow¶
Recall from the lecture that there are at least three types of execution flows. Our statements can be simple and structured sequentially, when one instruction is executed right after the previous one, but some more complex flows involve conditional branching (when the portion of the code to be executed depends on the value of some condition), or loops when a portion of the code is executed multiple times until a certain condition becomes False.
These portions of code are generally called blocks and Python, unlike most of the programming languages, uses indentation (and some keywords like else, ‘:’, ‘next’, etc.) to define blocks.
Conditionals¶
We can use conditionals any time a decision needs to be made depending on the value of some condition. A block of code will be executed if the condition is evaluated to the boolean True and another one if the condition is evaluated to False.
The basic if - else statement¶
The basic syntax of conditionals is an if statement like:
if condition :
#This is the True branch
#do something
else:
#This is the False branch (or else branch)
#do something else
where condition is a boolean expression that tells the interpreter which of the two blocks should be executed. If and only if the condition is True the first branch is executed, otherwise execution goes to the second branch (i.e. the else branch). Note that the condition is followed by a “:” character and that the two branches are indented. This is the way Python uses to identify the block of instructions that belong to the same branch. The else keyword is followed by “:” and is not indented (i.e. it is at the same level of the if statement. There is no keyword at the end of the “else branch”, but indentation tells when the block of code is finished.
Example: Let’s get an integer from the user and test if it is even or odd, printing the result to the screen.
[1]:
num = int(input("Dear user give me an integer:"))
res = ""
if num % 2 == 0:
#The number is even
res = "even"
else:
#The number is odd
res = "odd"
print("Number ", num, " is ", res)
Dear user give me an integer:27
Number 27 is odd
Note that the execution is sequential until the if keyword, then it branches until the indentation goes back to the same level of the if (i.e. the two branches rejoin at the print statement in the final line). Remember that the else branch is optional.
The if - elif - else statement¶
If statements can be chained in such a way that there are more than two possible branches to be followed. Chaining them with the if - elif - else statement will make execution follow only one of the possible paths.
The syntax is the following:
if condition :
#This is branch 1
#do something
elif condition1 :
#This is branch 2
#do something
elif condition2 :
#This is branch 3
#do something
else:
#else branch. Executed if all other conditions are false
#do something else
Note that branch 1 is executed if condition is True, branch 2 if and only if condition is False and condition1 is True, branch 3 if condition is False, condition 1 is False and condition2 is True. If all conditions are False the else branch is executed.
Example: The tax rate of a salary depends on the income. If the income is < 10000 euros, no tax is due, if the income is between 10000 euros and 20000 the tax rate is 25%, if between 20000 and 45000 it is 35% otherwise it is 40%. What is the tax due by a person earning 35000 euros per year?
[2]:
income = 35000
rate = 0.0
if income < 10000:
rate = 0
elif income < 20000:
rate = 0.25
elif income < 45000:
rate = 0.35
else:
rate = 0.4
tax = income*rate
print("The tax due is ", tax, " euros (i.e ", rate*100, "%)")
The tax due is 12250.0 euros (i.e 35.0 %)
Note the difference in the two following cases:
[3]:
#Example 1
val = 10
if val > 5:
print("Value >5")
elif val > 5:
print("I said value is >5!")
else:
print("Value is <= 5")
#Example 2
val = 10
if(val > 5):
print("\n\nValue is >5")
if(val > 5):
print("I said Value is >5!!!")
Value >5
Value is >5
I said Value is >5!!!
Loops¶
Looping is the ability of repeating a specific block of code several times (i.e. until a specific condition is True or there are no more elements to process).
For loop¶
The for loop is used to loop over a collection of objects (e.g. a string, list, tuple, …). The basic syntax of the for loop is the following:
for elem in collection :
#OK, do something with elem
# instruction 1
# instruction 2
the variable elem will get the value of each one of the elements present in collection one after the other. The end of the block of code to be executed for each element in the collection is again defined by indentation.
Depending on the type of the collection elem will get different values. Recall from the lecture that:
Let’s see this in action:
[4]:
S = "Hi there from python"
Slist = S.split(" ")
Stuple = ("Hi","there","from","python")
print("String:", S)
print("List:", Slist)
print("Tuple:", Stuple)
#for loop on string
print("On strings:")
for c in S:
print(c)
print("\nOn lists:")
#for loop on list
for item in Slist:
print(item)
print("\nOn tuples:")
#for loop on list
for item in Stuple:
print(item)
String: Hi there from python
List: ['Hi', 'there', 'from', 'python']
Tuple: ('Hi', 'there', 'from', 'python')
On strings:
H
i
t
h
e
r
e
f
r
o
m
p
y
t
h
o
n
On lists:
Hi
there
from
python
On tuples:
Hi
there
from
python
Looping over a range¶
It is possible to loop over a range of values with the pythom built-in function range. The range function accepts either two or three parameters (all of them are integers). Similarly to the slicing operator, it needs the starting point, end point and an optional step. Three distinct syntaxes are available:
range(E) # ranges from 0 to E-1
range(S,E) # ranges from S to E-1
range(S,E,step) # ranges from S to E-1 with +step jumps
Remember that S is included while E is excluded. Let’s see some examples.
Example: Given a list of integers, return a list with all the even numbers.
[5]:
myList = [1, 7, 9, 121, 77, 82]
onlyEven = []
for i in range(0, len(myList)): #this is equivalent to range(len(myList)):
if myList[i] % 2 == 0 :
onlyEven.append(myList[i])
print("original list:", myList)
print("only even numbers:", onlyEven)
original list: [1, 7, 9, 121, 77, 82]
only even numbers: [82]
Example: Store in a list the multiples of 19 between 1 and 100.
[6]:
multiples = []
for i in range(19,101,19): # equal to: list(range(19,101,19))
multiples.append(i) #
print("multiples of 19: ", multiples)
#alternative way:
multiples = []
for i in range(1, (100//19) + 1):
multiples.append(i*19)
print("multiples of 19:", multiples)
multiples of 19: [19, 38, 57, 76, 95]
multiples of 19: [19, 38, 57, 76, 95]
Note: range works differently in Python 2.x and 3.x
In Python 3 the range function returns an iterator rather storing the entire list.
[7]:
#Check out the difference:
print(range(0,10))
print(list(range(0,10)))
range(0, 10)
[0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
Example: Let’s consider the two DNA strings s1 = “ATACATATAGGGCCAATTATTATAAGTCAC” and s2 = “CGCCACTTAAGCGCCCTGTATTAAAGTCGC” that have the same length. Let’s create a third string \(out\) such that \(out[i]\) is \("|"\) if \(s1[i]==s2[i]\), \("\ "\) otherwise.
[8]:
s1 = "ATACATATAGGGCCAATTATTATAAGTCAC"
s2 = "CGCCACTTAAGCGCCCTGTATTAAAGTCGC"
outSTR = ""
for i in range(len(s1)):
if s1[i] == s2[i]:
outSTR = outSTR + "|"
else:
outSTR = outSTR + " "
print(s1)
print(outSTR)
print(s2)
ATACATATAGGGCCAATTATTATAAGTCAC
|| || | | | | ||||| |
CGCCACTTAAGCGCCCTGTATTAAAGTCGC
Nested for loops¶
In some occasions it is useful to nest one (or more) for loops into another one. The basic syntax is:
for i in collection:
for j in another_collection:
#do some stuff with i and j
Example:
Given the matrix \(\begin{bmatrix}1 & 2 & 3\\4 & 5 & 6\\7 & 8 & 9\end{bmatrix}\) stored as a list of lists (i.e. matrix = [[1, 2, 3], [4, 5, 6], [7, 8, 9]].
Print it out as: \(\begin{matrix}1 & 2 & 3\\4 & 5 & 6\\7 & 8 & 9\end{matrix}\)
[9]:
matrix = [[1, 2, 3], [4, 5, 6], [7, 8, 9]]
for i in range(len(matrix)):
line = ""
for j in range(len(matrix[i])):
line = line + str(matrix[i][j]) + " " #note int --> str conversion!
print(line)
# Without nested for (but this is not exactly the same).
# NOTE: cannot do print(" ".join(row)) because we have integers
#for row in matrix:
# print(" ".join(str(row)))
#
#Outputs:
#[ 1 , 2 , 3 ]
#[ 4 , 5 , 6 ]
#[ 7 , 8 , 9 ]
1 2 3
4 5 6
7 8 9
While loops¶
The for loop is great when we have to iterate over a finite sequence of elements. But when one needs to loop until a specific condition holds true, another construct must be used: the while statement. The loop will end when the condition becomes false.
The basic syntax is the following:
while condition:
#do something
#update the value of condition
An example follows:
[10]:
i = 0
while i < 5:
print("i now is:", i)
i = i + 1 #THIS IS VERY IMPORTANT!
i now is: 0
i now is: 1
i now is: 2
i now is: 3
i now is: 4
Note that if condition is false at the beginning the block of code is never executed.
Note: The loop will continue until condition holds true and the only code executed is the block defined through the indentation. This block of code must update the value of condition otherwise the interpreter will get stuck in the loop and will never exit.
We can combine for loops and while loops one into the code block of the other:
[11]:
for i in range(1,10):
j = 1
output = ""
while j<= i:
output = str(j) + " " + output
j = j + 1
print(output)
1
2 1
3 2 1
4 3 2 1
5 4 3 2 1
6 5 4 3 2 1
7 6 5 4 3 2 1
8 7 6 5 4 3 2 1
9 8 7 6 5 4 3 2 1
Note the way the numbers are concatenated together to form the output string. Check the difference of the previous code to the following:
[12]:
for i in range(1,10):
j = 1
while j<=i:
print(j, end = " ")
j = j + 1
print("")
1
1 2
1 2 3
1 2 3 4
1 2 3 4 5
1 2 3 4 5 6
1 2 3 4 5 6 7
1 2 3 4 5 6 7 8
1 2 3 4 5 6 7 8 9
Exercises¶
Given the integer 134479170, print if it is divisible for the numbers from 2 to 16. Hint: use for and if.
Show/Hide Solution
Given the DNA string
DNA="GATTACATATATCAGTACAGATATATACGCGCGGGCTTACTATTAAAAACCCC"
write a Python script that reverse-complements it. To reverse-complement a string of DNA, one needs to replace any A with T, T with A, C with G and G with C, while any other character is complemented in N. Finally, the sequence has to be reversed (e.g. the first base becomes the last). For example, ATCG becomes CGAT.
Show/Hide Solution
Count how many of the first 100 integers are divisible by 2, 3, 5, 7 but not by 10 and print these counts. Be aware that a number can be divisible by more than one of these numbers (e.g. 6) and therefore it must be counted as divisible by all of them (e.g. 6 must be counted as divisible by 2 and 3).
Show/Hide Solution
Write a python script that creates the following pattern:
+
++
+++
++++
+++++
++++++
+++++++ <-- 7
++++++
+++++
++++
+++
++
+
Show/Hide Solution
@HWI-ST1296:75:C3F7CACXX:1:1101:19142:14904
CCAACAACTTTGACGCTAAGGATAGCTCCATGGCAGCATATCTGGCACAA
+
FHIIJIJJGIJJJJJ1HHHFFFFFEE:;CIDDDDDDDDDDDDEDDD-./0
Store the sequence and the quality in two strings. Create a list with all the quality phred scores (given a quality character “X” the phred score is: ord(“X”) -33. Finally print all the bases that have quality lower than 25, reporting the base, its position, quality character and phred score.
Output example: base: C index: 15 qual:1 phred: 16.
Show/Hide Solution
Given the following sequence:
seq=AUGCUGUCUCCCUCACUGUAUGUAAAUUGCAUCUAGAAUAGCA
UCUGGAGCACUAAUUGACACAUAGUGGGUAUCAAUUAUUA
UUCCAGGUACUAGAGAUACCUGGACCAUUAACGGAUAAAU
AGAAGAUUCAUUUGUUGAGUGACUGAGGAUGGCAGUUCCU
GCUACCUUCAAGGAUCUGGAUGAUGGGGAGAAACAGAGAA
CAUAGUGUGAGAAUACUGUGGUAAGGAAAGUACAGAGGAC
UGGUAGAGUGUCUAACCUAGAUUUGGAGAAGGACCUAGAA
GUCUAUCCCAGGGAAAUAAAAAUCUAAGCUAAGGUUUGAG
GAAUCAGUAGGAAUUGGCAAAGGAAGGACAUGUUCCAGAU
GAUAGGAACAGGUUAUGCAAAGAUCCUGAAAUGGUCAGAG
CUUGGUGCUUUUUGAGAACCAAAAGUAGAUUGUUAUGGAC
CAGUGCUACUCCCUGCCUCUUGCCAAGGGACCCCGCCAAG
CACUGCAUCCCUUCCCUCUGACUCCACCUUUCCACUUGCC
CAGUAUUGUUGGUGU
and considering the genetic code and the first forward open reading frame (i.e. the string as it is remembering to remove newlines).
How many start codons are present in the whole sequence (i.e. AUG)?
How many stop codons (i.e. UAA,UAG, UGA)
Create another string in which any codon with except the start and stop codons are substituted with “—” and print the resulting string.
Show/Hide Solution
Playing time! Write a python scripts that:
Picks a random number from 1 to 10, with: import random myInt = random.randint(1,10)
Asks the user to guess a number and checks if the user has guessed the right one
If the guess is right the program will stop with a congratulation message
If the guess is wrong the program will continue asking a number, reporting the numbers already guessed (hint: store them in a list and print it).
Modify the program to notify the user if he/she inputs the same number more than once.
Show/Hide Solution
Practical 5¶
In this practical we will add some information on loops and introduce dictionaries.
More on loops¶
As seen in the previous practical and in the lecture, there are three different ways of execution flow:
We have already seen the if, for and while loops and their variants. Please remember that the code block of each of these statements is defined by the indentation (i.e. spacing).
Ternary operator¶
In some cases it is handy to be able to initialize a variable depending on the value of another one.
Example: The discount rate applied to a purchase depends on the amount of the sale. Create a variable discount setting its value to 0 if the variable amount is lower than 100 euros, to 10% if it is higher.
[1]:
amount = 110
discount = 0
if amount >100:
discount = 0.1
else:
discount = 0 # not necessary
print("Total amount:", amount, "discount:", discount)
Total amount: 110 discount: 0.1
The previous code can be written more coincisely as:
[2]:
amount = 110
discount = 0.1 if amount > 100 else 0
print("Total amount:", amount, "discount:", discount)
Total amount: 110 discount: 0.1
The basic syntax of the ternary operator is:
variable = value if condition else other_value
meaning that the variable is initialized to value if the condition holds, otherwise to other_value.
Python also allows in line operations separated by a “;”. This is a compact way of specifying several instructions on a single line, but it makes the code more difficult to read.
[3]:
a = 10; b = a + 1; c = b +2
print(a,b,c)
10 11 13
Note: Although the ternary operator and in line operations are sometimes useful and less verbose than the explicit definition, they are considered “non-pythonic” and advised against.
Break and continue¶
Sometimes it is useful to skip an entire iteration of a loop or end the loop before its supposed end. This can be achieved with two different statements: continue and break.
Continue statement¶
Within a for or while loop, continue makes the interpreter skip that iteration and move on to the next.
Example: Print all the odd numbers from 1 to 20.
[4]:
#Two equivalent ways
#1. Testing remainder == 1
for i in range(21):
if i % 2 == 1:
print(i, end = " ")
print("")
#2. Skipping if remainder == 0 in for
for i in range(21):
if i % 2 == 0:
continue
print(i, end = " ")
1 3 5 7 9 11 13 15 17 19
1 3 5 7 9 11 13 15 17 19
Continue can be used also within while loops but we need to be careful to update the value of the variable before reaching the continue statement or we will get stuck in never-ending loops. Example: Print all the odd numbers from 1 to 20.
[ ]:
#Wrong code:
i = 0
while i < 21:
if i % 2 == 0:
continue
print(i, end = " ")
i = i + 1 # NEVER EXECUTED IF i % 2 == 0!!!!
a possible correct solution using while:
[5]:
i = -1
while i< 20: #i is incremented in the loop, so 20!!!
i = i + 1 #the variable is updated no matter what
if i % 2 == 0:
continue
print(i, end = " ")
1 3 5 7 9 11 13 15 17 19
Break statement¶
Within a for or while loop, break makes the interpreter exit the loop and continue with the sequential execution. Sometimes it is useful to get out of the loop if to complete our task we do not need to get to the end of it.
Example: Given the following list of integers [1,5,6,4,7,1,2,3,7] print them until a number already printed is found.
[6]:
L = [1,5,6,4,7,1,2,3,7]
found = []
for i in L:
if i in found:
break
found.append(i)
print(i, end = " ")
1 5 6 4 7
Example: Pick a random number from 1 and 50 and count how many times it takes to randomly choose number 27. Limit the number of random picks to 40 (i.e. if more than 40 picks have been done and 27 has not been found exit anyway with a message).
[7]:
import random
iterations = 1
picks = []
while iterations <= 40:
pick = random.randint(1,50)
picks.append(pick)
if pick == 27:
break
iterations += 1 #equal to: iterations = iterations + 1
if iterations == 41:
print("Sorry number 27 was never found!")
else:
print("27 found in ", iterations, "iterations")
print(picks)
27 found in 9 iterations
[9, 16, 8, 37, 42, 7, 14, 28, 27]
An alternative way without using the break statement makes use of a flag variable (that when changes value will make the loop end):
[8]:
import random
found = False # This is called flag
iterations = 1
picks = []
while iterations <= 40 and found == False: #the flag is used to exit
pick = random.randint(1,50)
picks.append(pick)
if pick == 27:
found = True #update the flag, will exit at next iteration
iterations += 1
if iterations == 41 and not found:
print("Sorry number 27 was never found!")
else:
print("27 found in ", iterations -1, "iterations")
print(picks)
Sorry number 27 was never found!
[14, 32, 28, 25, 49, 28, 31, 6, 11, 17, 21, 13, 35, 15, 3, 30, 34, 19, 38, 20, 47, 38, 14, 42, 32, 19, 23, 49, 40, 21, 17, 35, 47, 1, 39, 41, 31, 33, 21, 35]
List comprehension¶
List comprehension is a quick way of creating a list. The resulting list is normally obtained by applying a function or a method to the elements of another list that remains unchanged.
The basic syntax is:
new_list = [ some_function (x) for x in start_list]
or
new_list = [ x.some_method() for x in start_list]
List comprehension can also be used to filter elements of a list and produce another list as sublist of the first one (remember that the original list is not changed).
In this case the syntax is:
new_list = [ some_function (x) for x in start_list if condition]
or
new_list = [ x.some_method() for x in start_list if condition]
where the element x in start_list becomes part of new_list if and only if the condition holds True.
Let’s see some examples:
Example: Given a list of strings [“hi”, “there”, “from”, “python”] create a list with the length of the corresponding element (i.e. the one with the same index).
[9]:
elems = ["hi", "there", "from", "python"]
newList = [len(x) for x in elems]
for i in range(0,len(elems)):
print(elems[i], " has length ", newList[i])
hi has length 2
there has length 5
from has length 4
python has length 6
Example: Given a list of strings [“dog”, “cat”, “rabbit”, “guinea pig”, “hamster”, “canary”, “goldfish”] create a list with the elements starting with a “c” or “g”.
[10]:
pets = ["dog", "cat", "rabbit", "guinea pig", "hamster", "canary", "goldfish"]
cg_pets = [x for x in pets if x.startswith("c") or x.startswith("g")]
print("Original:")
print(pets)
print("Filtered:")
print(cg_pets)
Original:
['dog', 'cat', 'rabbit', 'guinea pig', 'hamster', 'canary', 'goldfish']
Filtered:
['cat', 'guinea pig', 'canary', 'goldfish']
Example: Create a list with all the numbers divisible by 17 from 1 to 200.
[11]:
values = [ x for x in range(1,200) if x % 17 == 0]
print(values)
[17, 34, 51, 68, 85, 102, 119, 136, 153, 170, 187]
Example: Transpose the matrix \(\begin{bmatrix}1 & 10\\2 & 20\\3 & 30\\4 & 40\end{bmatrix}\) stored as a list of lists (i.e. matrix = [[1, 10], [2,20], [3,30], [4,40]]). The output matrix should be: \(\begin{bmatrix}1 & 2 & 3 & 4\\10 & 20 & 30 & 40\end{bmatrix}\), represented as [[1, 2, 3, 4], [10, 20, 30, 40]]
[12]:
matrix = [[1, 10], [2,20], [3,30], [4,40]]
print(matrix)
transpose = [[row[i] for row in matrix] for i in range(2)]
print (transpose)
[[1, 10], [2, 20], [3, 30], [4, 40]]
[[1, 2, 3, 4], [10, 20, 30, 40]]
Example: Given the list: [“Hotel”, “Icon”,” Bus”,”Train”, “Hotel”, “Eye”, “Rain”, “Elephant”] create a list with all the first letters.
[13]:
myList = ["Hotel", "Icon"," Bus","Train", "Hotel", "Eye", "Rain", "Elephant"]
initials = [x[0] for x in myList]
print(myList)
print(initials)
print("".join(initials))
['Hotel', 'Icon', ' Bus', 'Train', 'Hotel', 'Eye', 'Rain', 'Elephant']
['H', 'I', ' ', 'T', 'H', 'E', 'R', 'E']
HI THERE
With list comprehension we can copy a list into another one, but this is a shallow copy:
[10]:
a = [1,2,3]
b = [a, [[a]]]
print("B:", b)
c = [x for x in b]
print("C:", c)
a.append(4)
print("B now:" , b)
print("C now:", c)
B: [[1, 2, 3], [[[1, 2, 3]]]]
C: [[1, 2, 3], [[[1, 2, 3]]]]
B now: [[1, 2, 3, 4], [[[1, 2, 3, 4]]]]
C now: [[1, 2, 3, 4], [[[1, 2, 3, 4]]]]
Dictionaries¶
A dictionary is a map between one object, the key, and another object, the value. Dictionaries are mutable objects and contain sequences of mappings key –> object but there is not specific ordering among them. Dictionaries are defined using the curly braces {key1 : value1, key2 : value2} and : to separate keys from values.
Some examples on how to define dictionaries follow:
[14]:
first_dict = {"one" : 1, "two": 2, "three" : 3, "four" : 4}
print("First:", first_dict)
empty_dict = dict()
print("Empty:",empty_dict)
second_dict = {1 : "one", 2 : "two", "three" :3 } #BAD IDEA BUT POSSIBLE!!!
print(second_dict)
third_dict = dict(zip(["one","two","three","four"],[1,2,3,4]))
print(third_dict)
print(first_dict == third_dict)
First: {'one': 1, 'two': 2, 'three': 3, 'four': 4}
Empty: {}
{1: 'one', 2: 'two', 'three': 3}
{'one': 1, 'two': 2, 'three': 3, 'four': 4}
True
Note that there is no ordering of the keys, and that the order in which they have been inserted is not preserved. Moreover, keys and values can be dishomogeneous (e.g. keys can be strings and values integers). An interesting case is third_dict where the function zip followed by dict is used to map the keys of the first list into the values present in the second.
Note that keys can be dishomogeneous, even though this is a bad idea normally. The only requirement for the keys is that they must be immutable objects. Trying to use a mutable object as a key will make the interpreter crash with the error: unhashable type. Finally, keys must be unique. We cannot associate more than one value to the same key.
[15]:
a = (1,2,3) #a,b are tuples: hence immutable
b = (1,3,5)
my_dict = {a : 6, b : 9 }
print(my_dict)
c = [1,2,3] #c,d are lists: hence mutable
d = [1,3,5]
dict2 = {c : 6, d : 9}
print(dict2)
{(1, 2, 3): 6, (1, 3, 5): 9}
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-15-0fe98c7f5acd> in <module>
8 d = [1,3,5]
9
---> 10 dict2 = {c : 6, d : 9}
11 print(dict2)
TypeError: unhashable type: 'list'
Functions working on dictionaries¶
As for the other data types, python provides several operators that can be applied to dictionaries. The following operators are available and they basically work as in lists. The only exception being that the operator in checks whether the specified object is present among the keys.
Some usage examples follow:
[16]:
myDict = {"one" : 1, "two" : 2, "twentyfive" : 25}
print(myDict)
myDict["ten"] = 10
myDict["twenty"] = 20
print(myDict)
myDict["ten"] = "10-again"
print(myDict)
print("The dictionary has ", len(myDict), " elements")
print("The value of \"ten\" is:", myDict["ten"])
print("The value of \"two\" is:", myDict["two"])
print("Is \"twentyfive\" in dictionary?", "twentyfive" in myDict)
print("Is \"seven\" in dictionary?", "seven" in myDict)
{'one': 1, 'two': 2, 'twentyfive': 25}
{'one': 1, 'two': 2, 'twentyfive': 25, 'ten': 10, 'twenty': 20}
{'one': 1, 'two': 2, 'twentyfive': 25, 'ten': '10-again', 'twenty': 20}
The dictionary has 5 elements
The value of "ten" is: 10-again
The value of "two" is: 2
Is "twentyfive" in dictionary? True
Is "seven" in dictionary? False
Dictionary methods¶
Recall what seen in the lecture, the following methods are available for dictionaries:
These methods are new to dictionaries and can be used to loop through the elements in them.
ERRATUM: dict.keys() returns a dict_keys object not a list. To cast it to list, we need to call list(dict.keys()). The same applies to dict.values() that returns a dict_values object that needs conversion to a list with list(dict.values()).
[17]:
D = {"k1" : 1, "k2" : 2 , "k3" : 3}
print("keys:" , D.keys(), "values:", D.values())
print("")
print("keys:", list(D.keys()), "values:", list(D.values()))
keys: dict_keys(['k1', 'k2', 'k3']) values: dict_values([1, 2, 3])
keys: ['k1', 'k2', 'k3'] values: [1, 2, 3]
Example Given the protein sequence below, store in a dictionary all the aminoacids present and count how many times they appear. Finally print out the stats (e.g. how many amino-acids are present, the most frequent, the least frequent and the frequency of all of them in alphabetical order).
>sp|P00517|KAPCA_BOVIN cAMP-dependent protein kinase catalytic subunit alpha
MGNAAAAKKGSEQESVKEFLAKAKEDFLKKWENPAQNTAHLDQFERIKTLGTGSFGRVML
VKHMETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMV
MEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGY
IQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFF
ADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFAT
TDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF
[1]:
protein = """MGNAAAAKKGSEQESVKEFLAKAKEDFLKKWENPAQNTAHLDQFERIKTLGTGSFGRVML
VKHMETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMV
MEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGY
IQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFF
ADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFAT
TDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF"""
protein = protein.replace("\n","")
print(protein)
amino_acids = dict()
for a in protein:
if a in amino_acids:
amino_acids[a] = amino_acids[a] + 1 # amino_acids[a] += 1
else:
amino_acids[a] = 1
num_aminos = len(amino_acids)
print("The number of amino-acids present is ", num_aminos)
#let's get all aminoacids
#and sort them alphabetically
a_keys = list(amino_acids.keys())
a_keys.sort()
# Another example of dictionaries
mostF = {"frequency" : -1, "aminoacid" : "-"}
leastF = {"frequency" : len(protein), "aminoacid" : "-"}
for a in a_keys:
freq = amino_acids[a]
if(mostF["frequency"] < freq):
mostF["frequency"] = freq
mostF["aminoacid"] = a
if(leastF["frequency"] > freq):
leastF["frequency"] = freq
leastF["aminoacid"] = a
print(a, " is present", freq, "times")
print("Amino", leastF["aminoacid"], "has the lowest freq. (",leastF["frequency"],")")
print("Amino", mostF["aminoacid"], "has the highest freq. (",mostF["frequency"],")")
MGNAAAAKKGSEQESVKEFLAKAKEDFLKKWENPAQNTAHLDQFERIKTLGTGSFGRVMLVKHMETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF
The number of amino-acids present is 20
A is present 23 times
C is present 2 times
D is present 18 times
E is present 27 times
F is present 25 times
G is present 22 times
H is present 9 times
I is present 21 times
K is present 34 times
L is present 32 times
M is present 8 times
N is present 17 times
P is present 14 times
Q is present 14 times
R is present 15 times
S is present 16 times
T is present 14 times
V is present 20 times
W is present 6 times
Y is present 14 times
Amino C has the lowest freq. ( 2 )
Amino K has the highest freq. ( 34 )
Important NOTE. Accessing a value through the key of a dictionary requires that the pair key-value one searches for is present in the dictionary. If the searched key is not present the interpreter crashes out throwing a KeyError as follows:
[19]:
myDict = {"one" : 1, "two" : 2, "three" : 3}
print(myDict["one"])
print(myDict["seven"])
1
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
<ipython-input-19-a05b31e54a02> in <module>
2
3 print(myDict["one"])
----> 4 print(myDict["seven"])
KeyError: 'seven'
This could be avoided by checking that the key is present in the dictionary beforehand:
[20]:
myDict = {"one" : 1, "two" : 2, "three" : 3}
search_keys = ["one", "seven"]
for s in search_keys:
if s in myDict:
print("key:", s, "value:", myDict[s])
else:
print("key", s, "not found in dictionary")
key: one value: 1
key seven not found in dictionary
or by using the dictionary method get that has two inputs: the key and a default value to return in case key is not present in the dictionary:
[21]:
myDict = {"one" : 1, "two" : 2, "three" : 3}
search_keys = ["one", "seven"]
for s in search_keys:
print("key:", s, "value:", myDict.get(s, "not found"))
key: one value: 1
key: seven value: not found
Exercises¶
Given the following two lists of integers: [1, 13, 22, 7, 43, 81, 77, 12, 15,21, 84,100] and [44,32,7, 100, 81, 13, 1, 21, 71]:
Sort the two lists
Create a third list as intersection of the two lists (i.e. an element is in the intersection if it is present in both lists).
Print the three lists.
Show/Hide Solution
The sequence below is the Sars-Cov2 ORF1a polyprotein. 1. Count and print how many aminoacids it is composed of and 2. put in a dictionary all the indexes of the occurrences of the following four aminoacids:
TTTL, GFAV, KMLL(i.e. the key of the dictionary is the sequence and the value is the list of all positions at which the four-mers appear).
ORF1a = """MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVF
IKRSDARTAPHGHVMVELVAELEGIQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADL
KSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLARAGK
ASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSI
IKTIQPRVEKKKLDGFMGRIRSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLT
KEGATTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKC
AYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVET
VKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEAARVVRSIFSRTLETAQNSVR
VLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDW
LEEKFKEGVEFLRDGWEIVKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKL
KALNLGETFVTHSKGLYRKCVKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPT
SEAVEAPLVGTPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGGAPTKVTFGDDTVIEVQGYKSVN
ITFELDERIDKVLNEKCSAYTVELGTEVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDE
SGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEYGTEDDYQGKPLEFGATSAALQPEEEQEEDWL
DDDSQQTVGQQDGSEDNQTTTIQTIVEVQPQLEMELTPVVQTIEVNSFSGYLKLTDNVYIKNADIVEEAK
KVKPTVVVNAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGP
NVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSF
LEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDIN
GNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAKALRKVPTDNYITTYP
GQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVS
TIQRKYKGIKIQEGVVDYGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLK
VPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGIEFLKRGDKSVYYTSN
PTTFHLDGEVITFDNLKTLLSLREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPH
NSHEGKTFYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNCYLATAL
LTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNV
VCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT
FTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCT
EIDPKLDNYYKKDNSYFTEQPIDLVPNQPYPNASFDNFKFVCDNIKFADDLNQLTGYKKPASRELKVTFF
PDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKS
EDAQGMDNLACEDLKPVSEEVVENPTIQKDVLECNVKTTEVVGDIILKPANNSLKIIEEVGHTDLMAAYV
DNSSLTIKKPNELSRVLGLKTLATHGLAAVNSVPWDTIANYAKPFLNKVVSTTTNIVTRCLNRVCTNYMP
YFFTLLLQLCTFTRSTNSRIKASMPTTIAKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFLLLSVCL
GSLIYSTAALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCTGSIPCSVCLSGLDSLDTYPSLETIQIT
ISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSWLMWLIINLVQMAPISAM
VRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNW
NCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSH
FVNLDNLRANNTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKM
FDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQGFVDSDVETKDVVECLKLSHQ
SDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIR
SAAKKNNLPFKLTCATTRQVVNVVTTKIALKGGKIVNNWLKQLIKVTLVFLFVAAIFYLITPVHVMSKHT
DFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQRGGSYTNDKACPLIAAVITREVGFVVPGLP
GTILRTTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLE
GSVAYESLRPDTRYVLMDGSIIQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDY
YRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAF
NTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICIST
KHFYWFFSNYLKRRVVFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGA
MDTTSYREAACCHLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTL
NGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPK
TPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMEL
PTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKY
NYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQS
AVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFL
LPSLATVAYFNMVYMPASWVMRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWT
LMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIM
LVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKLLGVGGK
PCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLS
MQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSE
FDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLN
IIPLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTA
LRANSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSD
GTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFC
AFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPK
GFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNGFAV"""
Show/Hide Solution
Given the string “nOBody Said iT was eAsy, No oNe Ever saId it WoulD be tHis hArd…”
Create a list with all the letters that are capitalized (use str.isupper)
Print the list
Use the string method join to concatenate all the letters in a string, using “*” as separator. The syntax of join is str.join(list) and it outputs a string with all the elements in list joined with the character in str (es. “+”.join([1,2,3]) returns “1+2+3”).
The expected output:
['O', 'B', 'S', 'T', 'A', 'N', 'N', 'E', 'I', 'W', 'D', 'H', 'A']
O*B*S*T*A*N*N*E*I*W*D*H*A
Show/Hide Solution
Given the following sequence:
AUGCUGUCUCCCUCACUGUAUGUAAAUUGCAUCUAGAAUAGCA
UCUGGAGCACUAAUUGACACAUAGUGGGUAUCAAUUAUUA
UUCCAGGUACUAGAGAUACCUGGACCAUUAACGGAUAAAU
AGAAGAUUCAUUUGUUGAGUGACUGAGGAUGGCAGUUCCU
GCUACCUUCAAGGAUCUGGAUGAUGGGGAGAAACAGAGAA
CAUAGUGUGAGAAUACUGUGGUAAGGAAAGUACAGAGGAC
UGGUAGAGUGUCUAACCUAGAUUUGGAGAAGGACCUAGAA
GUCUAUCCCAGGGAAAUAAAAAUCUAAGCUAAGGUUUGAG
GAAUCAGUAGGAAUUGGCAAAGGAAGGACAUGUUCCAGAU
GAUAGGAACAGGUUAUGCAAAGAUCCUGAAAUGGUCAGAG
CUUGGUGCUUUUUGAGAACCAAAAGUAGAUUGUUAUGGAC
CAGUGCUACUCCCUGCCUCUUGCCAAGGGACCCCGCCAAG
CACUGCAUCCCUUCCCUCUGACUCCACCUUUCCACUUGCC
CAGUAUUGUUGGUG
considering only first forward open reading frame (i.e. the string as it is remembering to remove newlines): 1. create a list of all the codons and print it (considering only first forward open reading frame we will have the codons: AUG, CUG, UCU,…).
2. create then a dictionary in which codons are keys and values are how many times that codon is present in the first forward open reading frame and print it; 3. retrieve from the dictionary and print the number of times codons: “AUG”, “AGA”, “GGG”, “AUA” are present. If a codon is not present the script should print “NOT present” rather than crash.
Show/Hide Solution
Given the following list of gene correlations:
geneCorr = [["G1C2W9", "G1C2Q7", 0.2], ["G1C2W9", "G1C2Q4", 0.9], ["Q6NMS1", "G1C2W9", 0.8],["G1C2W9", "Q6NMS1",0.4], ["G1C2Q7", "G1C2Q4",0.76]]
where each sublist [“gene1”, “gene2”, corr] represents a correlation between gene1 and gene2 with correlation corr, create another list containing only the elements having an high correlation (i.e. > 0.75). Print this list.
Expected result:
[['G1C2W9', 'G1C2Q4', 0.9], ['Q6NMS1', 'G1C2W9', 0.8], ['G1C2Q7', 'G1C2Q4', 0.76]]
Show/Hide Solution
Given the following sequence of DNA:
DNA = “GATTACATATATCAGTACAGATATATACGCGCGGGCTTACTATTAAAAACCCC”
1. Create a dictionary reporting the frequency of each base (i.e. key is the
base and value is the frequency).
2. Create a dictionary representing an index of all possible dimers (i.e. 2
bases, 16 dimers in total): AA, AT, AC, AG, TA, TT, TC, TG, ... . In this case,
keys of the dictionary are dimers and values are lists with all possible starting
positions of the dimer.
3. Print the DNA string.
4. Print for each base its frequency
4. Print all positions of the dimer "AT"
The expected result is:
sequence: GATTACATATATCAGTACAGATATATACGCGCGGGCTTACTATTAAAAACCCC
G has frequency: 0.1509433962264151
C has frequency: 0.22641509433962265
A has frequency: 0.3584905660377358
T has frequency: 0.2641509433962264
{'GG': [32, 33], 'TC': [11], 'GT': [14], 'CA': [5, 12, 17], 'TT': [2, 36, 42],
'CG': [27, 29, 31], 'TA': [3, 7, 9, 15, 21, 23, 25, 37, 40, 43], 'AG': [13, 18],
'GA': [0, 19], 'CT': [35, 39], 'GC': [28, 30, 34], 'AT': [1, 6, 8, 10, 20, 22, 24, 41],
'CC': [49, 50, 51], 'AA': [44, 45, 46, 47], 'AC': [4, 16, 26, 38, 48]}
Dimer AT is found at: [1, 6, 8, 10, 20, 22, 24, 41]
Show/Hide Solution
Given the following table, reporting molecular weights for each amino acid, store them in a dictionary where the key is the one letter code and the value is the molecular weight (e.g. {“A” : 89, “R”:174”}).
Write a python script to answer the following questions:
1. What is the average molecular weight of an amino acid?
2. What is the total molecular weight and number of aminoacids
of the P53 peptide GSRAHSSHLKSKKGQSTSRHK?
3. What is the total molecular weight and number of aminoacids
of the peptide YTSLIHSLIEESQNQQEKNEQELLELDKWASLWNWF?
Show/Hide Solution
The following string is an extract of a blast alignment with compacted textual output. This is a comma (“,”) separated text file where the columns report the following info: the first column is the query_id, the second the subject_id (i.e. the reference on which we aligned the query), the third is the percentage of identity and then we have the alignment length, number of mismatches, gap opens, start point of the alignment on the query, end point of the alignment on the query, start point of the alignment on the subject, end point of the alignment on the subject and evalue of the alignment.
#Fields:q.id,s.id,% ident,align len,mismatches,gap opens,q.start,q.end,s.start,s.end,evalue
ab1_400a,scaffold16155,98.698,384,4,1,12,394,6700,7083,0.0
ab1_400b,scaffold14620,98.698,384,4,1,12,394,1240,857,0.0
92A2_SP6_344a,scaffold14394,95.575,113,5,0,97,209,250760,250648,2.92e-44
92A2_SP6_344b,scaffold10682,97.849,93,2,0,18,110,898,990,3.81e-38
92A2_T7_558a,scaffold277,88.746,311,31,3,21,330,26630,26937,5.81e-103
92A2_T7_558b,scaffold277,89.545,220,21,2,27,246,27167,26950,6.06e-73
92A2_T7_558c,scaffold1125,88.125,320,31,5,30,346,231532,231847,7.51e-102
ab1_675a,scaffold4896,100.000,661,0,0,15,675,79051,78391,0.0
ab1_676b,scaffold4896,99.552,670,0,3,7,673,78421,79090,0.0
For each alignment, store the subject id, the percentage of identity and evalue, subject start and end in a dictionary using the query id as key. All this information can be stored in a dictionary having subject id as key and a dictionary with all the information as value:
alignments["ab1_400"] = {"subjectid" : scaffold16155, "perc_id" : 98.698, "evalue" : 0.0}Print the whole dictionary
Print only the alignments having percentage of identity > 90%
Note: skip the first comment line (i.e. skip line if starts with “#”). Note1: when storing the percentage of identity remember to convert the string into a float.
The expected output is:
{'92A2_T7_558a': {'perc_id': 88.746, 'subjectid': 'scaffold277', 'evalue': '5.81e-103'},
'92A2_T7_558b': {'perc_id': 89.545, 'subjectid': 'scaffold277', 'evalue': '6.06e-73'},
'92A2_SP6_344b': {'perc_id': 97.849, 'subjectid': 'scaffold10682', 'evalue': '3.81e-38'},
'92A2_T7_558c': {'perc_id': 88.125, 'subjectid': 'scaffold1125', 'evalue': '7.51e-102'},
'ab1_400a': {'perc_id': 98.698, 'subjectid': 'scaffold16155', 'evalue': '0.0'},
'ab1_675a': {'perc_id': 100.0, 'subjectid': 'scaffold4896', 'evalue': '0.0'},
'ab1_400b': {'perc_id': 98.698, 'subjectid': 'scaffold14620', 'evalue': '0.0'},
'92A2_SP6_344a': {'perc_id': 95.575, 'subjectid': 'scaffold14394', 'evalue': '2.92e-44'},
'ab1_676b': {'perc_id': 99.552, 'subjectid': 'scaffold4896', 'evalue': '0.0'}}
Alignments with identity > 90%:
Query id Subject id % ident evalue
92A2_SP6_344b scaffold10682 97.849 3.81e-38
ab1_400a scaffold16155 98.698 0.0
ab1_675a scaffold4896 100.0 0.0
ab1_400b scaffold14620 98.698 0.0
92A2_SP6_344a scaffold14394 95.575 2.92e-44
ab1_676b scaffold4896 99.552 0.0
Show/Hide Solution
The following text (separated with a comma “,”) is an extract of protein-protein interactions network stored in the database STRING involving PKLR (Pyruvate kinase, liver and RBC) that plays a key role in glycolysis:
#node1,node2,node1_ext_id,node2_ext_id,
ENO1,TPI1,ENSP00000234590,ENSP00000229270
PKLR,ENO1,ENSP00000339933,ENSP00000234590
PKLR,ENO3,ENSP00000339933,ENSP00000324105
PGK1,ENO1,ENSP00000362413,ENSP00000234590
PGK1,TPI1,ENSP00000362413,ENSP00000229270
GPI,TPI1,ENSP00000405573,ENSP00000229270
PKLR,ENO2,ENSP00000339933,ENSP00000229277
PGK1,ENO3,ENSP00000362413,ENSP00000324105
PGK1,ENO2,ENSP00000362413,ENSP00000229277
GPI,PKLR,ENSP00000405573,ENSP00000339933
ENO2,TPI1,ENSP00000229277,ENSP00000229270
PGK2,ENO1,ENSP00000305995,ENSP00000234590
ENO3,PGK2,ENSP00000324105,ENSP00000305995
PGK2,TPI1,ENSP00000305995,ENSP00000229270
ENO3,TPI1,ENSP00000324105,ENSP00000229270
PGK2,ENO2,ENSP00000305995,ENSP00000229277
GPI,ENO3,ENSP00000405573,ENSP00000324105
PKLR,LDHB,ENSP00000339933,ENSP00000229319
PKLR,LDHC,ENSP00000339933,ENSP00000280704
PKLR,TPI1,ENSP00000339933,ENSP00000229270
PGK1,PKLR,ENSP00000362413,ENSP00000339933
GPI,ENO2,ENSP00000405573,ENSP00000229277
PKLR,PGK2,ENSP00000339933,ENSP00000305995
GPI,PGK1,ENSP00000405573,ENSP00000362413
ME3,PKLR,ENSP00000352657,ENSP00000339933
ME3,LDHB,ENSP00000352657,ENSP00000229319
ME3,LDHC,ENSP00000352657,ENSP00000280704
GPI,PGK2,ENSP00000405573,ENSP00000305995
GPI,ENO1,ENSP00000405573,ENSP00000234590
GPI,LDHB,ENSP00000405573,ENSP00000229319
ENO3,ENO2,ENSP00000324105,ENSP00000229277
GPI,LDHC,ENSP00000405573,ENSP00000280704
ENO3,LDHB,ENSP00000324105,ENSP00000229319
ENO3,LDHC,ENSP00000324105,ENSP00000280704
ENO1,LDHB,ENSP00000234590,ENSP00000229319
LDHB,TPI1,ENSP00000229319,ENSP00000229270
LDHC,TPI1,ENSP00000280704,ENSP00000229270
PGK2,LDHC,ENSP00000305995,ENSP00000280704
PGK1,LDHB,ENSP00000362413,ENSP00000229319
PGK1,PGK2,ENSP00000362413,ENSP00000305995
ENO1,ENO2,ENSP00000234590,ENSP00000229277
LDHC,ENO1,ENSP00000280704,ENSP00000234590
LDHB,ENO2,ENSP00000229319,ENSP00000229277
LDHC,ENO2,ENSP00000280704,ENSP00000229277
ENO3,ENO1,ENSP00000324105,ENSP00000234590
PGK1,LDHC,ENSP00000362413,ENSP00000280704
GPI,ME3,ENSP00000405573,ENSP00000352657
PGK2,LDHB,ENSP00000305995,ENSP00000229319
ME3,TPI1,ENSP00000352657,ENSP00000229270
Here is a graphic representation of the protein-protein interactions:
Note: we can assume that relations between nodes are transitive. node1 --> node2
implies node2 --> node1.
1. Store the network information in a dictionary having node1 as key and
the list of all nodes2 associated to it as value (remember to skip the first
line that is the header). Remember transitivity, therefore add also node2 -->node1
2. Find all first neighbours of "PKLR" (i.e. the nodes that are directly connected
to "PKLR") and print them
3. Find all first neighbours of "ME3" (i.e. the nodes that are directly connected
to "PKLR") and print them
4. Find all the second neighbours of "ME3" (i.e. the nodes that are connected to nodes
directly connected to "ME3", but not directly to "ME3").
Show/Hide Solution
Practical 6¶
In this practical we will see how to define functions to reuse code, we will talk about the scope of variables and finally will see how to deal with files in Python.
Functions¶
A function is a block of code that has a name and that performs a task. A function can be thought of as a box that gets an input and returns an output.
Why should we use functions? For a lot of reasons including:
Reduce code duplication: put in functions parts of code that are needed several times in the whole program so that you don’t need to repeat the same code over and over again;
Decompose a complex task: make the code easier to write and understand by splitting the whole program into several easier functions;
both things improve code readability and make your code easier to understand.
The basic definition of a function is:
def function_name(input) :
#code implementing the function
...
...
return return_value
Functions are defined with the def keyword that proceeds the function_name and then a list of parameters is passed in the brackets. A colon : is used to end the line holding the definition of the function. The code implementing the function is specified by using indentation. A function might or might not return a value. In the first case a return statement is used.
Consider the following example in which we want to compute the sum of the square root of the values in lists X, Y, Z.
[1]:
import math
X = [1, 5, 4, 4, 7, 2, 1]
Y = [9, 4, 7, 1, 2]
Z = [9, 9, 4, 7]
sum_x = 0
sum_y = 0
sum_z = 0
for el in X:
sum_x += math.sqrt(el)
for el in Y:
sum_y += math.sqrt(el)
for el in Z:
sum_z += math.sqrt(el)
print(X, "sum_sqrt:", sum_x)
print(Y, "sum_sqrt:", sum_y)
print(Z, "sum_sqrt:", sum_z)
[1, 5, 4, 4, 7, 2, 1] sum_sqrt: 12.296032850937475
[9, 4, 7, 1, 2] sum_sqrt: 10.059964873437686
[9, 9, 4, 7] sum_sqrt: 10.64575131106459
In the above code there is a lot of duplication. Let’s try and rewrite the above code taking advantage of functions.
[2]:
import math
X = [1, 5, 4, 4, 7, 2, 1]
Y = [9, 4, 7, 1, 2]
Z = [9, 9, 4, 7]
# This function does not return anything
def print_sum_sqrt(vals):
tmp = 0
for el in vals:
tmp += math.sqrt(el)
print(vals, "sum_sqrt:", tmp)
print_sum_sqrt(X)
print_sum_sqrt(Y)
print_sum_sqrt(Z)
[1, 5, 4, 4, 7, 2, 1] sum_sqrt: 12.296032850937475
[9, 4, 7, 1, 2] sum_sqrt: 10.059964873437686
[9, 9, 4, 7] sum_sqrt: 10.64575131106459
If we want, we can modify print_sum_sqrt to output the values:
[3]:
import math
X = [1, 5, 4, 4, 7, 2, 1]
Y = [9, 4, 7, 1, 2]
Z = [9, 9, 4, 7]
# This function returns the sum
def sum_sqrt(vals):
tmp = 0
for el in vals:
tmp += math.sqrt(el)
return tmp
x = sum_sqrt(X)
y = sum_sqrt(Y)
z = sum_sqrt(Z)
print(X, "sum_sqrt:", x)
print(Y, "sum_sqrt:", y)
print(Z, "sum_sqrt:", z)
# we have the sums as numbers, can use them
print("Sum of all: ", x + y + z)
[1, 5, 4, 4, 7, 2, 1] sum_sqrt: 12.296032850937475
[9, 4, 7, 1, 2] sum_sqrt: 10.059964873437686
[9, 9, 4, 7] sum_sqrt: 10.64575131106459
Sum of all: 33.00174903543975
Example: Define a function that implements the sum of two lists of integers (note that there is no check that the two lists actually contain integers and that they have the same size).
[4]:
def int_list_sum(l1,l2):
"""implements the sum of two lists of integers having the same size
"""
ret =[]
for i in range(len(l1)):
ret.append(l1[i] + l2[i])
return ret
L1 = list(range(1,10))
L2 = list(range(20,30))
print("L1:", L1)
print("L2:", L2)
res = int_list_sum(L1,L2)
print("L1+L2:", res)
res = int_list_sum(L1,L1)
print("L1+L1", res)
L1: [1, 2, 3, 4, 5, 6, 7, 8, 9]
L2: [20, 21, 22, 23, 24, 25, 26, 27, 28, 29]
L1+L2: [21, 23, 25, 27, 29, 31, 33, 35, 37]
L1+L1 [2, 4, 6, 8, 10, 12, 14, 16, 18]
Note that once the function has been defined, it can be called as many times as wanted with different input parameters. Moreover, a function does not do anything until it is actually called. A function can return 0 (in this case the return value would be “None”), 1 or more results. Notice also that collecting the results of a function is not mandatory.
Example: Let’s write a function that, given a list of elements, prints only the even-placed ones without returning anything.
[5]:
def get_even_placed(myList):
"""returns the even placed elements of myList"""
ret = [myList[i] for i in range(len(myList)) if i % 2 == 0]
print(ret)
L1 = ["hi", "there", "from","python","!"]
L2 = list(range(13))
print("L1:", L1)
print("L2:", L2)
print("even L1:")
get_even_placed(L1)
print("even L2:")
get_even_placed(L2)
L1: ['hi', 'there', 'from', 'python', '!']
L2: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12]
even L1:
['hi', 'from', '!']
even L2:
[0, 2, 4, 6, 8, 10, 12]
Note that the function above is polymorphic (i.e. it works on several data types, provided that we can iterate through them).
Example: Let’s write a function that, given a list of integers, returns the number of elements, the maximum and minimum.
[6]:
"""easy! this changes the original list!!!"""
def get_info(myList):
"""returns len of myList, min and max value
(assumes elements are integers) but it would work with str"""
myList.sort()
return len(myList), myList[0], myList[-1] #return type is a tuple
A = [7, 1, 125, 4, -1, 0]
print("Original A:", A, "\n")
result = get_info(A)
print("Len:", result[0], "Min:", result[1], "Max:",result[2], "\n" )
print("A now:", A)
Original A: [7, 1, 125, 4, -1, 0]
Len: 6 Min: -1 Max: 125
A now: [-1, 0, 1, 4, 7, 125]
We need to make a copy if we do not want to affect the caller (see why below):
[39]:
def get_info(myList):
"""returns len of myList, min and max value
(assumes elements are integers) but it would work with str"""
tmp = myList[:] #copy the input list
tmp.sort()
return len(tmp), tmp[0], tmp[-1] #return type is a tuple
A = [7, 1, 125, 4, -1, 0]
print("Original A:", A, "\n")
result = get_info(A)
print("Len:", result[0], "Min:", result[1], "Max:",result[2], "\n" )
print("A now:", A)
Original A: [7, 1, 125, 4, -1, 0]
Len: 6 Min: -1 Max: 125
A now: [7, 1, 125, 4, -1, 0]
[8]:
def my_sum(myList):
ret = 0
for el in myList:
ret += el # == ret = ret + el
return ret
A = [1,2,3,4,5,6]
B = [7, 9, 4]
s = my_sum(A)
print("List A:", A)
print("Sum:", s)
s = my_sum(B)
print("List B:", B)
print("Sum:", s)
List A: [1, 2, 3, 4, 5, 6]
Sum: 21
List B: [7, 9, 4]
Sum: 20
Please note that the return value above is actually a tuple. Importantly enough, a function needs to be defined (i.e. its code has to be written) before it can actually be used otherwise the Python interpreter does not know what to do when the function is actually called with some parameters.
[9]:
A = [1,2,3]
my_sum_new(A)
def my_sum_new(myList):
ret = 0
for el in myList:
ret += el
return ret
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-9-50f5bebe9695> in <module>
1 A = [1,2,3]
----> 2 my_sum_new(A)
3
4 def my_sum_new(myList):
5 ret = 0
NameError: name 'my_sum_new' is not defined
Namespace and variable scope¶
Namespaces are the way Python makes sure that names in a program are unique and can be safely used without any conflicts. They are mappings from names to objects, or in other words places where names are associated to objects. Namespaces can be considered as the context and in Python are implemented as dictionaries that map the name to the object. According to Python’s reference a scope is a textual region of a Python program, where a namespace is directly accessible, which means that Python will look into that namespace to find the object associated to a name. Four namespaces are made available by Python:
1. **Local**: the innermost that contains local names (inside a function or a class);
2. **Enclosing**: the scope of the enclosing function,
it does not contain local nor global names (nested functions) ;
3. **Global**: contains the global names;
4. **Built-in**: contains all built in names
(e.g. print, if, while, for,...)
When one refers to a name, Python tries to find it in the current namespace, if it is not found it continues looking in the namespace that contains it until the built-in namespace is reached. If the name is not found there either, the Python interpreter will throw a NameError exception, meaning it cannot find the name. The order in which namespaces are considered is: Local, Enclosing, Global and Built-in (LEGB).
Consider the following example:
[10]:
def my_function():
var = 1 #local variable
print("Local:", var)
b = "my string"
print("Local:", b)
var = 7 #global variable
my_function()
print("Global:", var)
print(b)
Local: 1
Local: my string
Global: 7
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-10-da11a41b34ff> in <module>
8 my_function()
9 print("Global:", var)
---> 10 print(b)
11
NameError: name 'b' is not defined
Variables defined within a function can only be seen within the function. That is why variable b is defined only within the function. Variables defined outside all functions are global to the whole program. The namespace of the local variable is within the function my_function, while outside it the variable will have its global value.
And the following:
[11]:
def outer_function():
var = 1 #outer
def inner_function():
var = 2 #inner
print("Inner:", var)
print("Inner:", B)
inner_function()
print("Outer:", var)
var = 3 #global
B = "This is B"
outer_function()
print("Global:", var)
print("Global:", B)
Inner: 2
Inner: This is B
Outer: 1
Global: 3
Global: This is B
Note in particular that the variable B is global, therefore it is accessible everywhere and also inside the inner_function. On the contrary, the value of var defined within the inner_function is accessible only in the namespace defined by it, outside it will assume different values as shown in the example.
In a nutshell, remember the three simple rules seen in the lecture. Within a def:
1. Name assignments create local names by default;
2. Name references search the following four scopes in the order:
local, enclosing functions (if any), then global and finally built-in (LEGB)
3. Names declared in global and nonlocal statements map assigned names to
enclosing module and function scopes.
Argument passing¶
Arguments are the parameters and data we pass to functions. When passing arguments, there are three important things to bear in mind:
Passing an argument is actually assigning an object to a local variable name;
Assigning an object to a variable name within a function does not affect the caller;
Changing a mutable object variable name within a function affects the caller
Consider the following examples:
[15]:
"""Assigning the argument does not affect the caller"""
def my_f(x):
x = "local value" #local
print("Local: ", x)
x = "global value" #global
my_f(x)
print("Global:", x)
my_f(x)
Local: local value
Global: global value
Local: local value
[16]:
"""Changing a mutable affects the caller"""
def my_f(myList):
myList[1] = "new value1"
myList[3] = "new value2"
print("Local: ", myList)
myList = ["old value"]*4
print("Global:", myList)
my_f(myList)
print("Global now: ", myList)
Global: ['old value', 'old value', 'old value', 'old value']
Local: ['old value', 'new value1', 'old value', 'new value2']
Global now: ['old value', 'new value1', 'old value', 'new value2']
Recall what seen in the lecture:
The behaviour above is because immutable objects are passed by value (therefore it is like making a copy), while mutable objects are passed by reference (therefore changing them effectively changes the original object).
To avoid making changes to a mutable object passed as parameter one needs to explicitely make a copy of it.
Consider the example seen before. Example: Let’s write a function that, given a list of integers, returns the number of elements, the maximum and minimum.
[17]:
def get_info(myList):
"""returns len of myList, min and max value (assumes elements are integers)"""
myList.sort()
return len(myList), myList[0], myList[-1] #return type is a tuple
def get_info_copy(myList):
"""returns len of myList, min and max value (assumes elements are integers)"""
tmp = myList[:] #copy the input list!!!!
tmp.sort()
return len(tmp), tmp[0], tmp[-1] #return type is a tuple
A = [7, 1, 125, 4, -1, 0]
B = [70, 10, 1250, 40, -10, 0, 10]
print("A:", A)
result = get_info(A)
print("Len:", result[0], "Min:", result[1], "Max:",result[2] )
print("A now:", A) #whoops A is changed!!!
print("\n###### With copy now ########")
print("\nB:", B)
result = get_info_copy(B)
print("Len:", result[0], "Min:", result[1], "Max:",result[2] )
print("B now:", B) #B is not changed!!!
A: [7, 1, 125, 4, -1, 0]
Len: 6 Min: -1 Max: 125
A now: [-1, 0, 1, 4, 7, 125]
###### With copy now ########
B: [70, 10, 1250, 40, -10, 0, 10]
Len: 7 Min: -10 Max: 1250
B now: [70, 10, 1250, 40, -10, 0, 10]
Positional arguments¶
Arguments can be passed to functions following the order in which they appear in the function definition.
Consider the following example:
[18]:
def print_parameters(a,b,c,d):
print("1st param:", a)
print("2nd param:", b)
print("3rd param:", c)
print("4th param:", d)
print_parameters("A", "B", "C", "D")
1st param: A
2nd param: B
3rd param: C
4th param: D
Passing arguments by keyword¶
Given the name of an argument as specified in the definition of the function, parameters can be passed using the name = value syntax.
For example:
[19]:
def print_parameters(a,b,c,d):
print("1st param:", a)
print("2nd param:", b)
print("3rd param:", c)
print("4th param:", d)
print_parameters(a = 1, c=3, d=4, b=2)
print("\n###############\n")
print_parameters("first","second",d="fourth",c="third")
print("\n###############\n")
1st param: 1
2nd param: 2
3rd param: 3
4th param: 4
###############
1st param: first
2nd param: second
3rd param: third
4th param: fourth
###############
Arguments passed positionally and by name can be used at the same time, but parameters passed by name must always be to the left of those passed by name. The following code in fact is not accepted by the Python interpreter:
[20]:
def print_parameters(a,b,c,d):
print("1st param:", a)
print("2nd param:", b)
print("3rd param:", c)
print("4th param:", d)
#The following won't work
print_parameters(d="fourth",c="third", "first","second")
#Correct code instead:
print_parameters("first","second", d="fourth",c="third")
File "<ipython-input-20-0aba188b6596>", line 9
print_parameters(d="fourth",c="third", "first","second")
^
SyntaxError: positional argument follows keyword argument
Specifying default values¶
During the definition of a function it is possible to specify default values. The syntax is the following:
def my_function(par1 = val1, par2 = val2, par3 = val3):
Consider the following example:
[21]:
def print_parameters(a="defaultA", b="defaultB",c="defaultC"):
print("a:",a)
print("b:",b)
print("c:",c)
print_parameters("param_A")
print("\n#################\n")
print_parameters(b="PARAMETER_B")
print("\n#################\n")
print_parameters()
print("\n#################\n")
print_parameters(c="PARAMETER_C", b="PAR_B")
a: param_A
b: defaultB
c: defaultC
#################
a: defaultA
b: PARAMETER_B
c: defaultC
#################
a: defaultA
b: defaultB
c: defaultC
#################
a: defaultA
b: PAR_B
c: PARAMETER_C
Another example.
Example. Write a function that rounds a float at a precision (i.e. number of decimals) specified in input. If no precision is specified then the whole number should be returned. Examples:
my_round(1.1717413, 3) = 1.172 my_round(1.1717413, 1) = 1.2 my_round(1.1717413) = 1.17174.
[22]:
import math
def my_round(val, precision = 0):
if precision == 0:
return val
else:
return round(val * 10** precision)/ 10**precision
my_val = 1.717413
print(my_val, " precision 2: ", my_round(my_val,2))
print(my_val, " precision 1: ", my_round(my_val,1))
print(my_val, " precision max: ", my_round(my_val))
print("")
my_val = math.pi
print(my_val, " precision 10: ", my_round(my_val,10))
1.717413 precision 2: 1.72
1.717413 precision 1: 1.7
1.717413 precision max: 1.717413
3.141592653589793 precision 10: 3.1415926536
We can also use the function implemented and apply it to a list of values through list comprehension.
Example: create a list with the square root values of the first 20 integers with 3 digits of precision.
[23]:
import math
def my_round(val, precision = 0):
if precision == 0:
return val
else:
return round(val * 10** precision)/ 10**precision
result = [my_round(math.sqrt(x), 3) for x in range(1,21)]
print(result)
[1.0, 1.414, 1.732, 2.0, 2.236, 2.449, 2.646, 2.828, 3.0, 3.162, 3.317, 3.464, 3.606, 3.742, 3.873, 4.0, 4.123, 4.243, 4.359, 4.472]
As a final example of list comprehension, let’s print only the values of the list result above whose digits sum up to a certain value x. Hint: write another function!
[24]:
import math
def my_round(val, precision = 0):
if precision == 0:
return val
else:
return round(val * 10** precision)/ 10**precision
#version without list comprehension
def sum_of_digits_noList(num, total):
tmp = str(num)
tot = 0
for d in tmp:
if d != ".":
tot += int(d)
if tot == total:
return True
else:
return False
#with list comprehension
def sum_of_digits(num, total):
tmp = [int(x) for x in str(num) if x != "."]
return sum(tmp) == total
result = [my_round(math.sqrt(x), 3) for x in range(1,21)]
print("sum is 10:", [x for x in result if sum_of_digits(x, 10)])
print("sum is 13:",[x for x in result if sum_of_digits(x, 13)])
sum is 10: [1.414, 4.123]
sum is 13: [1.732, 2.236, 4.243]
File input and output¶
Files are non volatile data stored at specific locations in memory. To read or write from/to a file, one first needs to create a reference to the file. This is called the handle to the file.
Recall from the lecture that Python provides programmers with the following functions and methods:
To read or write to a file one first needs to open it with the python’s built-in function open that returns a handler to the file. The handler can then be used to read or write the content of the file.
Example: Download the file textFile.txt to your favourite location and read it from python, printing out all its content. NOTE: the path of your file might be different from mine.
[25]:
fh = open("file_samples/textFile.txt", "r") #read-only mode
print("--- File content ---")
for line in fh:
print(line, end ="") #no need to add a new line
fh.close()
print("\n--- File closed ---")
--- File content ---
Hi everybody,
This is my first file
and it contains a total of
four lines!
--- File closed ---
The usual interaction with files is done in three steps: open the file, read or write its content, close the file.
Opening a file¶
As said, a file needs to be opened before working with it. This can be done by using the function open.
The standard syntax is:
file_handle = open("file_name", "file_mode")
where file_name is a string representing the path to reach the file (either absolute or relative to the .py module we are writing) and file_mode is the string representing the opening mode of the file. file_mode can be:
"r"which is the default and opens the file in read only mode;"w"write only mode. Note that this would overwrite an existing file;"a"append mode (i.e. add information at the end of an existing file or create a new file)"t"text mode. The file will be a text file (this is the default)."b"binary mode. The file will not be a textual file."x"exclusive creation. This will fail if the file already exists."+"update mode. The file will be opened with read and write permissions.
Opening modes can be combined (ex. "ra" would read and append, "wb" would write (and overwrite) a binary file, "r+b" read and write a binary file).
Closing a file¶
A opened file always needs to be closed. The basic syntax is:
file_handle.close()
this will free up resources and will not allow any more operations on the same file.
The following code will in fact crash, because the file has been closed and therefore no more operations can be performed on it.
[26]:
fh = open("file_samples/textFile.txt", "r") #read-only mode
print("--- File content ---")
for line in fh:
print(line, end ="") #no need to add a new line
fh.close()
print("\n--- File closed ---")
print(fh.readline())
--- File content ---
Hi everybody,
This is my first file
and it contains a total of
four lines!
--- File closed ---
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-26-0367c74d60af> in <module>
10 print("\n--- File closed ---")
11
---> 12 print(fh.readline())
ValueError: I/O operation on closed file.
An alternative way to open and implicitly close the file is by using the with keyword. The basic syntax is:
with open("file") as f:
#do some stuff
#until done with it
The previous example would become:
[27]:
print("--- File content ---")
with open("file_samples/textFile.txt", "r") as f:
for line in f:
print(line, end ="") #no need to add a new line
print("\n--- File closed ---")
--- File content ---
Hi everybody,
This is my first file
and it contains a total of
four lines!
--- File closed ---
Reading from a file¶
There are several ways for reading a file that has been opened in read mode having file handle fh:
content = fh.read()reads the whole file in the content string. Good for small and not structured files.line = fh.readline()reads the file one line at a time storing it in the stringlinelines = fh.readlines()reads all the lines of the file storing them as a listlinesusing the iterator:
for line in f: #process the information
which is the most convenient way for big files.
Let’s see some examples. Note that to restart reading a file from the beginning we need to close it and open it gain.
[28]:
fh = open("file_samples/textFile.txt", "r") #read-only mode
content = fh.read()
print("--- Mode1 (the whole file in a string) ---")
print(content)
fh.close()
print("")
print("--- Mode2 (line by line) ---")
with open("file_samples/textFile.txt","r") as f:
print("Line1: ", f.readline(), end = "")
print("Line2: ", f.readline(), end = "")
print("")
print("--- Mode3 (all lines as a list) ---")
with open("file_samples/textFile.txt","r") as f:
print(f.readlines())
print("")
print("--- Mode4 (as a stream) ---")
with open("file_samples/textFile.txt","r") as f:
for line in f:
print(line, end = "")
--- Mode1 (the whole file in a string) ---
Hi everybody,
This is my first file
and it contains a total of
four lines!
--- Mode2 (line by line) ---
Line1: Hi everybody,
Line2: This is my first file
--- Mode3 (all lines as a list) ---
['Hi everybody,\n', 'This is my first file\n', 'and it contains a total of\n', 'four lines!']
--- Mode4 (as a stream) ---
Hi everybody,
This is my first file
and it contains a total of
four lines!
Writing to a file¶
To write some data to a file it must first be opened in write mode (i.e. “w”) or append mode (“a”, “+”). The actual writing can be performed by the method write that has the following basic syntax:
file_handle.write(data_to_be_written)
To make sure all data is written to the file, we must remember to close the file after writing on it.
Example: Given the matrix represented as list of lists, M = [[1,2,3], [4,5,6], [7,8,9]] let’s write it on a file my_matrix.txt as \(\begin{matrix}1 & 2 & 3\\4 & 5 & 6\\7 & 8 & 9\end{matrix}\)
[45]:
M = [[1,2,3], [4,5,6], [7,8,9]]
with open("file_samples/my_matrix.txt", "w") as f:
for line in M:
str_line = [str(x) for x in line] #to make this "joinable"
f.write(" ".join(str_line))
f.write("\n")
#no need to put the close because we used with
#Equivalent code (without with clause):
M = [[1,2,3], [4,5,6], [7,8,9]]
f = open("file_samples/my_matrix.txt", "w")
for line in M:
str_line = [str(x) for x in line]
f.write(" ".join(str_line))
f.write("\n")
f.close()
String formatting with format¶
Strings can be formatted with the method format. A lot of information on the use of format can be found here.
Format can be used to add values to a string in specific placeholders (normally defined with the syntax {}) or to format values according to the user specifications (e.g. number of decimal places for floating point numbers).
In the following we will see some simple examples.
[30]:
#simple empty placeholders
print("I like {} more than {}.\n".format("python", "java"))
#indexed placeholders, note order
print("I like {0} more than {1} or {2}.\n".format("python", "java", "C++"))
print("I like {2} more than {1} or {0}.\n".format("python", "java", "C++"))
#indexed and named placeholders
print("I like {1} more than {c} or {0}.\n".format("python", "java", c="C++"))
#with type specification
import math
print("The square root of {0} is {1:f}.\n".format(2, math.sqrt(2)))
#with type and format specification (NOTE: {.2f})
print("The square root of {0} is {1:.2f}.\n".format(2, math.sqrt(2)))
#spacing data properly
print("{:2s}|{:5}|{:6}".format("N","sqrt","square"))
for i in range(0,20):
print("{:2d}|{:5.3f}|{:6d}".format(i,math.sqrt(i),i*i))
I like python more than java.
I like python more than java or C++.
I like C++ more than java or python.
I like java more than C++ or python.
The square root of 2 is 1.414214.
The square root of 2 is 1.41.
N |sqrt |square
0|0.000| 0
1|1.000| 1
2|1.414| 4
3|1.732| 9
4|2.000| 16
5|2.236| 25
6|2.449| 36
7|2.646| 49
8|2.828| 64
9|3.000| 81
10|3.162| 100
11|3.317| 121
12|3.464| 144
13|3.606| 169
14|3.742| 196
15|3.873| 225
16|4.000| 256
17|4.123| 289
18|4.243| 324
19|4.359| 361
Exercises¶
Implement a function that takes in input a string representing a DNA sequence and computes its reverse-complement. Take care to reverse complement any character other than (A,T,C,G,a,t,c,g) to N. The function should preserve the case of each letter (i.e. A becomes T, but a becomes t). For simplicity all bases that do not represent nucleotides are converted to a capital N. Hint: create a dictionary revDict with bases as keys and their complements as values. Ex. revDict = {“A” : “T” , “a” : “t”, …}.
Apply the function to the DNA sequence “ATTACATATCATACTATCGCNTTCTAAATA”
Apply the function to the DNA sequence “acaTTACAtagataATACTaccataGCNTTCTAAATA”
Apply the function to the DNA sequence “TTTTACCKKKAKTUUUITTTARRRRRAIUTYYA”
Check that the reverse complement of the reverse complement of the sequence in 1. is exactly as the original sequence.
Show/Hide Solution
Write the following python functions and test them with some parameters of your choice:
getDivisors: the function has a positive integer as parameter and returns a list of all the positive divisors of the integer in input (excluding the number itself). Example:
getDivisors(6) --> [1,2,3]checkSum: the function has a list and an integer as parameters and returns True if the sum of all elements in the list equals the integer, False otherwise. Example:
checkSum([1,2,3], 6) --> True,checkSum([1,2,3],1) --> False.checkPerfect: the function gets an integer as parameter and returns True if the integer is a perfect number, False otherwise. A number is perfect if all its divisors (excluding itself) sum to its value. Example:
checkPerfect(6) --> Truebecause 1+2+3 = 6. Hint: use the functions implemented before.
Use the three implemented functions to write a fourth function:
getFirstNperfects: the function gets an integer N as parameter and returns a dictionary with the first N perfect numbers. The key of the dictionary is the perfect number, while the value of the dictionary is the list of its divisors. Example: getFirstNperfects(1) --> {6 : [1,2,3]}
Get and print the first 4 perfect numbers and finally test if 33550336 is a perfect number.
WARNING: do not try to find more than 4 perfect numbers as it might take a while!!!
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A pangram is a sentence that contains all the letters of the alphabet at least once (let’s ignore numbers and other characters for simplicity). 1. Write a function that gets a text in input and returns True if it is a pangram. 2. Write a function that computes how many unique characters an input sentence has; 3. Modify the function at 1. in such a way that a user can specify an alphabet and check if the provided text is a pangram in that reference alphabet.
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A restriction enzyme is an enzyme that cleaves DNA into fragments at or near specific recognition sites within molecules known as restriction sites. A lot of restriction enzymes exist that cleave the DNA at different sites. For simplicity let’s focus on only the 5’-3’ orientation of DNA. Consider the following enzymes, stored as a dictionary:
restriction_enzymes = {'EcoRI' : ('GAATTC','G','AATTC'), 'TaqI': ('TCGA','T','CGA'), 'PvII: ('CAGCTG','CAG','CTG')}
meaning for example that enzyme ‘EcoRI’ would split a sequence xxxxGAATTCxxxxx into the two sequences xxxxG and AATTCxxxxx.
A. Implement a function (restrict_DNA(sequence, enzyme)) that takes a DNA string in input, and the specification of a restriction enzyme (e.g. “TaqI”) and returns a list with all the possible pairs of cleaved DNA sequences. B. Extend this code in such a way that it can process a list of DNA sequences rather than a single one and returns a list of lists (write a function restrict_DNA_sequences(list_of_sequences, enzyme). If the enzyme specified in input is not recognized, the script should output a warning message without crashing.
Test your function(s) with the following calls:
seq = "TACTACCTACGAATTCAAATGAATTCCCTTAAGAATTCATTCGATCGATTAAAGAGCTGATTAGAATATCCAGCTG"
print("Restriction with EcoRI")
print(restrict_DNA(seq, 'EcoRI'))
print("\nRestriction with PvII")
print(restrict_DNA(seq, 'PvII'))
print("\nRestriction with TaqI")
R = restrict_DNA(seq, 'TaqI')
print(R)
print("\nSecond restriction with EcoRI")
print(restrict_DNA_sequences(R, 'EcoRI'))
print(restrict_DNA_sequences(R, 'MyEnzyme'))
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Blast is a well known tool to perform sequence alignment between a pool of query sequences and a pool of subject sequences. Among the other formats, it can produce an text output that is tab separated (
\t) capturing user specified output. Comments in the file are written in lines starting with an hash key (“#”). A sample blast output file is blast_sample.tsv, please download it and spend some time to look at it. The meaning of all columns is specified in the file header:# Fields: query id, subject id, query length, % identity, alignment length, identical, gap opens, q. start, q. end, s. start, s. end, evalue
Write a python program with:
A function (readBlast) that reads in the blast .tsv file (storing each line in a list) ignoring comment lines;
A function (filterBlast) that gets a string in input representing a blast alignment and filters it according to the user specified parameters below. It should return True if all filters are passed, false otherwise:
% identity > identity_threshold (default 0%)
evalue < evalue_thrshold (default 0.5)
alignment length / query length > align_threshold (default 0)
The program should report how many entries out of the total passed the filter.
Test several combinations of filters like:
1. identity_theshold = 97, all others default
2. evalue_threshold = 0.5, all others default
3. align_threshold = 0.9, all others default
4. align_threshold = 0.9, identity_threshold = 97
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Fasta is a format representing nucleotide or peptide sequences. Each entry of a fasta file starts with a “>” followed by the identifier of the entry (the header of the sequence). All the lines following a header represent the sequence belonging to that identifier. Here you can find an example of fasta file: contigs82.fasta. Please download it and have a look at its content.
Write a python program that reads a fasta file and prints to screen the identifier of the sequence and the frequency of all the characters in the sequence (note that sequences might contain all IUPAC codes in case of SNPs). Hint: use a dictionary.
Sample output:
MDC020656.85 :
N has freq 0.052
T has freq 0.273
A has freq 0.308
G has freq 0.203
C has freq 0.163
MDC001115.177 :
N has freq 0.018
G has freq 0.157
A has freq 0.302
T has freq 0.316
C has freq 0.207
...
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Write a python program that reads two files. The first is a one column text file (contig_ids.txt) with the identifiers of some contigs that are present in the second file, which is a fasta formatted file (contigs82.fasta). The program will write on a third, fasta formatted file (e.g. filtered_contigs.fasta) only those entries in contigs82.fasta having identifier in contig_ids.txt.
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Write a python program that:
reads the text file sample_text.txt and stores in a dictionary how many times each word appears (hint: the key is the word and the count is the value);
prints to screen how many lines the file has and how many distinct words are in the file;
writes to a text file (scientist_histo.csv) the histogram of the words in comma separated value format (i.e. word,count). Words must be sorted alphabetically;
Finally, write a function that prints to screen (alphabetically) all the words that have a count higher than a threshold N and apply it with N = 5.
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Practical 7¶
In this practical we will keep practicing with functions and will see how to get input from the command line.
Functions¶
Reminder. The basic definition of a function is:
def function_name(input) :
#code implementing the function
...
...
return return_value
Functions are defined with the def keyword that proceeds the function_name and then a list of parameters is passed in the brackets. A colon : is used to end the line holding the definition of the function. The code implementing the function is specified by using indentation. A function might or might not return a value. In the first case a return statement is used.
Getting input from the command line¶
To call a program my_python_program.py from command line, you just have to open a terminal (in Linux) or the command prompt (in Windows) and, assuming that python is present in the path, you can cd into the folder containing your python program, (eg. cd C:\python\my_exercises\) and just type in python3 my_python_program.py or python my_python_program.py In case of arguments to be passed by command line, one has to put them after the specification of the program name (eg.
python my_python_program.py parm1 param2 param3).
Python provides the module sys to interact with the interpreter. In particular, sys.argv is a list representing all the arguments passed to the python script from the command line.
Consider the following code:
[ ]:
import sys
"""Test input from command line in systest.py"""
if len(sys.argv) != 4: #note that this is the number of params +1!!!
print("Dear user, I was expecting 3 params. You gave me ",len(sys.argv)-1)
exit(1)
else:
for i in range(0,len(sys.argv)):
print("Param {}:{} ({})".format(i,sys.argv[i],type(sys.argv[i])))
Invoking the systest.py script from command line with the command python3 exercises/systest.py 1st_param 2nd 3 will return:
Param 0: exercises/systest.py (<class 'str'>)
Param 1: 1st_param (<class 'str'>)
Param 2: 2nd (<class 'str'>)
Param 3: 3 (<class 'str'>)
Invoking the systest.py script from command line with the command python3 exercises/systest.py 1st_param will return:
Dear user, I was expecting three parameters. You gave me 1
Note that the parameter at index 0, sys.argv[0] holds the name of the script, and that all parameters are actually strings (and therefore need to be cast to numbers if we want to do mathematical operations on them).
Example: Write a script that takes two integers in input, i1 and i2, and computes the sum, difference, multiplication and division on them.
[ ]:
import sys
"""Maths example with input from command line"""
if len(sys.argv) != 3:
print("Dear user, I was expecting 2 params. You gave me ",len(sys.argv)-1)
exit(1)
else:
i1 = int(sys.argv[1])
i2 = int(sys.argv[2])
print("{} + {} = {}".format(i1,i2, i1 + i2))
print("{} - {} = {}".format(i1,i2, i1 - i2))
print("{} * {} = {}".format(i1,i2, i1 * i2))
if i2 != 0:
print("{} / {} = {}".format(i1,i2, i1 / i2))
else:
print("{} / {} = Infinite".format(i1,i2))
Which, depending on user input, should give something like:
note that we need to check if the values given in input are actually numbers, otherwise the execution will crash (third example). This is easy in case of integers (str.isdigit()) but in case of floats it is more complex and might require Exception handling.
A more flexible and powerful way of getting input from command line makes use of the Argparse module.
Argparse¶
Argparse is a command line parsing module which deals with user specified parameters (positional arguments) and optional arguments.
Very briefly, the basic syntax of the Argparse module (for more information check the official documentation) is the following.
Import the module:
import argparse
Define a argparse object:
parser = argparse.ArgumentParser(description="This is the description of the program")
note the parameter description that is a string to describe the program;
Add positional arguments:
parser.add_argument("arg_name", type = obj, help = "Description of the parameter)where
arg_nameis the name of the argument (which will be used to retrieve its value). The argument has typeobj(the type will be automatically checked for us) and a description specified in thehelpstring.Add optional arguments:
parser.add_argument("-p", "--optional_arg", type = obj, default = def_val, help = "Description of the parameter)where
-pis a short form of the parameter (and it is optional),--optional_argis the extended name and it requires a value after it is specified,typeis the data type of the parameter passed (e.g. str, int, float, ..),defaultis optional and gives a default value to the parameter. If not specified and no argument is passed, the argument will get the value “None”.Helpis again the description string.Parse the arguments:
args = parser.parse_args()
the parser checks the arguments and stores their values in the
argparseobject that we calledargs.Retrieve and process arguments:
myArgName = args.arg_name myOptArg = args.optional_arg
now variables contain the values specified by the user and we can use them.
Let’s see the example above again.
Example: Write a script that takes two integers in input, i1 and i2, and computes the sum, difference, multiplication and division on them.
[ ]:
import argparse
"""Maths example with input from command line"""
parser = argparse.ArgumentParser(description="""This script gets two integers in input
and performs some operations on them""")
parser.add_argument("i1", type=int,
help="The first integer")
parser.add_argument("i2", type=int,
help="The second integer")
args = parser.parse_args()
i1 = args.i1
i2 = args.i2
print("{} + {} = {}".format(i1,i2, i1 + i2))
print("{} - {} = {}".format(i1,i2, i1 - i2))
print("{} * {} = {}".format(i1,i2, i1 * i2))
if i2 != 0:
print("{} / {} = {}".format(i1,i2, i1 / i2))
else:
print("{} / {} = Infinite".format(i1,i2))
That returns the following:
Note that we did not have to check the types of the inputs (i.e. the last time we run the script) but this is automatically done by argparse.
Example: Let’s write a program that gets a string (S) and an integer (N) in input and prints the string repeated N times. Three optional parameters are specified: verbosity (-v) to make the software print a more descriptive output, separator (-s) to separate each copy of the string (defaults to ” “) and trailpoints (-p) to add several “.” at the end of the string (defaults to 1).
[ ]:
import argparse
parser = argparse.ArgumentParser(description="""This script gets a string
and an integer and repeats the string N times""")
parser.add_argument("string", type=str,
help="The string to be repeated")
parser.add_argument("N", type=int,
help="The number of times to repeat the string")
parser.add_argument("-v", "--verbose", action="store_true",
help="increase output verbosity")
parser.add_argument("-p", "--trailpoints", type = int, default = 1,
help="Adds these many trailing points")
parser.add_argument("-s", "--separator", type = str, default = " ",
help="The separator between repeated strings")
args = parser.parse_args()
mySTR = args.string + args.separator
trailP = "." * args.trailpoints
answer = mySTR * args.N
answer = answer[:-len(args.separator)] + trailP #to remove the last separator
if args.verbose:
print("the string {} repeated {} is:".format(args.str, args.N, answer))
else:
print(answer)
Executing the program from command line without parameters gives the message:
Calling it with the -h flag:
With the positional arguments "ciao a tutti" and 3:
With the positional arguments "ciao a tutti" and 3, and with the optional parameters -s "___" -p 3 -v
Example: Let’s write a program that reads and prints to screen a text file specified by the user. Optionally, the file might be compressed with gzip to save space. The user should be able to read also gzipped files. Hint: use the module gzip which is very similar to the standard file management method (more info here). You can find a text file here textFile.txt and its gzipped version here text.gz:
[ ]:
import argparse
import gzip
parser = argparse.ArgumentParser(description="""Reads and prints a text file""")
parser.add_argument("filename", type=str, help="The file name")
parser.add_argument("-z", "--gzipped", action="store_true",
help="If set, input file is assumed gzipped")
args = parser.parse_args()
inputFile = args.filename
fh = ""
if args.gzipped:
fh = gzip.open(inputFile, "rt")
else:
fh = open(inputFile, "r")
for line in fh:
line = line.strip("\n")
print(line)
fh.close()
The output:
Example: Let’s write a program that reads the content of a file and prints to screen some stats like the number of lines, the number of characters and maximum number of characters in one line. Optionally (if flag -v is set) it should print the content of the file. You can find a text file here textFile.txt:
[ ]:
import argparse
def readText(f):
"""reads the file and returns a list with
each line as separate element"""
myF = open(f, "r")
ret = myF.readlines() #careful with big files!
return ret
def computeStats(fileList):
"""returns a tuple (num.lines, num.characters,max_char.line)"""
num_lines = len(fileList)
lines_len = [len(x.replace("\n", "")) for x in fileList]
num_char = sum(lines_len)
max_char = max(lines_len)
return (num_lines, num_char, max_char)
parser = argparse.ArgumentParser(description="Computes file stats")
parser.add_argument("inputFile", type=str, help="The input file")
parser.add_argument(
"-v", "--verbose", action="store_true", help="if set, prints the file content")
args = parser.parse_args()
inFile = args.inputFile
lines = readText(inFile)
stats = computeStats(lines)
if args.verbose:
print("File content:\n{}\n".format("".join(lines)))
print(
"Stats:\nN.lines:{}\nN.chars:{}\nMax. char in line:{}".format(
stats[0], stats[1], stats[2]))
Output with -v flag:
Output without -v flag:
Exercises¶
Modify the program of Exercise 6 of Practical 6 in order to allow users to specify the input and output files from command line. Then test it with the provided files. The text of the exercise follows:
Write a python program that reads two files. The first is a one column text file (contig_ids.txt) with the identifiers of some contigs that are present in the second file, which is a fasta formatted file (contigs82.fasta). The program will write on a third, fasta formatted file (e.g. filtered_contigs.fasta) only those entries in contigs82.fasta having identifier in contig_ids.txt.
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Write a python script that takes in input a single-entry .fasta file (specified from the command line) of the amino-acidic sequence of a protein and prints off 1) the total number of aminoacids, 2) for each aminoacid, its count and percentage of the whole. Optionally, it the user specifies the flag “-S” (–search) followed by a string representing an aminoacid sequence, the program should count and print how many times that input sequence appears. Download the Sars-Cov-2 Spike Protein and test your script on it. Please use functions.
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Cytoscape is a well known tool to perform network analysis. It is well integrated with several online databases housing for example protein-protein interactions like EBI’s IntAct. It is also able to read and write a very simple text file called
.sifto represent interactions between the nodes of a network. Sif formatted files are tab separated (\t) and each line represents a connection between the nodes of the network. For example:node1 interaction1 node2 node1 interaction2 node3 node2 interaction1 node3
represents two types of interactions between node1, node2 and node3. Normally nodes are represented as circles in a network (graph) and interactions as lines (that can be of different kinds) connecting nodes (edges). The following is an extract from the file pka.sif that has been downloaded by Cytoscape from the database IntAct and represents the interactions of the Protein Kinase A (PKA) of E.coli:
P75742 EBI-9168813 P76594 P21513 EBI-888473 P76594 P21513 EBI-15543881 P76594
the first and third columns represent proteins and the second is the interaction joining them. All the values are identifiers from the IntAct database. The cytoscape representation of the full set of interactions is:
Write a python script that reads in the .sif file (pka.sif is here but even better if any .sif file specified in input by the user) and stores the information in one (or more) suitable objects to be able to:
1. Print the interaction that is more present among the nodes;
2. Print the node that is connected to the highest number of
other nodes (no matter if on the left or right of the interaction);
Hint: you can store the information in a dictionary having the interaction as key and a list of tuples (node1,node2) as value. Although redundant, it is convenient to keep a list of unique nodes. Note: This will use more memory but it is acceptable for small examples as it allows to quickly answer the questions.
Optional: check what these ids refer to on the IntAct database.
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Given a fasta file like contigs82.fasta specified in input by a user, write a python script that counts, for each sequence, the number of times that a DNA or protein string specified in input appears.
If we run something like: python3 find_stringInFasta.py contigs82.fasta TGCTCACAG
the result should print lines like:
TGCTCACAG in MDC052568.000: 1 times
TGCTCACAG in MDC002479.192: 1 times
TGCTCACAG in MDC040033.7: 1 times
Modify the program so that it outputs also the list of all the indexes where the string appears in each sequence in the fasta file. Try to look for the following sequences:
TTTTCCTAGG
TGCTCCGAGCATGTGATAATCATTCCAAGCTCCAT
TAAACAT
GATTACA
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The Fisher’s dataset regarding Petal and Sepal length and width in csv format can be found here. These are the measurements of the flowers of fifty plants each of the two species Iris setosa and Iris versicolor.
The header of the file is:
Species Number,Species Name,Petal width,Petal length,Sepal length,Sepal width
Write a python script that reads this file in input (feel free to hard-code the filename in the code) and computes the average petal length and width and sepal length and width for each of the three different Iris species. Print them to the screen alongside the number of elements.
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Practical 8¶
In this practical we will will practice Pandas.
Libraries installation¶
First things first. Let’s start off by installing the required libraries. In particular we will need three libraries. Try and see if they are already available by typing the following commands in the console or put them in a python script:
import pandas as pd
import matplotlib.pyplot as plt
import numpy as np
if, upon execution, you do not get any error messages, you are sorted. Otherwise, you need to install them.
In Linux you can install the libraries by typing in a terminal sudo pip3 install matplotlib, sudo pip3 install pandas and sudo pip3 install numpy (or sudo python3.X -m pip install matplotlib, sudo python3.X -m pip install pandas and sudo python3.X -m pip install numpy), where X is your python version.
In Windows you can install the libraries by typing in the command prompt (to open it type cmd in the search box) pip3 install matplotlib, pip3 install pandas and pip3 install numpy. If you are using anaconda you need to run these commands from the anaconda prompt.
Please install them in this order (i.e. matplotlib first, then pandas and finally numpy). You might not need to install numpy as matplotlib requires it. Once done that, try to perform the above imports again and they should work this time around.
Pandas¶
Pandas (the name comes from panel data) is a very efficient library to deal with numerical tables and time series. It is a quite complex library and here we will only scratch the surface of it. You can find a lot of information including the documentation on the Pandas website.
In particular the library pandas provides two data structures: Series and DataFrames.
Series¶
Series are 1-dimensional structures (like lists) containing data. Series are characterized by two types of information: the values and the index (a list of labels associated to the data), therefore they are a bit like a list and a bit like a dictionary. The index is optional and can be added by the library if not specified.
How to define and access a Series¶
There are several ways to define a Series. We can specify both the values and the index explicitly, or through a dictionary, or let python add the default index for us. We can access the index with the Series.index method and the values with the Series.values.
[1]:
import pandas as pd
import random
print("Values and index explicitly defined")
#values and index explicitely defined
S = pd.Series([random.randint(0,20) for x in range(0,10)],
index = list("ABCDEFGHIL"))
print(S)
print("The index:", S.index)
print("The values:", S.values)
print("------------------------\n")
print("From dictionary")
#from a dictionary
S1 = pd.Series({"one" : 1, "two" : 2, "ten": 10,
"three" : 3, "four": 4, "forty" : 40})
print(S1)
print(S1.index)
print(S1.values)
print("------------------------\n")
print("Default index")
#index added by default
myData = [random.randint(0,10) for x in range(10)]
S2 = pd.Series(myData)
print(S2)
print(S2.index)
print(S2.values)
print("------------------------\n")
print("Same value repeated")
S3 = pd.Series(1.27, range(10))
print(S3)
print(S3.index)
print(S3.values)
Values and index explicitly defined
A 1
B 9
C 4
D 7
E 20
F 7
G 13
H 10
I 4
L 8
dtype: int64
The index: Index(['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'L'], dtype='object')
The values: [ 1 9 4 7 20 7 13 10 4 8]
------------------------
From dictionary
one 1
two 2
ten 10
three 3
four 4
forty 40
dtype: int64
Index(['one', 'two', 'ten', 'three', 'four', 'forty'], dtype='object')
[ 1 2 10 3 4 40]
------------------------
Default index
0 3
1 3
2 2
3 0
4 3
5 8
6 2
7 3
8 7
9 7
dtype: int64
RangeIndex(start=0, stop=10, step=1)
[3 3 2 0 3 8 2 3 7 7]
------------------------
Same value repeated
0 1.27
1 1.27
2 1.27
3 1.27
4 1.27
5 1.27
6 1.27
7 1.27
8 1.27
9 1.27
dtype: float64
RangeIndex(start=0, stop=10, step=1)
[1.27 1.27 1.27 1.27 1.27 1.27 1.27 1.27 1.27 1.27]
Data in a series can be accessed by using the label (i.e. the index) as in a dictionary or through its position as in a list. Slicing is also allowed both by position and index. In the latter case, we can do Series[S:E] with S and E indexes, both S and E are included.
It is also possible to retrieve some elements by passing a list of positions or indexes. Head and tail methods can also be used to retrieve the top or bottom N elements with Series.head(N) or Series.tail(N).
Note: When the method returns more than one element, the return type is a Series.
[2]:
import pandas as pd
import random
#values and index explicitely defined
S = pd.Series([random.randint(0,20) for x in range(0,10)],
index = list("ABCDEFGHIL"))
print(S)
print("")
print("Value at label \"A\":", S["A"])
print("Value at index 1:", S[1])
print("")
print("Slicing from 1 to 3:") #note 3 excluded
print(S[1:3])
print("")
print("Slicing from C to H:") #note H included!
print(S["C":"H"])
print("")
print("Retrieving from list:")
print(S[[1,3,5,7,9]])
print(S[["A","C","E","G"]])
print("")
print("Top 3")
print(S.head(3))
print("")
print("Bottom 3")
print(S.tail(3))
A 1
B 19
C 10
D 5
E 9
F 12
G 9
H 4
I 12
L 10
dtype: int64
Value at label "A": 1
Value at index 1: 19
Slicing from 1 to 3:
B 19
C 10
dtype: int64
Slicing from C to H:
C 10
D 5
E 9
F 12
G 9
H 4
dtype: int64
Retrieving from list:
B 19
D 5
F 12
H 4
L 10
dtype: int64
A 1
C 10
E 9
G 9
dtype: int64
Top 3
A 1
B 19
C 10
dtype: int64
Bottom 3
H 4
I 12
L 10
dtype: int64
Operator broadcasting¶
Operations can automatically be broadcast to the entire Series. This is a quite cool feature and saves us from looping through the elements of the Series.
Example: Given a list of 10 integers and we want to divide them by 2. Without using pandas we would:
[3]:
import random
listS = [random.randint(0,20) for x in range(0,10)]
print(listS)
for el in range(0,len(listS)):
listS[el] /=2 #compact of X = X / 2
print(listS)
[11, 9, 18, 16, 3, 19, 12, 7, 14, 17]
[5.5, 4.5, 9.0, 8.0, 1.5, 9.5, 6.0, 3.5, 7.0, 8.5]
With pandas instead:
[4]:
import pandas as pd
import random
S = pd.Series([random.randint(0,20) for x in range(0,10)],
index = list("ABCDEFGHIL"))
print(S)
print("")
S1 = S / 2
print(S1)
A 9
B 0
C 5
D 7
E 1
F 18
G 10
H 18
I 4
L 18
dtype: int64
A 4.5
B 0.0
C 2.5
D 3.5
E 0.5
F 9.0
G 5.0
H 9.0
I 2.0
L 9.0
dtype: float64
Filtering¶
We can also apply boolean operators to obtain only the sub-Series with all the values satisfying a specific condition. This allows us to filter the Series.
Calling the boolean operator on the series alone (e.g. S > 10) will return a Series with True at the indexes where the condition is met, False at the others. Passing such a Series to a Series of the same length will return only the elements where the condition is True. Check the code below to see this in action.
[5]:
import pandas as pd
import random
S = pd.Series([random.randint(0,20) for x in range(0,10)],
index = list("ABCDEFGHIL"))
print(S)
print("")
S1 = S>10
print(S1)
print("")
S2 = S[S > 10]
print(S2)
A 0
B 5
C 0
D 11
E 6
F 14
G 18
H 15
I 0
L 0
dtype: int64
A False
B False
C False
D True
E False
F True
G True
H True
I False
L False
dtype: bool
D 11
F 14
G 18
H 15
dtype: int64
Missing data¶
Operations involving Series might have to deal with missing data or non-valid values (both cases are represented as NaN, that is not a number). Operations are carried out by aligning the Series based on their indexes. Indexes not in common end up in NaN values. Although most of the operations that can be performed on series quite happily deal with NaNs, it is possible to drop NaN values or to fill them (i.e. replace their value with some other value). The sytax is:
Series.dropna()
or
Series.fillna(some_value)
Note that these operations do not modify the Series but rather return a new Series.
[6]:
import pandas as pd
import random
S = pd.Series([random.randint(0,10) for x in range(0,10)],
index = list("ABCDEFGHIL"))
S1 = pd.Series([random.randint(0,10) for x in range(0,8)],
index = list("DEFGHAZY"))
print("The dimensions of these Series:", S.shape)
print("")
print(S1)
print("---- S + S1 ----")
Ssum = S + S1
print(Ssum)
print("---- Dropping NaNs ----")
print(Ssum.dropna())
print("---- Filling NaNs ----")
print(Ssum.fillna("my_value"))
The dimensions of these Series: (10,)
D 8
E 3
F 0
G 8
H 9
A 5
Z 1
Y 1
dtype: int64
---- S + S1 ----
A 5.0
B NaN
C NaN
D 15.0
E 12.0
F 4.0
G 9.0
H 18.0
I NaN
L NaN
Y NaN
Z NaN
dtype: float64
---- Dropping NaNs ----
A 5.0
D 15.0
E 12.0
F 4.0
G 9.0
H 18.0
dtype: float64
---- Filling NaNs ----
A 5
B my_value
C my_value
D 15
E 12
F 4
G 9
H 18
I my_value
L my_value
Y my_value
Z my_value
dtype: object
Computing stats¶
Pandas offers several operators to compute stats on the data stored in a Series. These include basic stats like min, max (and relative indexes with argmin and argmax) mean, std, quantile (to get the quantiles). A description of the data can be obtained by using the method describe and the counts for each value can be obtained by value_counts. Other methods available are sum and cumsum (for the sum and cumulative sum of the elements), autocorr and corr (for autocorrelation and correlation) and many others. For a complete list check the Pandas reference.
Note: as said before, when these methods do not return a single value, they return a Series.
Example: Fill the previous Series with the mean values of the series rather than NaNs.
[7]:
Ssum = S + S1
print(Ssum)
print("---- Filling with avg value ----")
print(Ssum.fillna(Ssum.mean()))
print("Min:{} (index: {}) Max: {} (index: {})".format(Ssum.min(),
Ssum.argmin(),
Ssum.max(),
Ssum.argmax()))
A 5.0
B NaN
C NaN
D 15.0
E 12.0
F 4.0
G 9.0
H 18.0
I NaN
L NaN
Y NaN
Z NaN
dtype: float64
---- Filling with avg value ----
A 5.0
B 10.5
C 10.5
D 15.0
E 12.0
F 4.0
G 9.0
H 18.0
I 10.5
L 10.5
Y 10.5
Z 10.5
dtype: float64
Min:4.0 (index: 5) Max: 18.0 (index: 7)
Let’s see some operators introduced above in action.
[8]:
import pandas as pd
import random
S = pd.Series([random.randint(0,10) for x in range(0,10)],
index = list("ABCDEFGHIL"))
print("The data:")
print(S)
print("")
print("Its description")
print(S.describe())
print("")
print("Specifying different quantiles:")
print(S.quantile([0.1,0.2,0.8,0.9]))
print("")
print("Histogram:")
print(S.value_counts())
print("")
print("The type is a Series:")
print(type(S.value_counts()))
print("Summing the values:")
print(S.sum())
print("")
print("The cumulative sum:")
print(S.cumsum())
The data:
A 0
B 8
C 5
D 10
E 5
F 7
G 0
H 7
I 9
L 9
dtype: int64
Its description
count 10.000000
mean 6.000000
std 3.559026
min 0.000000
25% 5.000000
50% 7.000000
75% 8.750000
max 10.000000
dtype: float64
Specifying different quantiles:
0.1 0.0
0.2 4.0
0.8 9.0
0.9 9.1
dtype: float64
Histogram:
9 2
7 2
5 2
0 2
10 1
8 1
dtype: int64
The type is a Series:
<class 'pandas.core.series.Series'>
Summing the values:
60
The cumulative sum:
A 0
B 8
C 13
D 23
E 28
F 35
G 35
H 42
I 51
L 60
dtype: int64
Example:
Create two Series from the lists [2, 4, 6, 8, 10, 12, 13, 14, 15, 16], [1, 3, 5, 7, 9, 11, 13, 14, 15, 16] using the same index for both: [‘9B47’, ‘468B’, ‘B228’, ‘3C52’, ‘AE2E’, ‘DFF6’, ‘C38B’, ‘2CE5’, ‘0325’, ‘398F’].
Let’s compare the distribution stats of the two Series (mean value, max, min, quantiles) and get the index and value of the positions where the two series are the same. Finally, let’s get the sub-series where the first has a value higher than the first quartile of the second and compute its stats.
[9]:
import pandas as pd
L1 = [2, 4, 6, 8, 10, 12, 13, 14, 15, 16]
L2 = [1, 3, 5, 7, 9, 11, 13, 14, 15, 16]
I = ['9B47', '468B', 'B228', '3C52', 'AE2E', 'DFF6', 'C38B', '2CE5', '0325', '398F']
L1Series = pd.Series(L1,index = I)
L2Series = pd.Series(L2, index = I)
#Let's describe the stats
print("Stats of L1Series")
print(L1Series.describe())
print("")
print("Stats of L2Series")
print(L2Series.describe())
print("")
#This is a Series with boolean values (True means the two Series where the same)
Leq = L1Series == L2Series
print("Equality series")
print(Leq)
print("")
#Get the subseries where both are the same
Lsub = L1Series[Leq]
print("Subseries of identicals")
print(Lsub)
print("")
#Get the values that are the same
print("Identical values:")
print(Lsub.values)
print("")
#Get the indexes where the two series are the same
print("Indexes of identical values:")
print(Lsub.index)
print("")
firstQuartile = L2Series.quantile(0.25)
print("The first quartile of L2Series:",firstQuartile)
print("")
#Get the subseries in which L1 is bigger than L2
Lbig = L1Series[L1Series > firstQuartile]
print("The subseries with L1 > L2")
print(Lbig)
Stats of L1Series
count 10.000000
mean 10.000000
std 4.830459
min 2.000000
25% 6.500000
50% 11.000000
75% 13.750000
max 16.000000
dtype: float64
Stats of L2Series
count 10.00000
mean 9.40000
std 5.25357
min 1.00000
25% 5.50000
50% 10.00000
75% 13.75000
max 16.00000
dtype: float64
Equality series
9B47 False
468B False
B228 False
3C52 False
AE2E False
DFF6 False
C38B True
2CE5 True
0325 True
398F True
dtype: bool
Subseries of identicals
C38B 13
2CE5 14
0325 15
398F 16
dtype: int64
Identical values:
[13 14 15 16]
Indexes of identical values:
Index(['C38B', '2CE5', '0325', '398F'], dtype='object')
The first quartile of L2Series: 5.5
The subseries with L1 > L2
B228 6
3C52 8
AE2E 10
DFF6 12
C38B 13
2CE5 14
0325 15
398F 16
dtype: int64
Plotting data¶
Using python’s matplotlib it is possible to plot data. The basic syntax is Series.plot(kind = "type") the parameter kind can be used to produce several types of plots (examples include line, hist, pie, bar, see here for all possible choices). Note that matplotlib needs to be imported and the pyplot needs to be shown with pyplot.show() to display the plot.
Typically, the following syntax is used to import pyplot (remember also to import pandas):
import pandas as pd
import matplotlib.pyplot as plt
note the use of the alias plt for simplicity.
[10]:
import pandas as pd
import matplotlib.pyplot as plt
import random
S = pd.Series([random.randint(0,10) for x in range(0,10)],
index = list("ABCDEFGHIL"))
print("The data:")
print(S)
S1 = pd.Series([random.randint(0,10) for x in range(0,100)])
S.plot()
plt.show()
plt.close()
S1.plot(kind = "hist")
plt.show()
plt.close()
S.plot(kind = "pie")
plt.show()
plt.close()
The data:
A 1
B 10
C 0
D 5
E 6
F 8
G 4
H 5
I 10
L 3
dtype: int64
<matplotlib.figure.Figure at 0x7f964c553630>
<matplotlib.figure.Figure at 0x7f95f8b2eb38>
<matplotlib.figure.Figure at 0x7f9601b9eb00>
Example: Let’s create a series representing the sin, cos and sqrt functions and plot them.
[11]:
import math
import matplotlib.pyplot as plt
import pandas as pd
x = [i/10 for i in range(0,500)]
y = [math.sin(2*i/3.14 ) for i in x]
y1 = [math.cos(2*i/3.14 ) for i in x]
y2 = [math.sqrt(i) for i in x]
#print(x)
ySeries = pd.Series(y)
ySeries1 = pd.Series(y1)
ySeries2 = pd.Series(y2)
ySeries.plot()
plt.title("Sin function")
plt.show()
plt.close()
ySeries1.plot()
plt.title("Cos function")
plt.show()
plt.close()
plt.title("Sin and Cos functions")
ySeries.plot()
ySeries1.plot()
plt.legend(["Sin", "Cos"])
plt.show()
plt.close()
ySeries2.plot()
plt.title("Sqrt function")
plt.show()
plt.close()
ySeries2 = (ySeries + 2*ySeries1)/ySeries2
ySeries2.plot()
plt.title("(sin(x) + 2cos(x)) / sqrt(x)")
plt.show()
Pandas DataFrames¶
DataFrames in pandas are the 2D analogous of Series. Dataframes are spreadsheet-like data structures with an ordered set of columns that can also be dishomogeneous. We can think about Dataframes as dictionaries of Series, each one representing a named column. Dataframes are described by an index that contains the labels of rows and a columns structure that holds the labels of the columns.
Note that the operation of extracting a column from a DataFrame returns a Series. Moreover, most (but not all!) of the operations that apply to Series also apply to DataFrames.
Define a DataFrame¶
There are several different ways to define a DataFrame. It is possible to create a DataFrame starting from a dictionary having Series as values. In this case, they keys of the dictionary are the columns of the DataFrame.
[12]:
import pandas as pd
myData = {
"temperature" : pd.Series([1, 3, 8, 13, 17, 20, 22, 22,18 ,13,6,2],
index = ["Jan","Feb", "Mar","Apr","May","Jun",
"Jul","Aug","Sep","Oct","Nov","Dec"]
),
"dayLength" : pd.Series([9.7, 10.9, 12.5, 14.1, 15.6, 16.3, 15.9,
14.6,13,11.4,10,9.3],
index = ["Jan","Feb", "Mar","Apr","May","Jun",
"Jul","Aug","Sep","Oct","Nov","Dec"]
)
}
DF = pd.DataFrame(myData)
print(DF)
print(DF.columns)
print(DF.index)
temperature dayLength
Jan 1 9.7
Feb 3 10.9
Mar 8 12.5
Apr 13 14.1
May 17 15.6
Jun 20 16.3
Jul 22 15.9
Aug 22 14.6
Sep 18 13.0
Oct 13 11.4
Nov 6 10.0
Dec 2 9.3
Index(['temperature', 'dayLength'], dtype='object')
Index(['Jan', 'Feb', 'Mar', 'Apr', 'May', 'Jun', 'Jul', 'Aug', 'Sep', 'Oct',
'Nov', 'Dec'],
dtype='object')
If the index is not specified, it is given by default:
[13]:
import pandas as pd
import matplotlib.pyplot as plt
myData = {
"temperature" : pd.Series([1, 3, 8, 13, 17, 20,
22, 22,18 ,13,6,2]),
"dayLength" : pd.Series([9.7, 10.9, 12.5, 14.1, 15.6,
16.3,15.9,14.6,13,11.4,10,9.3])
}
DF = pd.DataFrame(myData)
print(DF)
print(DF.index)
DF.plot()
plt.show()
plt.close()
DF.plot(kind ="box")
plt.show()
temperature dayLength
0 1 9.7
1 3 10.9
2 8 12.5
3 13 14.1
4 17 15.6
5 20 16.3
6 22 15.9
7 22 14.6
8 18 13.0
9 13 11.4
10 6 10.0
11 2 9.3
RangeIndex(start=0, stop=12, step=1)
It is also possible to define a DataFrame from a list of dictionaries holding a set of values rather than Series. Note that when columns do not have the corresponding information a NaN is added. Indexes and columns can be changed after they have been defined.
[14]:
import pandas as pd
myData = [{"A" : 1, "B" : 2, "C" : 3.2, "D" : 10},
{"A" : 1, "B" : 2, "F" : 3.2, "G" : 10, "H":1},
{"A" : 1, "B" : 2, "C" : 3.2, "D" : 1,
"E": 4.1, "F" : 3.2, "G" : 10, "H":1}
]
DF = pd.DataFrame(myData)
print(DF)
print("")
#Let's change the columns and indexes
columns = "val1,val2,val3,val4,val5,val6,val7,val8".split(',')
inds = ["Day1", "Day2", "Day3"]
DF.columns = columns
DF.index = inds
print(DF)
A B C D F G H E
0 1 2 3.2 10.0 NaN NaN NaN NaN
1 1 2 NaN NaN 3.2 10.0 1.0 NaN
2 1 2 3.2 1.0 3.2 10.0 1.0 4.1
val1 val2 val3 val4 val5 val6 val7 val8
Day1 1 2 3.2 10.0 NaN NaN NaN NaN
Day2 1 2 NaN NaN 3.2 10.0 1.0 NaN
Day3 1 2 3.2 1.0 3.2 10.0 1.0 4.1
Loading data from external files¶
Pandas also provides methods to load data from external files. In particular, to load data from a .cvs file, we can use the method pandas.read_csv(filename). This method has a lot of parameters, you can see all the details on its usage on the official documentation. Some useful optional parameters are the separator (to specify the column separator like sep="\t" for tab separated files),
the character to identify comments (comment="#") or that to skip some lines (like the header for example or any initial comments to the file) skiprows=N. The rows to use as column header can be specified with the parameter header that accepts a number or a list of numbers. Similarly, the columns to use as index can be specified with the parameter index_col.
Another method to read data in is pandas.read_excel(filename) that works in a similar way but can load excel files (see here).
Example: Let’s load the data stored in a csv datafile sampledata_orders.csv in a pandas DataFrame.
[15]:
import pandas as pd
orders = pd.read_csv("file_samples/sampledata_orders.csv",
sep=",", index_col = 0, header = 0)
print("First 5 entries:")
print(orders.head())
print("")
print("The index:")
print(orders.index)
print("")
print("The column names:")
print(orders.columns)
print("")
print("A description of the numerical values:")
print(orders.describe())
First 5 entries:
Order ID Order Date Order Priority Order Quantity Sales \
Row ID
1 3 10/13/2010 Low 6 261.5400
49 293 10/1/2012 High 49 10123.0200
50 293 10/1/2012 High 27 244.5700
80 483 7/10/2011 High 30 4965.7595
85 515 8/28/2010 Not Specified 19 394.2700
Discount Ship Mode Profit Unit Price Shipping Cost \
Row ID
1 0.04 Regular Air -213.25 38.94 35.00
49 0.07 Delivery Truck 457.81 208.16 68.02
50 0.01 Regular Air 46.71 8.69 2.99
80 0.08 Regular Air 1198.97 195.99 3.99
85 0.08 Regular Air 30.94 21.78 5.94
Customer Name Province Region Customer Segment \
Row ID
1 Muhammed MacIntyre Nunavut Nunavut Small Business
49 Barry French Nunavut Nunavut Consumer
50 Barry French Nunavut Nunavut Consumer
80 Clay Rozendal Nunavut Nunavut Corporate
85 Carlos Soltero Nunavut Nunavut Consumer
Product Category Product Sub-Category \
Row ID
1 Office Supplies Storage & Organization
49 Office Supplies Appliances
50 Office Supplies Binders and Binder Accessories
80 Technology Telephones and Communication
85 Office Supplies Appliances
Product Name Product Container \
Row ID
1 Eldon Base for stackable storage shelf, platinum Large Box
49 1.7 Cubic Foot Compact "Cube" Office Refrigera... Jumbo Drum
50 Cardinal Slant-D® Ring Binder, Heavy Gauge Vinyl Small Box
80 R380 Small Box
85 Holmes HEPA Air Purifier Medium Box
Product Base Margin Ship Date
Row ID
1 0.80 10/20/2010
49 0.58 10/2/2012
50 0.39 10/3/2012
80 0.58 7/12/2011
85 0.50 8/30/2010
The index:
Int64Index([ 1, 49, 50, 80, 85, 86, 97, 98, 103, 107,
...
6492, 6526, 6657, 7396, 7586, 7765, 7766, 7906, 7907, 7914],
dtype='int64', name='Row ID', length=8399)
The column names:
Index(['Order ID', 'Order Date', 'Order Priority', 'Order Quantity', 'Sales',
'Discount', 'Ship Mode', 'Profit', 'Unit Price', 'Shipping Cost',
'Customer Name', 'Province', 'Region', 'Customer Segment',
'Product Category', 'Product Sub-Category', 'Product Name',
'Product Container', 'Product Base Margin', 'Ship Date'],
dtype='object')
A description of the numerical values:
Order ID Order Quantity Sales Discount Profit \
count 8399.000000 8399.000000 8399.000000 8399.000000 8399.000000
mean 29965.179783 25.571735 1775.878179 0.049671 181.184423
std 17260.883447 14.481071 3585.050525 0.031823 1196.653372
min 3.000000 1.000000 2.240000 0.000000 -14140.700000
25% 15011.500000 13.000000 143.195000 0.020000 -83.315000
50% 29857.000000 26.000000 449.420000 0.050000 -1.500000
75% 44596.000000 38.000000 1709.320000 0.080000 162.750000
max 59973.000000 50.000000 89061.050000 0.250000 27220.690000
Unit Price Shipping Cost Product Base Margin
count 8399.000000 8399.000000 8336.000000
mean 89.346259 12.838557 0.512513
std 290.354383 17.264052 0.135589
min 0.990000 0.490000 0.350000
25% 6.480000 3.300000 0.380000
50% 20.990000 6.070000 0.520000
75% 85.990000 13.990000 0.590000
max 6783.020000 164.730000 0.850000
Extract values by row and column¶
Once a DataFrame is populated we can access its content. Several options are available:
Select by column
DataFrame[col]returns a SeriesSelect by row label
DataFrame.loc[row_label]returns a SeriesSelect row by integer location
DataFrame.iloc[row_position]returns a SeriesSlice rows
DataFrame[S:E](S and E are labels, both included) returns a DataFrameSelect rows by boolean vector
DataFrame[bool_vect]returns a DataFrame
Note that if names are well formed (i.e. no spaces, no strange characters…) we can use DataFrame.col instead of DataFrame[col]. Here are some ways to extract data from the orders dataframe:
[16]:
import pandas as pd
orders = pd.read_csv("file_samples/sampledata_orders.csv", sep=",", index_col =0, header=0)
print("The Order Quantity column (top 5)")
print(orders["Order Quantity"].head(5))
print("")
print("The Sales column (top 10)")
print(orders.Sales.head(10))
print("")
print("The row with ID:50")
r50 = orders.loc[50]
print(r50)
print("")
print("The third row:")
print(orders.iloc[3])
print("The Order Quantity, Sales, Discount and Profit of the 2nd,4th, 6th and 8th row:")
print(orders[1:8:2][["Order Quantity", "Sales","Discount", "Profit"]])
print("The Order Quantity, Sales, Discount and Profit of orders with discount > 10%:")
print(orders[orders["Discount"] > 0.1][["Order Quantity", "Sales","Discount", "Profit"]])
The Order Quantity column (top 5)
Row ID
1 6
49 49
50 27
80 30
85 19
Name: Order Quantity, dtype: int64
The Sales column (top 10)
Row ID
1 261.5400
49 10123.0200
50 244.5700
80 4965.7595
85 394.2700
86 146.6900
97 93.5400
98 905.0800
103 2781.8200
107 228.4100
Name: Sales, dtype: float64
The row with ID:50
Order ID 293
Order Date 10/1/2012
Order Priority High
Order Quantity 27
Sales 244.57
Discount 0.01
Ship Mode Regular Air
Profit 46.71
Unit Price 8.69
Shipping Cost 2.99
Customer Name Barry French
Province Nunavut
Region Nunavut
Customer Segment Consumer
Product Category Office Supplies
Product Sub-Category Binders and Binder Accessories
Product Name Cardinal Slant-D® Ring Binder, Heavy Gauge Vinyl
Product Container Small Box
Product Base Margin 0.39
Ship Date 10/3/2012
Name: 50, dtype: object
The third row:
Order ID 483
Order Date 7/10/2011
Order Priority High
Order Quantity 30
Sales 4965.76
Discount 0.08
Ship Mode Regular Air
Profit 1198.97
Unit Price 195.99
Shipping Cost 3.99
Customer Name Clay Rozendal
Province Nunavut
Region Nunavut
Customer Segment Corporate
Product Category Technology
Product Sub-Category Telephones and Communication
Product Name R380
Product Container Small Box
Product Base Margin 0.58
Ship Date 7/12/2011
Name: 80, dtype: object
The Order Quantity, Sales, Discount and Profit of the 2nd,4th, 6th and 8th row:
Order Quantity Sales Discount Profit
Row ID
49 49 10123.0200 0.07 457.81
80 30 4965.7595 0.08 1198.97
86 21 146.6900 0.05 4.43
98 22 905.0800 0.09 127.70
The Order Quantity, Sales, Discount and Profit of orders with discount > 10%:
Order Quantity Sales Discount Profit
Row ID
176 11 663.784 0.25 -481.04
3721 22 338.520 0.21 -17.75
37 43 586.110 0.11 98.44
2234 1 27.960 0.17 -9.13
4900 49 651.900 0.16 -74.51
Broadcasting, filtering and computing stats¶
These work pretty much like on Series and pandas takes care of adding NaNs when it cannot perform some operations due to missing values and so on.
Obviously some operators, when applied to entire tables, might not always make sense (like mean or sum of strings).
[17]:
import pandas as pd
orders = pd.read_csv("file_samples/sampledata_orders.csv", sep=",", index_col =0, header=0)
orders_10 = orders[["Sales","Profit", "Product Category"]].head(10)
orders_5 = orders[["Sales","Profit", "Product Category"]].head()
orders_20 = orders[["Sales","Profit", "Product Category"]].head(20)
print(orders_20)
print("")
#Summing over the entries, does not make sense but...
print("Top10 + Top5:")
print(orders_10 + orders_5)
print("")
prod_cost = orders_20["Sales"] - orders_20["Profit"]
print(prod_cost)
print("")
print("Technology orders")
print(orders_20[orders_20["Product Category"] == "Technology"])
print("")
print("Office Supplies positive profit")
print(orders_20[ (orders_20["Product Category"] == "Office Supplies") & (orders_20["Profit"] >0) ])
Sales Profit Product Category
Row ID
1 261.5400 -213.25 Office Supplies
49 10123.0200 457.81 Office Supplies
50 244.5700 46.71 Office Supplies
80 4965.7595 1198.97 Technology
85 394.2700 30.94 Office Supplies
86 146.6900 4.43 Furniture
97 93.5400 -54.04 Office Supplies
98 905.0800 127.70 Office Supplies
103 2781.8200 -695.26 Office Supplies
107 228.4100 -226.36 Office Supplies
127 196.8500 -166.85 Office Supplies
128 124.5600 -14.33 Office Supplies
134 716.8400 134.72 Office Supplies
135 1474.3300 114.46 Technology
149 80.6100 -4.72 Office Supplies
160 1815.4900 782.91 Furniture
161 248.2600 93.80 Office Supplies
175 4462.2300 440.72 Furniture
176 663.7840 -481.04 Furniture
203 834.9040 -11.68 Technology
Top10 + Top5:
Sales Profit Product Category
Row ID
1 523.080 -426.50 Office SuppliesOffice Supplies
49 20246.040 915.62 Office SuppliesOffice Supplies
50 489.140 93.42 Office SuppliesOffice Supplies
80 9931.519 2397.94 TechnologyTechnology
85 788.540 61.88 Office SuppliesOffice Supplies
86 NaN NaN NaN
97 NaN NaN NaN
98 NaN NaN NaN
103 NaN NaN NaN
107 NaN NaN NaN
Row ID
1 474.7900
49 9665.2100
50 197.8600
80 3766.7895
85 363.3300
86 142.2600
97 147.5800
98 777.3800
103 3477.0800
107 454.7700
127 363.7000
128 138.8900
134 582.1200
135 1359.8700
149 85.3300
160 1032.5800
161 154.4600
175 4021.5100
176 1144.8240
203 846.5840
dtype: float64
Technology orders
Sales Profit Product Category
Row ID
80 4965.7595 1198.97 Technology
135 1474.3300 114.46 Technology
203 834.9040 -11.68 Technology
Office Supplies positive profit
Sales Profit Product Category
Row ID
49 10123.02 457.81 Office Supplies
50 244.57 46.71 Office Supplies
85 394.27 30.94 Office Supplies
98 905.08 127.70 Office Supplies
134 716.84 134.72 Office Supplies
161 248.26 93.80 Office Supplies
Statistics can be computed by column (normally the default) or by row (specifying axis=1) or on the entire table.
Here you can find the complete list of methods that can be applied.
[18]:
import pandas as pd
data = pd.read_csv("file_samples/random.csv", sep=",", header=0)
print("Global description")
print(data.describe())
print("")
print(data)
print("")
print("Let's reduce A in [0,1]")
print(data["A"]/ data["A"].max())
print("Let's reduce first row in [0,1]")
print(data.iloc[0]/ data.loc[0].max())
print("Mean and std values (by column)")
print(data.mean())
print(data.std())
print("")
print("Mean and std values (by column) - top 10 values")
print(data.head(10).mean(axis=1))
print(data.head(10).std(axis=1))
print("Cumulative sum (by column)- top 10 rows")
print(data.head(10).cumsum())
print("Cumulative sum (by row) - top 10 rows")
print(data.head(10).cumsum(axis = 1 ))
Global description
A B C D E F \
count 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000
mean 45.240000 49.760000 54.120000 50.500000 57.860000 49.180000
std 28.393417 32.193015 25.165282 28.321226 32.443364 28.488229
min 0.000000 0.000000 5.000000 1.000000 2.000000 1.000000
25% 21.750000 18.000000 35.750000 28.250000 29.250000 25.000000
50% 42.000000 49.500000 52.500000 49.500000 68.000000 52.000000
75% 63.250000 76.250000 73.750000 76.000000 86.750000 75.500000
max 99.000000 99.000000 100.000000 95.000000 100.000000 97.000000
G H I L
count 50.000000 50.00000 50.000000 50.000000
mean 49.780000 47.78000 46.920000 51.780000
std 29.673248 29.75978 31.056788 30.613649
min 1.000000 1.00000 0.000000 3.000000
25% 26.500000 24.50000 19.000000 26.250000
50% 51.000000 42.50000 44.000000 46.500000
75% 76.750000 72.00000 73.000000 82.000000
max 100.000000 99.00000 98.000000 100.000000
A B C D E F G H I L
0 28 69 5 41 12 62 90 32 33 85
1 91 59 64 94 4 51 45 52 96 5
2 54 74 53 92 20 84 85 21 98 73
3 99 0 39 12 90 15 62 38 4 67
4 98 10 35 77 46 97 88 72 15 37
5 44 9 91 57 98 63 52 77 62 7
6 76 17 12 41 69 34 100 29 0 91
7 52 25 43 59 87 91 1 90 23 90
8 56 33 38 91 13 1 34 17 22 82
9 29 18 42 48 34 16 64 7 46 9
10 81 77 38 93 63 90 57 58 52 100
11 57 97 23 59 38 93 46 49 88 86
12 57 0 79 78 100 76 16 31 79 8
13 18 1 67 44 2 17 53 51 6 23
14 77 95 94 88 9 25 54 23 36 35
15 87 42 63 33 95 53 11 58 53 3
16 34 24 24 28 74 79 86 98 42 90
17 1 31 20 63 70 3 29 39 5 87
18 35 17 77 15 9 63 86 95 95 21
19 0 85 13 13 60 74 44 78 7 56
20 61 20 47 21 85 78 53 14 37 70
21 81 15 89 54 38 59 72 35 59 12
22 20 81 76 15 64 18 9 47 11 81
23 57 94 73 19 21 79 81 45 71 40
24 2 58 83 67 99 46 76 70 50 45
25 64 13 52 60 32 70 32 4 73 20
26 27 49 100 48 70 30 58 48 42 36
27 82 89 93 73 30 64 18 54 93 82
28 19 85 98 7 84 71 77 20 18 63
29 34 95 68 23 68 38 73 1 28 10
30 33 60 66 80 94 41 53 99 29 57
31 0 99 18 2 29 28 11 30 36 56
32 20 61 33 89 52 59 50 55 4 33
33 82 72 41 33 92 16 18 99 73 91
34 8 28 22 29 83 53 47 10 42 34
35 64 50 24 59 6 83 92 91 87 98
36 42 73 50 17 91 9 39 37 97 50
37 27 49 67 61 21 25 94 96 16 98
38 44 44 48 70 86 85 9 31 4 46
39 36 93 64 1 96 89 14 75 10 84
40 20 13 34 87 11 10 2 5 91 27
41 54 2 61 80 98 53 96 40 2 26
42 42 88 79 31 41 23 50 95 77 26
43 7 14 56 95 70 28 78 31 34 95
44 40 65 34 44 97 36 3 90 55 13
45 97 61 45 32 91 26 84 33 57 80
46 60 49 47 92 81 51 7 18 66 47
47 39 98 90 33 68 5 26 72 76 37
48 6 18 74 51 77 19 28 21 81 46
49 20 69 54 26 25 80 36 8 65 31
Let's reduce A in [0,1]
0 0.282828
1 0.919192
2 0.545455
3 1.000000
4 0.989899
5 0.444444
6 0.767677
7 0.525253
8 0.565657
9 0.292929
10 0.818182
11 0.575758
12 0.575758
13 0.181818
14 0.777778
15 0.878788
16 0.343434
17 0.010101
18 0.353535
19 0.000000
20 0.616162
21 0.818182
22 0.202020
23 0.575758
24 0.020202
25 0.646465
26 0.272727
27 0.828283
28 0.191919
29 0.343434
30 0.333333
31 0.000000
32 0.202020
33 0.828283
34 0.080808
35 0.646465
36 0.424242
37 0.272727
38 0.444444
39 0.363636
40 0.202020
41 0.545455
42 0.424242
43 0.070707
44 0.404040
45 0.979798
46 0.606061
47 0.393939
48 0.060606
49 0.202020
Name: A, dtype: float64
Let's reduce first row in [0,1]
A 0.311111
B 0.766667
C 0.055556
D 0.455556
E 0.133333
F 0.688889
G 1.000000
H 0.355556
I 0.366667
L 0.944444
Name: 0, dtype: float64
Mean and std values (by column)
A 45.24
B 49.76
C 54.12
D 50.50
E 57.86
F 49.18
G 49.78
H 47.78
I 46.92
L 51.78
dtype: float64
A 28.393417
B 32.193015
C 25.165282
D 28.321226
E 32.443364
F 28.488229
G 29.673248
H 29.759780
I 31.056788
L 30.613649
dtype: float64
Mean and std values (by column) - top 10 values
0 45.7
1 56.1
2 65.4
3 42.6
4 57.5
5 56.0
6 46.9
7 56.1
8 38.7
9 31.3
dtype: float64
0 29.424291
1 33.013297
2 27.785688
3 35.647035
4 33.069792
5 30.342489
6 34.853503
7 32.942543
8 29.431842
9 18.826990
dtype: float64
Cumulative sum (by column)- top 10 rows
A B C D E F G H I L
0 28 69 5 41 12 62 90 32 33 85
1 119 128 69 135 16 113 135 84 129 90
2 173 202 122 227 36 197 220 105 227 163
3 272 202 161 239 126 212 282 143 231 230
4 370 212 196 316 172 309 370 215 246 267
5 414 221 287 373 270 372 422 292 308 274
6 490 238 299 414 339 406 522 321 308 365
7 542 263 342 473 426 497 523 411 331 455
8 598 296 380 564 439 498 557 428 353 537
9 627 314 422 612 473 514 621 435 399 546
Cumulative sum (by row) - top 10 rows
A B C D E F G H I L
0 28 97 102 143 155 217 307 339 372 457
1 91 150 214 308 312 363 408 460 556 561
2 54 128 181 273 293 377 462 483 581 654
3 99 99 138 150 240 255 317 355 359 426
4 98 108 143 220 266 363 451 523 538 575
5 44 53 144 201 299 362 414 491 553 560
6 76 93 105 146 215 249 349 378 378 469
7 52 77 120 179 266 357 358 448 471 561
8 56 89 127 218 231 232 266 283 305 387
9 29 47 89 137 171 187 251 258 304 313
Merging DataFrames¶
It is possible to merge together DataFrames having a common column name. The merge can be done with the pandas merge method. Upon merging, the two tables will be concatenated into a bigger one containing information from both DataFrames. The basic syntax is:
pandas.merge(DataFrame1, DataFrame2, on="col_name", how="inner/outer/left/right")
The column on which the merge has to be performed is specified with the parameter on followed by the column name, while the behaviour of the merging depends on the parameter how that tells pandas how to behave when dealing with non-matching data. In particular:
1. how = inner : non-matching entries are discarded;
2. how = left : ids are taken from the first DataFrame;
3. how = right : ids are taken from the second DataFrame;
4. how = outer : ids from both are retained.
[19]:
import pandas as pd
Snp1 = {"id": ["SNP_FB_0411211","SNP_FB_0412425","SNP_FB_0942385",
"CH01f09","Hi05f12x","SNP_FB_0942712" ],
"type" : ["SNP","SNP","SNP","SSR","SSR","SNP"]
}
Snp2 = {"id" : ["SNP_FB_0411211","SNP_FB_0412425",
"SNP_FB_0942385", "CH01f09","SNP_FB_0428218" ],
"chr" : ["1", "15","7","9","1"]
}
DFs1 = pd.DataFrame(Snp1)
DFs2 = pd.DataFrame(Snp2)
print(DFs1)
print(DFs2)
print("")
print("Inner merge (only common in both)")
inJ = pd.merge(DFs1,DFs2, on = "id", how = "inner")
print(inJ)
print("")
print("Left merge (IDS from DFs1)")
leftJ = pd.merge(DFs1,DFs2, on = "id", how = "left")
print(leftJ)
print("")
print("Right merge (IDS from DFs2)")
rightJ = pd.merge(DFs1,DFs2, on = "id", how = "right")
print(rightJ)
print("")
print("Outer merge (IDS from both)")
outJ = pd.merge(DFs1,DFs2, on = "id", how = "outer")
print(outJ)
id type
0 SNP_FB_0411211 SNP
1 SNP_FB_0412425 SNP
2 SNP_FB_0942385 SNP
3 CH01f09 SSR
4 Hi05f12x SSR
5 SNP_FB_0942712 SNP
id chr
0 SNP_FB_0411211 1
1 SNP_FB_0412425 15
2 SNP_FB_0942385 7
3 CH01f09 9
4 SNP_FB_0428218 1
Inner merge (only common in both)
id type chr
0 SNP_FB_0411211 SNP 1
1 SNP_FB_0412425 SNP 15
2 SNP_FB_0942385 SNP 7
3 CH01f09 SSR 9
Left merge (IDS from DFs1)
id type chr
0 SNP_FB_0411211 SNP 1
1 SNP_FB_0412425 SNP 15
2 SNP_FB_0942385 SNP 7
3 CH01f09 SSR 9
4 Hi05f12x SSR NaN
5 SNP_FB_0942712 SNP NaN
Right merge (IDS from DFs2)
id type chr
0 SNP_FB_0411211 SNP 1
1 SNP_FB_0412425 SNP 15
2 SNP_FB_0942385 SNP 7
3 CH01f09 SSR 9
4 SNP_FB_0428218 NaN 1
Outer merge (IDS from both)
id type chr
0 SNP_FB_0411211 SNP 1
1 SNP_FB_0412425 SNP 15
2 SNP_FB_0942385 SNP 7
3 CH01f09 SSR 9
4 Hi05f12x SSR NaN
5 SNP_FB_0942712 SNP NaN
6 SNP_FB_0428218 NaN 1
Note that the columns we merge on do not necessarily need to be the same, we can specify a correspondence between the row of the first dataframe (the one on the left) and the second dataframe (the one on the right) specifying which columns must have the same values to perform the merge. This can be done by using the parameters right_on = column_name and left_on = column_name:
[20]:
#%reset -s -f
%clear
import pandas as pd
d = dict({"A" : [1,2,3,4], "B" : [3,4,73,13]})
d2 = dict({"E" : [1,4,3,13], "F" : [3,1,71,1]})
DF = pd.DataFrame(d)
DF2 = pd.DataFrame(d2)
merged_onBE = DF.merge(DF2, left_on = 'B', right_on = 'E', how = "inner")
merged_onAF = DF.merge(DF2, right_on = "F", left_on = "A", how = "outer")
print("DF:")
print(DF)
print("DF2:")
print(DF2)
print("\ninner merge on BE")
print(merged_onBE)
print("\nouter merge on AF:")
print(merged_onAF)
DF:
A B
0 1 3
1 2 4
2 3 73
3 4 13
DF2:
E F
0 1 3
1 4 1
2 3 71
3 13 1
inner merge on BE
A B E F
0 1 3 3 71
1 2 4 4 1
2 4 13 13 1
outer merge on AF:
A B E F
0 1.0 3.0 4.0 1.0
1 1.0 3.0 13.0 1.0
2 2.0 4.0 NaN NaN
3 3.0 73.0 1.0 3.0
4 4.0 13.0 NaN NaN
5 NaN NaN 3.0 71.0
Grouping¶
Given a DataFrame, it is possible to apply the so called split-apply-aggregate processing method. Basically, this helps to group the data according to the value of some columns, apply a function on the different groups and aggregate the results in a new DataFrame.
Grouping of a DataFrame can be done by using the DataFrame.groupby(columnName) method which returns a pandas.DataFrameGroupBy object, which basically is composed of two information: the name shared by each group and a DataFrame containing all the elements belonging to that group.
Given a grouped DataFrame, each group can be obtained with the get_group(groupName) it is also possible to loop over the groups:
for groupName, groupDataFrame in grouped:
#do something
It is also possible to aggregate the groups by applying some functions to each of them (please refer to the documentation).
Let’s see these things in action.
Example Given a list of labels and integers group them by label and compute the mean of all values in each group.
[21]:
import pandas as pd
test = {"x": ["a","a", "b", "b", "c", "c" ],
"y" : [2,4,0,5,5,10]
}
DF = pd.DataFrame(test)
print(DF)
print("")
gDF = DF.groupby("x")
for i,g in gDF:
print("Group: ", i)
print(g)
print(type(g))
aggDF = gDF.aggregate(pd.DataFrame.mean)
print(aggDF)
#without looping through the groups...
print("\nThe 'a' group:")
print(gDF.get_group('a'))
print("\nThe 'c' group:")
print(gDF.get_group('c'))
x y
0 a 2
1 a 4
2 b 0
3 b 5
4 c 5
5 c 10
Group: a
x y
0 a 2
1 a 4
<class 'pandas.core.frame.DataFrame'>
Group: b
x y
2 b 0
3 b 5
<class 'pandas.core.frame.DataFrame'>
Group: c
x y
4 c 5
5 c 10
<class 'pandas.core.frame.DataFrame'>
y
x
a 3.0
b 2.5
c 7.5
The 'a' group:
x y
0 a 2
1 a 4
The 'c' group:
x y
4 c 5
5 c 10
Example Given the orders data seen above, let’s get the columns “Sales”, “Profit” and “Product Category” and compute the total sum and the mean of the sales and profits for each product category.
[22]:
import pandas as pd
import matplotlib.pyplot as plt
orders = pd.read_csv("file_samples/sampledata_orders.csv", sep=",",
index_col =0, header=0)
SPC = orders[["Sales","Profit", "Product Category"]]
print(SPC.head())
SPC.plot(kind = "hist", bins = 10)
plt.show()
print("")
grouped = SPC.groupby("Product Category")
for i,g in grouped:
print("Group: ", i)
print("")
print("Count elements per category:") #get the series corresponding to the column
#and apply the value_counts() method
print(orders["Product Category"].value_counts())
print("")
print("Total values:")
print(grouped.aggregate(pd.DataFrame.sum)[["Sales"]])
print("Mean values (sorted by profit):")
mv_sorted = grouped.aggregate(pd.DataFrame.mean).sort_values(by="Profit")
print(mv_sorted)
print("")
print("The most profitable is {}".format(mv_sorted.index[-1]))
Sales Profit Product Category
Row ID
1 261.5400 -213.25 Office Supplies
49 10123.0200 457.81 Office Supplies
50 244.5700 46.71 Office Supplies
80 4965.7595 1198.97 Technology
85 394.2700 30.94 Office Supplies
Group: Furniture
Group: Office Supplies
Group: Technology
Count elements per category:
Office Supplies 4610
Technology 2065
Furniture 1724
Name: Product Category, dtype: int64
Total values:
Sales
Product Category
Furniture 5178590.542
Office Supplies 3752762.100
Technology 5984248.182
Mean values (sorted by profit):
Sales Profit
Product Category
Furniture 3003.822820 68.116607
Office Supplies 814.048178 112.369072
Technology 2897.941008 429.207516
The most profitable is Technology
Exercises¶
The file top_3000_words.txt is a one-column file representing the top 3000 English words. Read the file and for each letter, count how many words start with that letter. Store this information in a dictionary. Create a pandas series from the dictionary and plot an histogram of all initials counting more than 100 words starting with them.
Show/Hide Solution
The file filt_aligns.tsv is a tab separated value file representing alignments of paired-end reads on some apple chromosomes. Paired end reads have the property of being X bases apart from each other as they have been sequenced from the two ends of some size-selected DNA molecules.
Each line of the file has the following information readID\tChrPE1\tAlignmentPosition1\tChrPE2\tAlignmentPosition2. The two ends of the same pair have the same readID. Load the read pairs aligning on the same chromosome into two dictionaries. The first (inserts) having readID as keys and the insert size (i.e. the absolute value of AlignmentPosition1 - AlignmentPosition2) as value. The second dictionary (chrs)will have readID as key and chromosome ID as value. Example:
readID Chr11 31120 Chr11 31472
readID1 Chr7 12000 Chr11 11680
will result in:
inserts = {"readID" : 352, "readID1" : 320}
chrs = {"readID" : "Chr11", "readID1" : "Chr7"}
Once you have the two dictionaries:
1. Create a Series with all the insert sizes and show some
of its stats with the method **describe**. What is the mean
insert size? How many paried end are we using to create
this distribution?
2. Display the first 5 values of the series
3. Make a box plot to assess the distribution of the values.
4. Make an histogram to see the values in a different way.
How does this distribution look like?
5. Create another series from the chromosome info and print
the first 10 elements
6. Create a DataFrame starting from the two Series and print
the first 10 elements
7. For each chromosome, get the average insert size of the
paired aligned to it (hint:use group by).
8. Make a box plot of the average insert size per chromosome.
Show/Hide Solution
Download the train.csv dataset. As the name says it is a .csv file. The file contains information regarding loans given or refused to applicants. Information on the gender, marital status, education, work and income of the applicant is reported alongside the amount and length of the loan and credit history (i.e. 0 if no previous loan was given, 1 otherwise). Open it in a text editor or excel and inspect it first. Then, answer the following questions (if you have any doubts check here):
Load it into a pandas DataFrame (use column
Loan_IDas index. Hint: use parm index_col).Get an idea of the data by visualizing its first 5 entries;
How many total entries are present in the file? How many males and females?
What is the average applicant income? Does the gender affect the income? Compute the average of the applicant income on the whole dataset and the average of the data grouped by Gender. How many Females have an income > than the average?
How many loans have been given (i.e. Loan_Status equals Y)? What is the percentage of the loans given and that of the loans refused?
What is the percentage of given/refused loans in the case of married people?
What is the percentage of given/refused loans in the case of applicants with positive credit history (i.e. Credit_History equals 1)?
Show/Hide Solution
[Thanks to Stefano Teso] DNA transcription and translation into proteins follows this schema:
The file gene_table.csv is a comma separated value file representing a summary of the annotation of several human genes based on the Ensembl annotation. For each gene it contains the following information:
gene_name,gene_biotype,chromosome,strand,transcript_count
where gene_name is based on the HGNC nomenclature. gene_biotype represents the biotype (refer to VEGA like protein_coding, pseudogene, lincRNA, miRNA etc. chromosome is where the feature is located, strand is a + or a - for the forward or reverse strand and transcript_count reports the number of isoforms of the gene.
A sample of the file follows:
TSPAN6,protein_coding,chrX,-,5
TNMD,protein_coding,chrX,+,2
DPM1,protein_coding,chr20,-,6
SCYL3,protein_coding,chr1,-,5
C1orf112,protein_coding,chr1,+,9
FGR,protein_coding,chr1,-,7
CFH,protein_coding,chr1,+,6
FUCA2,protein_coding,chr6,-,3
GCLC,protein_coding,chr6,-,13
Write a python program that: 0. Loads the gene_table.csv in a DataFrame (inspect the first entries with head to check the content of the file); 1. Computes the number of genes annotated for the human genome; 2. Computes the minimum, maximum, average and median number of known isoforms per gene (consider the transcript_count column as a series). 3. Plots a histogram and a boxplot of the number of known isoforms per gene 4. Computes the number of different biotypes. How many genes do we have for each genotype? Plot the number of genes per biotype in a horizontal bar plot (hint: use also figsize = (10,10) to make it visible; 5. Computes the number of different chromosomes 6. Computes, for each chromosome, the number of genes it contains, and prints a horizontal barplot with the number of genes per chromosome. 7. Computes, for each chromosome, the percentage of genes located on the + strand 8. Computes, for each biotype, the average number of transcripts associated to genes belonging to the biotype. Finally, plots them in a vertical bar plot
Show/Hide Solution
Write a function that creates and returns a data frame having columns with the labels specified through a list taken in input and ten rows of random data between 1 and 100.
Create two random DataFrames one with labels l = [“A”, “B”, “C” ,”D”,”E”] and l1 = [“W”, “X”,”Y”,”Z”]
Print the first 5 elements to inspect the two DataFrames and plot the valuse of the two DataFrames;
Create a new Series S1 with values: [1, 1, 1, 0, 0, 1, 1, 0, 0, 1]. Get the Series corresponding to the column “C” and multiply it point-to-point by the Series S1 (hint use: Series.multiply(S1))
Add this new series as a “C” column of the second DataFrame.
Merge the two DataFrames based on the value of C. Perform an inner, outer, left and right merge and see the difference
Show/Hide Solution
Practical 9¶
In this practical we will will practice Numpy and Matplotlib.
Numpy¶
Numpy is a fundamental library for high performance scientific computations. It provides fast and memory efficient data structures like ndarray with broadcasting capabilities, standard mathematical functions that can be applied on the arrays avoiding loops, linear algebra functions, I/O methods and it is well integrated with programming languages like C.
To use the functionalities of the library we always need to import it with (standard name is np):
import numpy as np
The official documentation of the numpy library can be found at http://www.numpy.org/.
Numpy ndarray¶
Numpy ndarray is an N-dimensional array object designed to contain homogeneous data (i.e. all data must have the same type). Every array (also called tensor) comes with two information: the shape (a tuple describing the dimensions of the array) and a dtype (the data type of the array).
Given a list of homogeneous values the ndarray can be obtained by using the np.array(list) method. Given the numpy array its shape, dimensionality and dtype can be obtained with array.shape, array.ndim and array.dtype.
An example follows:
[1]:
import numpy as np
Aint = np.array([[1,2,3], [4,5,6]])
Afloat = np.array([[1.1,2,3], [4.2,5,6], [1,2,3]])
print(Aint)
print(type(Aint))
print(Aint.shape)
print(Aint.dtype)
print("")
print(Afloat)
print("type: {}".format(type(Afloat)))
print("shape: {}".format(Afloat.shape))
print("dtype: {}".format(Afloat.dtype))
[[1 2 3]
[4 5 6]]
<class 'numpy.ndarray'>
(2, 3)
int64
[[1.1 2. 3. ]
[4.2 5. 6. ]
[1. 2. 3. ]]
type: <class 'numpy.ndarray'>
shape: (3, 3)
dtype: float64
Example:
Let’s create a ndarray holding the square root and one with the cubic root of the first five integers. Let’s put them together in a 2-d array and check its dimensions.
[2]:
import numpy as np
import math
mysqrt = [math.sqrt(x) for x in range(0,5)]
mycrt = [x**(1/3) for x in range(0,5)]
myOtherRt = [x**(1/5) for x in range(0,5)]
print("Original lists:")
print(mysqrt)
print(mycrt)
print("")
npData = np.array(mysqrt)
print("Numpy ndarray:")
print(npData)
print("")
print("The shape:", npData.shape)
print("The dimensionality:", npData.ndim)
print("The type:", npData.dtype)
print("")
npData = np.array([mysqrt]) #NOTE: brackets!
print("The 2D version of the ndarray:")
print(npData)
print("")
print("The shape:", npData.shape)
print("The dimensionality:", npData.ndim)
print("The type:", npData.dtype)
print("")
twoDarray = np.array([mysqrt, mycrt, myOtherRt])
print("Another 2D array:")
print(twoDarray)
print("")
print("The shape:", twoDarray.shape)
print("The dimensionality:", twoDarray.ndim)
print("The type:", twoDarray.dtype)
Original lists:
[0.0, 1.0, 1.4142135623730951, 1.7320508075688772, 2.0]
[0.0, 1.0, 1.2599210498948732, 1.4422495703074083, 1.5874010519681994]
Numpy ndarray:
[0. 1. 1.41421356 1.73205081 2. ]
The shape: (5,)
The dimensionality: 1
The type: float64
The 2D version of the ndarray:
[[0. 1. 1.41421356 1.73205081 2. ]]
The shape: (1, 5)
The dimensionality: 2
The type: float64
Another 2D array:
[[0. 1. 1.41421356 1.73205081 2. ]
[0. 1. 1.25992105 1.44224957 1.58740105]
[0. 1. 1.14869835 1.24573094 1.31950791]]
The shape: (3, 5)
The dimensionality: 2
The type: float64
We can also create arrays (matrices) full of zeros or ones or even diagonal matrices with the following numpy methods:
Array:
np.zeros(N)or matrix:np.zeros((N,M))Array:
np.ones(N)or matrix:np.ones((N,M))Matrix:
np.eye(N)
Numpy has its own range method that is called np.arange(N). Evenly spaced values in a range can be obtained also with np.linspace(S,E, num=N, endpoint=True/False) to obtain N linearly spaced values from S to E (included, unless endpoint = False is specified).
[3]:
import numpy as np
zeros = np.zeros(3)
zMat = np.zeros((4,3))
ones = np.ones(3)
oMat = np.ones((3,2))
diag = np.eye(4)
rng = np.arange(5) #5 excluded!
print("Zero array (1x3)")
print(zeros)
print("")
D = zMat.shape
print("Zero matrix ({}x{})".format(D[0],D[1]))
print(zMat)
print("")
print("Ones array (1x3)")
print(ones)
print("")
print("Ones matrix (3x2)")
print(oMat)
print("")
print("Diagonal matrix")
print(diag)
print("")
print("Range 0-4")
print(rng)
print("A diagonal matrix:")
dm = np.diag(rng)
print(dm)
print("Its shape:")
print(dm.shape)
rng = np.arange(7)
print("Range 0-6")
print(rng)
myRange = np.linspace(-5,2.5,num =6)
print("6 linearly spaced elements in [-5 - 2.5]:")
print(myRange)
myRange = np.linspace(0,21,num =7, endpoint=False)
print("7 linearly spaced elements in [0 - 21):")
print(myRange)
Zero array (1x3)
[0. 0. 0.]
Zero matrix (4x3)
[[0. 0. 0.]
[0. 0. 0.]
[0. 0. 0.]
[0. 0. 0.]]
Ones array (1x3)
[1. 1. 1.]
Ones matrix (3x2)
[[1. 1.]
[1. 1.]
[1. 1.]]
Diagonal matrix
[[1. 0. 0. 0.]
[0. 1. 0. 0.]
[0. 0. 1. 0.]
[0. 0. 0. 1.]]
Range 0-4
[0 1 2 3 4]
A diagonal matrix:
[[0 0 0 0 0]
[0 1 0 0 0]
[0 0 2 0 0]
[0 0 0 3 0]
[0 0 0 0 4]]
Its shape:
(5, 5)
Range 0-6
[0 1 2 3 4 5 6]
6 linearly spaced elements in [-5 - 2.5]:
[-5. -3.5 -2. -0.5 1. 2.5]
7 linearly spaced elements in [0 - 21):
[ 0. 3. 6. 9. 12. 15. 18.]
Random arrays¶
Random arrays can be created from several different distributions (check here for all options). Through the random number generator default_rng which has been added to the newest versions of numpy (e.g. >1.16). The older syntax has been kept for back-compatibility, but the newer one using the default_rng should be used. Some examples include uniform distribution, normal, binomial,…
Example:
Create a random array of 1000 values drawn from: 1. a gaussian distribution with \(\sigma = 20\) and \(\mu = 2\) 2. a uniform distribution from 0 to 5 3. a binomial distribution with \(p = 0.5\) and \(n = 12\)
and plot their histogram.
[4]:
import numpy as np
import matplotlib.pyplot as plt
#Create the random number generator
rng = np.random.default_rng()
#get the gaussian random array
g = rng.normal(20,2, 1000)
#a uniform random array with vals in [0,5]
u = rng.uniform(0,5, 1000)
#get the binomial random array
b = rng.binomial(12,0.5, 1000)
plt.hist(g, bins = 30)
plt.title("Gaussian(20,2)")
plt.xlabel("Random #")
plt.ylabel("Count")
plt.show()
plt.hist(u, bins = 10)
plt.title("Uniform(0,5)")
plt.xlabel("Random #")
plt.ylabel("Count")
plt.show()
plt.hist(b, bins = 10)
plt.title("Binomial(12,0.5)")
plt.xlabel("Random #")
plt.ylabel("Count")
plt.show()
<matplotlib.figure.Figure at 0x7f1fb241db00>
<matplotlib.figure.Figure at 0x7f1fb22507f0>
<matplotlib.figure.Figure at 0x7f1fad53d240>
It is also possible to specify the size of the output (with the tuple size) to get a matrix instead.
[5]:
import numpy as np
rng = np.random.default_rng()
u = rng.uniform(0,1, size = (4,3))
print("Uniform distr. in (0,1). 4x3 matrix:")
print("")
print(u)
Uniform distr. in (0,1). 4x3 matrix:
[[0.04319745 0.80810316 0.95688607]
[0.38279799 0.06599466 0.83906502]
[0.64017936 0.17292249 0.6691821 ]
[0.30912131 0.57479797 0.96046875]]
To always get the same values we need to initialize the random seed (a parameter of the pseudo-random sequence generator) always to the same value.
[6]:
import numpy as np
rng = np.random.default_rng()
u = rng.uniform(0,1,size=(3,2))
u1 = rng.uniform(0,1,size=(3,2))
u2 = rng.uniform(0,1,size=(3,2))
print(" u: {}\n\n u1:{}\n\n u2:{}".format(u,u1,u2))
print("")
print("With random seed reinit.")
rng = np.random.default_rng(0) #seed init at 0
u = rng.uniform(0,1,3)
rng = np.random.default_rng(0) #seed init at 0
u1 = rng.uniform(0,1,3)
rng = np.random.default_rng(0) #seed init at 0
u2 = rng.uniform(0,1,3)
#no reinit!!!
u3 = rng.uniform(0,1,3)
print(" u: {}\n u1:{}\n u2:{}\n u3:{}".format(u,u1,u2, u3))
u: [[0.76180262 0.30145968]
[0.42649499 0.6514337 ]
[0.46345338 0.27718304]]
u1:[[0.7564963 0.80978551]
[0.02806826 0.70233526]
[0.04354717 0.08700437]]
u2:[[0.53011366 0.61936712]
[0.67975182 0.85019137]
[0.04757717 0.2940392 ]]
With random seed reinit.
u: [0.63696169 0.26978671 0.04097352]
u1:[0.63696169 0.26978671 0.04097352]
u2:[0.63696169 0.26978671 0.04097352]
u3:[0.01652764 0.81327024 0.91275558]
Numpy to and from pandas¶
Pandas Series and DataFrames are actually built on top of numpy ndarrays. Moreover, given a numpy matrix (or array) it is quite easy to convert it into a DataFrame (or Series).
[7]:
import pandas as pd
import numpy as np
myDict = {"one" : 1, "two" : 2, "three" : 3, "four" : 4}
mySeries = pd.Series(myDict)
print(myDict)
print("")
print(mySeries)
print("")
print(type(mySeries))
print("")
print(type(mySeries.values))
print("")
myMat = np.diag(np.arange(6))
myDF = pd.DataFrame(myMat)
print("Numpy matrix")
print(myMat)
print("")
print("Pandas DataFrame")
print(myDF)
print("")
print("Reindexed DataFrame")
myDF = pd.DataFrame(myMat, index = list("ABCDEF"),
columns = ['a1','b2','c3','d4','e5','f6'])
print(myDF)
{'one': 1, 'two': 2, 'three': 3, 'four': 4}
one 1
two 2
three 3
four 4
dtype: int64
<class 'pandas.core.series.Series'>
<class 'numpy.ndarray'>
Numpy matrix
[[0 0 0 0 0 0]
[0 1 0 0 0 0]
[0 0 2 0 0 0]
[0 0 0 3 0 0]
[0 0 0 0 4 0]
[0 0 0 0 0 5]]
Pandas DataFrame
0 1 2 3 4 5
0 0 0 0 0 0 0
1 0 1 0 0 0 0
2 0 0 2 0 0 0
3 0 0 0 3 0 0
4 0 0 0 0 4 0
5 0 0 0 0 0 5
Reindexed DataFrame
a1 b2 c3 d4 e5 f6
A 0 0 0 0 0 0
B 0 1 0 0 0 0
C 0 0 2 0 0 0
D 0 0 0 3 0 0
E 0 0 0 0 4 0
F 0 0 0 0 0 5
Reshaping¶
The shape of a numpy ndarray can be changed at any time with the methods reshape((R,C)) where R and C are the rows and columns used to shape an array into a matrix, and ravel that is used to go the other way around from matrix to array.
[8]:
import numpy as np
myA = np.arange(12)
print("The array:")
print(myA)
print("")
myB = myA.reshape((2,6))
print("Reshaped (2x6):")
print(myB)
print("")
myC = myA.reshape((3,4))
print("Reshaped: (3x4)")
print(myC)
myD = myB.ravel()
print("")
print("Back to array:")
print(myD)
The array:
[ 0 1 2 3 4 5 6 7 8 9 10 11]
Reshaped (2x6):
[[ 0 1 2 3 4 5]
[ 6 7 8 9 10 11]]
Reshaped: (3x4)
[[ 0 1 2 3]
[ 4 5 6 7]
[ 8 9 10 11]]
Back to array:
[ 0 1 2 3 4 5 6 7 8 9 10 11]
Be careful though, if shapes don’t match an error cannot reshape array is returned:
Iterating over arrays and Indexing¶
It is possible to loop over the elements of an array by element or by row of the matrix. In the first case we use the method np.ndarray.flat to make a matrix accessible as a one dimensional array. Check out the following examples:
[9]:
import numpy as np
myA = np.arange(12)
print(myA)
print("")
print("Matrix:")
myA = myA.reshape((4,3))
print(myA)
print("Looping through elements:")# equivalent to:
for el in myA.flat: # for el in myA.ravel():
print("Element:", el) # print("Element:",el)
print("Looping row by row:")
for el in myA:
print("Row: ", el, "is a", type(el))
for j in el:
print("\tel:", j)
[ 0 1 2 3 4 5 6 7 8 9 10 11]
Matrix:
[[ 0 1 2]
[ 3 4 5]
[ 6 7 8]
[ 9 10 11]]
Looping through elements:
Element: 0
Element: 1
Element: 2
Element: 3
Element: 4
Element: 5
Element: 6
Element: 7
Element: 8
Element: 9
Element: 10
Element: 11
Looping row by row:
Row: [0 1 2] is a <class 'numpy.ndarray'>
el: 0
el: 1
el: 2
Row: [3 4 5] is a <class 'numpy.ndarray'>
el: 3
el: 4
el: 5
Row: [6 7 8] is a <class 'numpy.ndarray'>
el: 6
el: 7
el: 8
Row: [ 9 10 11] is a <class 'numpy.ndarray'>
el: 9
el: 10
el: 11
Indexing and slicing can be performed as usual with the [] operator. np.ndarray[i,j] returns the element at row i and column j.
A multi-dimensional matrix has more than 2 dimensions. They can be thought as several 2D matrices stacked one on top of the other:
Note that np.ndarray[0,:,:] is the whole first matrix. np.ndarray[:,0,:] is all the first rows, while np.ndarray[:,:,0] is all the first columns. Regarding slicing and indexing, the same reasoning applies to n-dimensional matrices. For example, myB below is a 3x3x3 matrix.
[10]:
import numpy as np
rng = np.random.default_rng()
myA = rng.integers(0,10, size = (3,4))
print(myA)
print("")
print("myA[2,2] = ", myA[2,2])
print("myA[1,3] = ", myA[1,3])
print("myA[0,3] = ", myA[0,3])
print("second row:", myA[1,:])
print("")
print("3D matrix ",)
myB = np.random.randint(0,10, size = (3,3,3))
print(" - shape:", myB.shape)
print(myB)
print("")
print("myB[0,2,2] = ", myB[0,2,2])
print("Second matrix:")
print(myB[1,:,:])
print("Third row of second matrix:")
print(myB[1,2,:])
print("Second column of second matrix:")
print(myB[1,:,1])
[[3 0 1 6]
[3 9 7 3]
[0 4 0 0]]
myA[2,2] = 0
myA[1,3] = 3
myA[0,3] = 6
second row: [3 9 7 3]
3D matrix
- shape: (3, 3, 3)
[[[0 3 1]
[2 6 0]
[0 7 9]]
[[9 3 7]
[0 4 4]
[1 7 2]]
[[1 4 1]
[5 9 9]
[4 5 1]]]
myB[0,2,2] = 9
Second matrix:
[[9 3 7]
[0 4 4]
[1 7 2]]
Third row of second matrix:
[1 7 2]
Second column of second matrix:
[3 4 7]
Broadcasting and arithmetic functions¶
Universal functions are very efficient element-wise functions that can be applied on ndarrays. As seen in Pandas, operations involving scalar values and arrays are broadcast to all the elements of the ndarray, while operations performed on arrays having the same size are done element by element.
Note also that it is possible to perform some operations only on a sub-part of an ndarray. Moreover, if operators are applied to differently sized, but compatible, ndarrays (es. matrix 3x3x3 and vector 3x1), numpy will perform broadcast of the operator. Let’s see some examples:
[11]:
import numpy as np
rng = np.random.default_rng()
A = rng.integers(0,10, size = (3,2))
B = rng.integers(0,10, size = (3,3,3))
C = rng.integers(0,10, size = (3,1))
print("Matrix A 3x2")
print(A)
print("")
print("Matrix B 3x3x3")
print(B)
print("")
print("Matrix C 3x1")
print(C)
print("")
print("A squared")
print(A**2)
print("")
print("A square-rooted")
print(np.sqrt(A))
print("")
print("B square-rooted")
print(np.sqrt(B))
print("A + C ")
print(A + C)
print("")
print("B + C ")
print(B + C)
print("")
print("B")
print(B)
print("Sub array B - 20")
B[:, 0:2 , 0:2 ] -= 20
print(B)
Matrix A 3x2
[[1 4]
[1 0]
[5 0]]
Matrix B 3x3x3
[[[5 5 8]
[2 7 5]
[3 2 7]]
[[6 7 8]
[5 2 7]
[1 4 1]]
[[4 3 5]
[2 4 5]
[9 1 7]]]
Matrix C 3x1
[[8]
[5]
[1]]
A squared
[[ 1 16]
[ 1 0]
[25 0]]
A square-rooted
[[1. 2. ]
[1. 0. ]
[2.23606798 0. ]]
B square-rooted
[[[2.23606798 2.23606798 2.82842712]
[1.41421356 2.64575131 2.23606798]
[1.73205081 1.41421356 2.64575131]]
[[2.44948974 2.64575131 2.82842712]
[2.23606798 1.41421356 2.64575131]
[1. 2. 1. ]]
[[2. 1.73205081 2.23606798]
[1.41421356 2. 2.23606798]
[3. 1. 2.64575131]]]
A + C
[[ 9 12]
[ 6 5]
[ 6 1]]
B + C
[[[13 13 16]
[ 7 12 10]
[ 4 3 8]]
[[14 15 16]
[10 7 12]
[ 2 5 2]]
[[12 11 13]
[ 7 9 10]
[10 2 8]]]
B
[[[5 5 8]
[2 7 5]
[3 2 7]]
[[6 7 8]
[5 2 7]
[1 4 1]]
[[4 3 5]
[2 4 5]
[9 1 7]]]
Sub array B - 20
[[[-15 -15 8]
[-18 -13 5]
[ 3 2 7]]
[[-14 -13 8]
[-15 -18 7]
[ 1 4 1]]
[[-16 -17 5]
[-18 -16 5]
[ 9 1 7]]]
A lot of mathematical and statistical functions can be applied. Examples include trigonometric functions like sin, cos, tan,…, statistical functions like mean, std, max, min, cumsum,… see the documentation for a complete list.
Example: Let’s create and plot a sin, cos and \(\log_2 (2 + sin+cos)\) from -2Pi to 2Pi
[12]:
import numpy as np
import matplotlib.pyplot as plt
A = np.arange(-2* np.pi, 2*np.pi, 0.01)
sA = np.sin(A)
cA = np.cos(A)
plt.plot(sA)
plt.plot(cA)
plt.plot(np.log2(2 + sA + cA))
plt.legend(["Sin(x)", "Cos(x)","$\log_2{2+sin(x)+cos(x)}$"])
plt.show()
Filtering¶
It is possible to filter np.ndarrays to retrieve the indexes (or the values) meeting specific conditions. The method where provides the index of those values. Note that if the np.ndarray is actually a matrix, where returns a tuple of indexes that are respectively the i and j coordinates of the elements fulfilling the condition.
Example: write a method that creates the np.ndarray with all the integers multiple of a certain number N that do not exceed M. The method should return also the indexes of those values in the original np.ndarray.
[13]:
import numpy as np
def getMultiples(N,M):
all = np.arange(1,M+1)
ind = np.where(all % N == 0)
filt = (all % N == 0)
return ind, all[filt]
res = getMultiples(13, 1000)
print("Indexes: {}\nValues:{}".format(res[0],res[1]))
Indexes: (array([ 12, 25, 38, 51, 64, 77, 90, 103, 116, 129, 142, 155, 168,
181, 194, 207, 220, 233, 246, 259, 272, 285, 298, 311, 324, 337,
350, 363, 376, 389, 402, 415, 428, 441, 454, 467, 480, 493, 506,
519, 532, 545, 558, 571, 584, 597, 610, 623, 636, 649, 662, 675,
688, 701, 714, 727, 740, 753, 766, 779, 792, 805, 818, 831, 844,
857, 870, 883, 896, 909, 922, 935, 948, 961, 974, 987]),)
Values:[ 13 26 39 52 65 78 91 104 117 130 143 156 169 182 195 208 221 234
247 260 273 286 299 312 325 338 351 364 377 390 403 416 429 442 455 468
481 494 507 520 533 546 559 572 585 598 611 624 637 650 663 676 689 702
715 728 741 754 767 780 793 806 819 832 845 858 871 884 897 910 923 936
949 962 975 988]
[14]:
import numpy as np
myA = np.arange(12).reshape((3,4))
print(myA)
print("Elements divisible by 3")
indexes = np.where(myA % 3 == 0)
print("Indexes:\n{}".format(indexes))
for ind in range(len(indexes[0])):
i = indexes[0][ind]
j = indexes[1][ind]
print("({},{}) -> {}".format(i,j, myA[i][j]))
[[ 0 1 2 3]
[ 4 5 6 7]
[ 8 9 10 11]]
Elements divisible by 3
Indexes:
(array([0, 0, 1, 2]), array([0, 3, 2, 1]))
(0,0) -> 0
(0,3) -> 3
(1,2) -> 6
(2,1) -> 9
Example: Let’s do some filtering on the sine and cosine series plotted above.
[15]:
import numpy as np
import matplotlib.pyplot as plt
A = np.arange(-2* np.pi, 2*np.pi, 0.01)
sA = np.sin(A)
cA = np.cos(A)
plt.plot(sA)
plt.plot(cA)
s0A_Y = sA[sA < 0] #get the values < 0
s0A_X = np.where(sA < 0) # the index of vaues < 0
c0A_Y = cA[np.all( [cA > 0.5 , cA < 0.75], axis = 0)]
c0A_X = np.where(np.all( [cA > 0.5 , cA < 0.75], axis = 0))
plt.scatter(s0A_X,s0A_Y, marker='o', c = 'red')
plt.scatter(c0A_X,c0A_Y, marker='X', c = 'green')
plt.legend(["Sin(x)", "Cos(x)","Sin(x) < 0", "Cos(x) in[0.5,0.75]"])
plt.show()
Note that in the code above, np.all tests if the two conditions are True at the same time (i.e. AND). If we want to test if at least one is True we use np.any. See np.all and np.any for more info:
[16]:
import numpy as np
v1 = [True, False,False, True]
v2 = [False, False,True, True]
v3 = [False, False, False, True]
print("vals:")
vals = np.array([v1,v2,v3])
print(vals)
print("\nANY(vals):")
print(np.any(vals, axis=0))
print("\nANY(vals) on rows:")
print(np.any(vals, axis=1))
print("\nALL(vals):")
print(np.all(vals, axis=0))
print("\nALL(vals) on rows:")
print(np.all(vals, axis=1))
vals:
[[ True False False True]
[False False True True]
[False False False True]]
ANY(vals):
[ True False True True]
ANY(vals) on rows:
[ True True True]
ALL(vals):
[False False False True]
ALL(vals) on rows:
[False False False]
We can apply all and any on 3D matrices as well, note the behaviour of axis in this case, that can assume values in [0,1,2] as in the following picture and example:
[17]:
import numpy as np
v1 = [[True, False],[False, True]]
v2 = [[False, False],[True, True]]
v3 = [[False, False], [False, True]]
print("vals:")
vals = np.array([v1,v2,v3])
print(vals)
print("\nThe matrix is {}D".format(vals.ndim))
print("First matrix:")
print(vals[0,:,:])
print("\nFirst row, all matrices:")
print(vals[:,0,:])
print("\nSecond column, all matrices:")
print(vals[:,:,1])
print("\nAXIS=0")
print("ANY:")
print(np.any(vals, axis=0))
print("ALL ")
print(np.all(vals, axis=0))
print("\nAXIS=1")
print("ANY:")
print(np.any(vals, axis=1))
print("ALL:")
print(np.all(vals, axis=1))
print("\nAXIS=2")
print("ANY:")
print(np.any(vals, axis=2))
print("ALL:")
print(np.all(vals, axis=2))
vals:
[[[ True False]
[False True]]
[[False False]
[ True True]]
[[False False]
[False True]]]
The matrix is 3D
First matrix:
[[ True False]
[False True]]
First row, all matrices:
[[ True False]
[False False]
[False False]]
Second column, all matrices:
[[False True]
[False True]
[False True]]
AXIS=0
ANY:
[[ True False]
[ True True]]
ALL
[[False False]
[False True]]
AXIS=1
ANY:
[[ True True]
[ True True]
[False True]]
ALL:
[[False False]
[False False]
[False False]]
AXIS=2
ANY:
[[ True True]
[False True]
[False True]]
ALL:
[[False False]
[False True]
[False False]]
Linear algebra¶
In numpy the product operator * is used to perform element-wise product, and therefore the arrays in input must have the same size. Matrix-matrix multiplication can be done through the np.dot(x,y) method, which is also a method of the object np.ndarray and therefore if x is a np.ndarray of compatible size with y, we can perform their product with x.dot(y).
A ndarray can be transposed by using the method T.
[18]:
import numpy as np
a = np.array([1, 2, 3, 1, 2, 3,1, 1 ,1])
A = a.reshape((3,3))
rng = np.random.default_rng()
B = rng.integers(0,10, size = (3,2))
print("A (3x3)")
print(A)
print("")
print("B (3x2)")
print(B)
print("")
print("AxB (3x2)")
print(A.dot(B))
print("")
print("A transposed:")
print(A.T)
A (3x3)
[[1 2 3]
[1 2 3]
[1 1 1]]
B (3x2)
[[8 4]
[1 0]
[4 5]]
AxB (3x2)
[[22 19]
[22 19]
[13 9]]
A transposed:
[[1 1 1]
[2 2 1]
[3 3 1]]
Numpy has a module called linalg providing several functions that implement matrix decompositions, inversions, determinant calculation and so on. Some of these methods are linalg.inv for the matrix inversion, linalg.qr for the QR decomposition, linalg.cholesky for the Cholesky decomposition, linalg.eig to find the eigenvalues of a matrix, linalg.solve to solve a system of linear equations and so on.
The complete list of all available methods can be found in the documentation.
Example: Let’s create a random 4x4 matrix and invert it. Let’s finally check that the product of the matrix by its inversion yields the 4x4 identity matrix.
[19]:
import numpy as np
from numpy import linalg
rng = np.random.default_rng()
A = rng.integers(0,10, size = (4,4))
print("Matrix A:")
print(A)
print("")
print("inv(A)")
A_1 = linalg.inv(A)
print(A_1)
print("")
print(np.dot(A,A_1)) # equivalent to print(A.dot(A_1))
Matrix A:
[[1 3 6 4]
[1 9 9 1]
[3 3 3 0]
[3 8 9 0]]
inv(A)
[[ 0.02222222 -0.08888889 0.42222222 -0.06666667]
[-0.13333333 0.53333333 0.46666667 -0.6 ]
[ 0.11111111 -0.44444444 -0.55555556 0.66666667]
[ 0.17777778 0.28888889 0.37777778 -0.53333333]]
[[ 1.00000000e+00 0.00000000e+00 2.22044605e-16 -4.44089210e-16]
[ 0.00000000e+00 1.00000000e+00 3.33066907e-16 -4.44089210e-16]
[-1.38777878e-17 -2.22044605e-16 1.00000000e+00 -1.11022302e-16]
[ 6.93889390e-17 2.22044605e-16 -1.11022302e-16 1.00000000e+00]]
Example: Let’s solve the following system of linear equations:\(\begin{cases} 2x + y - 2z = 3\\ x - y - z = 0\\ x + y + 3z = 12\end{cases}\)
[20]:
import numpy as np
from numpy import linalg
A = np.array([[2, 1, -2],[1,-1,-1], [1, 1 ,3]])
b = np.array([3, 0, 12])
print("A")
print(A)
print("")
print("b")
print(b)
print("")
#Let's find x such that: Ax = b
x = linalg.solve(A,b)
print("x")
print(x)
#Let's double check Ax = b:
print("")
print("Ax:")
print(np.dot(A,x))
A
[[ 2 1 -2]
[ 1 -1 -1]
[ 1 1 3]]
b
[ 3 0 12]
x
[3.5 1. 2.5]
Ax:
[ 3. 0. 12.]
Matplotlib¶
Matplotlib is a library created for producing publication quality plots. To use matplotlib one has to import it in the python program. Typically this is done with
import matplotlib.pyplot as plt
Documentation and several examples can be found at the matplotlib website.
Figures can also be saved to files with plt.savefig('filename').
Example: [adapted from documentation] Let’s plot the function \(cos(2 * \Pi * x)*sin(2 * \Pi * x)\) for x ranging from 0 to 10, annotating the point (5,0).
[21]:
import numpy as np
import matplotlib.pyplot as plt
x = np.arange(0, 10, 0.005)
y = np.cos(np.pi*x) * np.sin(2*np.pi*x)
fig = plt.figure()
ax = fig.add_subplot(111)
xdata = 5
ydata = 0
ax.plot(x, y)
ax.set_xlim(0, 10)
ax.set_ylim(-1, 1)
xdata = 5
ydata = 0
bbox = dict(boxstyle="round", fc="0.8")
arrowprops = dict(
arrowstyle = "->")
offset = 92
ax.annotate('(%.1f, %.1f)'%(xdata, ydata),
(xdata, ydata), xytext=(-1.5*offset, offset), textcoords='offset points',
bbox=bbox, arrowprops=arrowprops)
plt.show()
Example: Let’s plot simultaneusly \(sin(2 * \Pi * x)\), \(cos(2 \Pi x)\) and \(sin(2 \Pi x)*cos(2 \Pi x)\) for x ranging from 0 to 5.
[22]:
import numpy as np
import matplotlib.pyplot as plt
x = np.arange(0, 5, 0.005)
y = np.sin(2*np.pi*x)
y1 = np.cos(2*np.pi*x)
y2 = np.sin(2*np.pi*x)*np.cos(2*np.pi*x)
f, (ax1, ax2, ax3) = plt.subplots(3, sharex=True, sharey=True)
ax1.plot(x, y,'r')
ax2.plot(x, y1,'g')
ax3.plot(x,y2,'b')
ax1.legend(["sin"])
ax2.legend(["cos"])
ax3.legend(["sin * cos"])
plt.show()
Exercises¶
Write a function that converts a numpy ndarray of temperatures expressed in Degrees Celsius into Degrees Farenheit. The formula to convert a temperature C in Celsius into F in Farenheit is the following:
\[F = C * 9/5 + 32\]Write then a function that converts a numpy ndarray of temperatures in Farenheit into Celsius.
Finally:
apply the Celsius to Farenheit conversion on an ndarray containing the following October’s minimum and maximum temperatures in Trento: tmin = [12, 11, 11, 8, 9, 10, 3, 8, 4, 5, 10, 9, 8, 9, 8, 7, 6, 4, 5, 6, 9, 9, 3, 3, 5] and tmax =[15, 22, 18, 20, 22, 22, 20, 21, 21, 21, 21, 23, 24, 24, 24, 25, 22, 22, 20, 20, 19, 15, 20, 23, 19];
check that both functions work correctly by converting the values from Celsius to Farenheit and back to Celsius;
plot the minimum and maximum temperatures in celsius on the same graph. Since the temperatures refer to the first 25 days of the month of October 2017, the x coordinate can be a range(1,26);
Show/Hide Solution
Create the following functions:
createRadomList : with parameters, N, min, max. Creates a list of N random integers ranging from min to max;
getIdentical : with parameters two lists of integers L1 and L2 having the same size. It returns the list of indexes I where L1[I] == L2[I]
check : gets lists L1, L2, identities (as computed by getIdentical) and a number N and prints if the first N and last N values in identities correspond to indexes of identical values in L1 and L2;
implement getIdentical using numpy.ndarrays. Call it getIdenticalNpy (hint: subtract the two arrays and find zeros).
Test the software creating two lists of 100,000 random numbers from 0 to 10. You should get something similar to:
100000
100000
9032
Index: 4 L: 1 L1: 1
Index: 21 L: 10 L1: 10
Index: 32 L: 6 L1: 6
Index: 37 L: 5 L1: 5
Index: 47 L: 1 L1: 1
Index: 99974 L: 8 L1: 8
Index: 99982 L: 6 L1: 6
Index: 99983 L: 3 L1: 3
Index: 99984 L: 4 L1: 4
Index: 99987 L: 0 L1: 0
Identities are OK!
9032
Index: 4 L: 1 L1: 1
Index: 21 L: 10 L1: 10
Index: 32 L: 6 L1: 6
Index: 37 L: 5 L1: 5
Index: 47 L: 1 L1: 1
Index: 99974 L: 8 L1: 8
Index: 99982 L: 6 L1: 6
Index: 99983 L: 3 L1: 3
Index: 99984 L: 4 L1: 4
Index: 99987 L: 0 L1: 0
Identities are OK!
Show/Hide Solution
Write some python code to solve the following system of linear equations:
\[\begin{split}\begin{cases} 3x - 4y + 2z -5w = -9\\ -4x + 4y + 10z + w = 32\\ -x + 2y + -7z -w = -7\\ x + y + z + w = 1\end{cases}\end{split}\]Define then a function to compute the Euclidean norm of a ndarray in input.
Hint:
\[||X||_2 = \sqrt{{x_1}^2 + {x_2}^2 + ... + {x_n}^2}\]Compute then the Euclidean norm of the solution.
Implement a function that takes two N-dimensional vectors and computes the euclidean distance between them. Compute the distance between the solution of the system of equations above and the vector V = [7,120,11,33]. Check also that the distance between a vector and itself is zero. The Euclidean distance between two vectors P and Q can be computed as: \(\sqrt{\sum\limits_{i=1}^n (q_i -p_i)^2}\).
Show/Hide Solution
Implement the following functions working on numpy ndarrays:
The component form of a vector
comp(A,B)starting in point A and ending in point B is \(\overline{AB}\). Hint: if \(A=(a_1,...,a_n)\) and \(B=(b_1,...,b_n)\), \(\overline{AB} = (b_1 - a_1, ..., b_n - a_n)\).The direction cosines of a 3D vector
dirCos(A). If \(P=(x,y,z)\) the direction cosines are the cosines of the angles made by the vector with the three axes. They can be computed as:
\[\frac{x}{\sqrt(x^2+y^2+z^2}, \frac{y}{\sqrt(x^2+y^2+z^2}, \frac{z}{\sqrt(x^2+y^2+z^2}\]
The angle between two vectors
angle(A,B). Given two vectors \(A = (a_x,a_y,a_z)\) and \(B = (b_x,b_y,b_z)\), \(cos(\alpha) = \frac{A \cdot B}{||A||_2||B||_2}\) where the Euclidean norms are computed as in the previous example.
The volume of the pyramid described by three 3D vectors \(\overline{a},\overline{b},\overline{c}\):
the volume
pyrVol(a,b,c)can be computed as: \(\frac{1}{6} |det(M)|\), where \(M = \begin{bmatrix}\overline{a} \\ \overline{b} \\ \overline{c}\end{bmatrix}\), det is the determinant of the matrix anx || represents the absolute value.Define some numpy arrays starting from the following lists:
A = [10, 3, 4, 7, 12], B = [6, 7, 8, 1, 1] and test
comp(A,B)Va = [90,12,72] and test
dirCos(Va)VA = [70,9,12] and VB = [1,-10,30] and test
angle(VA,VB)a = [10, 20, 30], b = [ 4, 7, 21], c = [-5, 4, 12] and test
pyrVol(a,b,c)
Check your solutions here.
Show/Hide Solution
Implement the power iteration algorithm which is a method to obtain an approximation of the biggest (in absolute value) eigenvalue of a matrix A.
The algorithm starts from a random vector \(b_0\) and keeps computing \(b_{k+1} = \frac{A\cdot b_{k}}{min(A\cdot b_{k})}\). When the algorithm ends, the eigenvalue is actually the value: \(min(A\cdot b_{k})\)
The powerIteration function will have the maximum number of iterations and dThr as parameters powerIteration(A,maxIt, dThr). The computation will stop either when the maximum number of iterations maxIt is reached or when the Euclidean distance between b_{k-1} and b_k is lower than dThr.
Check the result against numpy eigenvalues obtained with np.linalg.eig() using various matrices.
Show/Hide Solution
Implement a function
movingAvg(A,n)where A is a numpy one dimensional array and n is the window size on which computing the average, that outputs the moving average over a numpy one dimensional array. Es. A = [1,2,3,4,5]movingAvg(A,2) = [1.5, 2.5, 3.5, 4.5], whilemovingAvg(A,3) = [2,3,4]without using for loops. Hint: use cumsum and clever slicing. Assess the smoothing effect of the moving average by creating a numpy array containing a sinusoidal wave with some additional noise (i.e. use np.sin and np.random.rand) and testing several values of the window size n.
Show/Hide Solution
Practical 10¶
In this practical we will will get acquainted with Biopython.
Biopython¶
From the Biopython tutorial: The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.
The goal of Biopython is to make it as easy as possible to use Python for bioinformatics by creating high-quality, reusable modules and classes. Biopython features include parsers for various Bioinformatics file formats (FASTA, FASTQ, BLAST, PDB, Clustalw, Genbank,…), access to online services (NCBI, Expasy,…), interfaces to common and not-so-common programs (Clustalw, DSSP, MSMS…), a standard sequence class, various clustering modules, a KD tree data structure etc. and even some documentation :-).
In this practical we will see some features of Biopython but please refer to biopython documentation to discover all its features, recipes etc.
These notes are largely based on the tutorial that is available here.
Installation of Biopython¶
To test if Biopython is installed in your system you can import the library with:
import Bio
if the execution gives:
Biopython needs to be installed.
In windows installing Biopython should be as easy as opening the command prompt as admininstrator (typing cmd and then right clicking on the link choosing run as admininstrator) and then pip3 install biopython. If that does not work, you should be able to install biopython with the following: python3.xx -m pip install biopython (where you should change python3.xx with the path to your python3.xx executable).
In linux sudo pip3 install biopython will install biopython for python3 up to python3.5. On python 3.6 and later the command is: python3.6 -m pip install biopython or, more in general, pythonX.X -m pip install biopython.
Detailed installation instructions can be found here.
General overview¶
Biopython provides the capability of parsing standard bioinformatics formats into python usable data structures. Some of the supported tools and formats are:
Blast output – both from standalone and WWW Blast
Clustalw
FASTA
GenBank
PubMed and Medline
ExPASy files, like Enzyme and Prosite
SCOP, including ‘dom’ and ‘lin’ files
UniGene
SwissProt
among the others. In particular it provides a sequence class to perform the most common operations on sequences, parsing of alignments, clustering etc. and it can quickly connect to the most popular databases to download data or parse information on the fly.
Sequence objects¶
Biopython has a specific object Seq to deal with biological sequences which is a lot more powerful than the str object of python when it comes to manage biological data. The object Seq has methods like translate() and reverse_complement() which are very handy.
As in the case of python’s str objects, the object Seq is immutable. The mutable version is MutableSeq.
All the information on Seq objects can be found here.
[1]:
from Bio.Seq import Seq
s = Seq("GATTACATAATA")
dna_seq = Seq("GATTATACGTAC")
print("S:", s)
print("dna_seq:", dna_seq)
my_prot = Seq("MGNAAAAKKGSEQE")
print("my_prot:", my_prot)
S: GATTACATAATA
dna_seq: GATTATACGTAC
my_prot: MGNAAAAKKGSEQE
Looping, slicing and concatenation¶
Note also that Seq objects behave like strings, and the consistency of the alphabet (i.e. if the sequence is DNA, RNA, aminoacid sequence…) is not checked anymore in the latest version. We can concatenate a sequence of DNA with that of aminoacids…
[2]:
from Bio.Seq import Seq
dna_seq = Seq("GATTATACGTAC")
my_prot = Seq("MGNAAAAKKGSEQE")
#Does it really make sense though?!?
print(dna_seq + my_prot)
GATTATACGTACMGNAAAAKKGSEQE
We can also loop through the elements and slice strings with the usual [S:E:step] operator (and as usual S is included, E is excluded). It is also possible to convert a Seq object into a string.
[3]:
from Bio.Seq import Seq
dna_seq = Seq("GATTATACGTACGGCTA")
for base in dna_seq:
print(base, end = " ")
print("")
sub_seq = dna_seq[4:10]
print(sub_seq)
#Let's reverse the string:
print("Reversed: ", dna_seq[::-1])
#from Seq to string:
dna_str = str(dna_seq)
print("As string:", dna_str)
print(type(dna_str))
G A T T A T A C G T A C G G C T A
ATACGT
Reversed: ATCGGCATGCATATTAG
As string: GATTATACGTACGGCTA
<class 'str'>
The object Seq provides several methods similar to the corresponding methods of strings:
Seq.count(s): counts the number of times s appears in the sequence;Seq.upper(): makes the sequence of the object Seq upper caseSeq.lower(): makes the sequence of the object Seq lower case
Example: Let’s compute the GC content of the sequence “GATTRWWACGTACGGCTASATTACSCCGGCTA”.
[4]:
from Bio.Seq import Seq
from Bio.SeqUtils import GC
dna_seq = Seq("GATTRWWACGTACGGCTASATTACSCCGGCTA")
gc = (dna_seq.count("G") + dna_seq.count("C"))/len(dna_seq)
print("GC % is {:.2f}".format(100*gc))
correct_gc = GC(dna_seq)
print("GC % is {:.2f}".format(correct_gc))
print("original:", dna_seq)
print("lower_case:",dna_seq.lower())
GC % is 40.62
GC % is 46.88
original: GATTRWWACGTACGGCTASATTACSCCGGCTA
lower_case: gattrwwacgtacggctasattacsccggcta
The difference in the results goes down to the fact that Biopython’s GC method takes into account ambiguous nucleotides like (S which stands for C or G ref iupac). This is a method provided in the SeqUtils module (more info on all the methods here).
Complement and reverse complement¶
A usual operation on DNA strings is the reverse complement. Biopython provides two specific methods to do that:
Seq.complement()to complement the sequenceSeq.reverse_complement()to reverse complement the sequence.
[5]:
from Bio.Seq import Seq
my_seq = Seq("GATCGATGGGCCTATATAGGATCGAAAATCGC")
print("Original sequence:\t{}".format(my_seq) )
comp = my_seq.complement()
print("")
print("Complement:\t\t{}".format(comp))
print("")
revcomp = my_seq.reverse_complement()
print("Reverse complement:\t{}".format(revcomp))
Original sequence: GATCGATGGGCCTATATAGGATCGAAAATCGC
Complement: CTAGCTACCCGGATATATCCTAGCTTTTAGCG
Reverse complement: GCGATTTTCGATCCTATATAGGCCCATCGATC
Transcription and translation¶
Remember that:
[taken from the Biopython tutorial].
Biopython has a method to transcribe a DNA sequence into a mRNA sequence (and one to go back):
Seq.transcribe()that transcribes a DNA sequence into mRNA (converting Ts in Us).Seq.back_transcribe()that back-transcribes a mRNA sequence into DNA (converting Us in Ts).
Note that transcribing a protein will result in a TranslationError.
Alike, a DNA or mRNA sequence can be translated into a protein with:
Seq.translate(table=N, to_stop=True/False, stop_symbol =symbol) that converts a DNA sequence or mRNA into the corresponding protein.
Optionally, the translate method accepts a parameter table to specify the NCBI translation table used (see below for codes). to_stop makes the translation stop at the first stop codon if True (in this case the stop codon is not translated!), stop_symbol to replace the asterisk with any other stop character (Es. “@”).
Stop codons will be represented by an asterisk.
Example: Let’s transcribe into mRNA and translate into protein the following coding sequence: ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG.
[6]:
from Bio.Seq import Seq
coding_dna = Seq("ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG")
print(coding_dna)
mrna = coding_dna.transcribe()
print(mrna)
print("")
print("... and back")
print(mrna.back_transcribe())
print("")
print("Translation to protein:")
prot = mrna.translate()
print(prot)
print("")
print("Up to first stop:")
print(mrna.translate(to_stop = True))
print("")
print("Mitocondrial translation: (TGA is W!)")
mit_prot = mrna.translate(table=2)
print(mit_prot)
#The following produces a translation error!
#print("RE-Translated protein: {}".format(prot.translate()))
ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG
AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG
... and back
ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG
Translation to protein:
MAIVMGR*KGAR*
Up to first stop:
MAIVMGR
Mitocondrial translation: (TGA is W!)
MAIVMGRWKGAR*
Translation tables can be accessed at runtime through:
[7]:
from Bio.Data import CodonTable
#equivalent to:
#standard_table = CodonTable.unambiguous_dna_by_id[1]
standard_table = CodonTable.unambiguous_dna_by_name["Standard"]
#equivalent to:
#standard_table = CodonTable.unambiguous_dna_by_id[2]
mito_table = CodonTable.unambiguous_dna_by_name["Vertebrate Mitochondrial"]
print(standard_table)
print("")
print(mito_table)
Table 1 Standard, SGC0
| T | C | A | G |
--+---------+---------+---------+---------+--
T | TTT F | TCT S | TAT Y | TGT C | T
T | TTC F | TCC S | TAC Y | TGC C | C
T | TTA L | TCA S | TAA Stop| TGA Stop| A
T | TTG L(s)| TCG S | TAG Stop| TGG W | G
--+---------+---------+---------+---------+--
C | CTT L | CCT P | CAT H | CGT R | T
C | CTC L | CCC P | CAC H | CGC R | C
C | CTA L | CCA P | CAA Q | CGA R | A
C | CTG L(s)| CCG P | CAG Q | CGG R | G
--+---------+---------+---------+---------+--
A | ATT I | ACT T | AAT N | AGT S | T
A | ATC I | ACC T | AAC N | AGC S | C
A | ATA I | ACA T | AAA K | AGA R | A
A | ATG M(s)| ACG T | AAG K | AGG R | G
--+---------+---------+---------+---------+--
G | GTT V | GCT A | GAT D | GGT G | T
G | GTC V | GCC A | GAC D | GGC G | C
G | GTA V | GCA A | GAA E | GGA G | A
G | GTG V | GCG A | GAG E | GGG G | G
--+---------+---------+---------+---------+--
Table 2 Vertebrate Mitochondrial, SGC1
| T | C | A | G |
--+---------+---------+---------+---------+--
T | TTT F | TCT S | TAT Y | TGT C | T
T | TTC F | TCC S | TAC Y | TGC C | C
T | TTA L | TCA S | TAA Stop| TGA W | A
T | TTG L | TCG S | TAG Stop| TGG W | G
--+---------+---------+---------+---------+--
C | CTT L | CCT P | CAT H | CGT R | T
C | CTC L | CCC P | CAC H | CGC R | C
C | CTA L | CCA P | CAA Q | CGA R | A
C | CTG L | CCG P | CAG Q | CGG R | G
--+---------+---------+---------+---------+--
A | ATT I(s)| ACT T | AAT N | AGT S | T
A | ATC I(s)| ACC T | AAC N | AGC S | C
A | ATA M(s)| ACA T | AAA K | AGA Stop| A
A | ATG M(s)| ACG T | AAG K | AGG Stop| G
--+---------+---------+---------+---------+--
G | GTT V | GCT A | GAT D | GGT G | T
G | GTC V | GCC A | GAC D | GGC G | C
G | GTA V | GCA A | GAA E | GGA G | A
G | GTG V(s)| GCG A | GAG E | GGG G | G
--+---------+---------+---------+---------+--
MutableSeq¶
Seq objects are immutable and therefore we cannot change their value. If we need to do so, we need to convert them into MutableSeq objects to avoid a runtime TypeError that will occur when we try to change a Seq. Seq to MutableSeq conversion can be done by:
Seq.tomutable()to convert a Seq to a MutableSeq.MutableSeq.toseq()to convert a MutableSeq to a Seq.
This will allow us to assign the value of characters within the MutableSeq with MutableSeq[ind] = newValue. Note also that methods like complement change the actual object if applied to a MutableSeq:
[8]:
from Bio.Seq import Seq
coding_dna = Seq("ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG")
#cannot do the following because Seq is immutable
#coding_dna[10:20] = "TATATATATA"
print("Coding DNA:")
print(coding_dna)
mut_dna = coding_dna.tomutable()
print("Mutable DNA:")
print(mut_dna)
mut_dna[10:20] = "TATATATATA"
print("Mutable DNA now:")
print(mut_dna)
print("")
print("Rev comp (Seq not changed!):")
coding_dna.reverse_complement()
print(coding_dna)
print("Rev comp (MutableSeq changed!):")
mut_dna.reverse_complement()
print(mut_dna)
Coding DNA:
ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG
Mutable DNA:
ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG
Mutable DNA now:
ATGGCCATTGTATATATATACTGAAAGGGTGCCCGATAG
Rev comp (Seq not changed!):
ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG
Rev comp (MutableSeq changed!):
CTATCGGGCACCCTTTCAGTATATATATACAATGGCCAT
Sequence annotation¶
Sequence records are annotations associated to sequences. In biopython there is a SeqRecord object to store this information. SeqRecord are part of the Bio.SeqRecord module which therefore needs to be imported before being used.
The SeqRecord class has the following attributes:
SeqRecord.seq: the sequence (the Seq object)SeqRecord.id: the identifier of the sequence, typically an accession numberSeqRecord.name: a “common” name or identifier sometimes identical to the accession numberSeqRecord.description: a human readable description of the sequenceSeqRecord.letter_annotations: a per letter annotation using a restricted dictionary (e.g. quality)SeqRecord.annotations: a dictionary of unstructured annotation (e.g. organism, publications,…)SeqRecord.features: a list of SeqFeature objects with more structured information (e.g. genes pos).SeqRecord.dbxrefs: a list of database cross references.
Information on SeqFeature objects can be found here.
Although you can manually create a SeqRecord, normally you will access SeqRecords populated by methods like SeqIO, here you can find how to manually create a SeqRecord.
Sequence I/O¶
The Bio.SeqIO module aims to provide a simple way to work with several different sequence file formats. Detailed information on the module can be found here.
Example:
Read a fasta file NC005816.fna containing the whole sequence for Yersinia pestis biovar Microtus str. 91001 plasmid pPCP1 and retrieve some information about the sequence.
[9]:
from Bio import SeqIO
record = SeqIO.read("file_samples/NC_005816.fna", "fasta")
print(record)
print("")
print("Sequence [first 30 bases]:")
print(record.seq[0:30])
print("")
print("The id:")
print(record.id)
print("")
print("The description:")
print(record.description)
print("")
print("The record is a: ", type(record))
ID: gi|45478711|ref|NC_005816.1|
Name: gi|45478711|ref|NC_005816.1|
Description: gi|45478711|ref|NC_005816.1| Yersinia pestis biovar Microtus str. 91001 plasmid pPCP1, complete sequence
Number of features: 0
Seq('TGTAACGAACGGTGCAATAGTGATCCACACCCAACGCCTGAAATCAGATCCAGG...CTG')
Sequence [first 30 bases]:
TGTAACGAACGGTGCAATAGTGATCCACAC
The id:
gi|45478711|ref|NC_005816.1|
The description:
gi|45478711|ref|NC_005816.1| Yersinia pestis biovar Microtus str. 91001 plasmid pPCP1, complete sequence
The record is a: <class 'Bio.SeqRecord.SeqRecord'>
WARNING: When dealing with very large FASTA or FASTQ files, the overhead of working with all these objects can make scripts too slow. In this case SimpleFastaParser and FastqGeneralIterator parsers might be better as they return just a tuple of strings for each record.
For example, to use SimpleFastaParser:
[10]:
from Bio.SeqIO.FastaIO import SimpleFastaParser
with open("file_samples/NC_005816.fna") as in_handle:
for title, seq in SimpleFastaParser(in_handle):
s = seq[0:50]+"\n"+seq[51:101]+"\n..."
print("Header:\n{}\nSequence:\n{}".format(title,s))
#Another example:
print("\n")
labels = ["1st","2nd","3rd"]
with open("file_samples/contigs82.fasta") as cont_handle:
for l in labels:
ID, seq = next(SimpleFastaParser(cont_handle))
print(l, "entry:")
print(ID, " has size ", len(seq))
print(seq[:50]+"...")
print("")
Header:
gi|45478711|ref|NC_005816.1| Yersinia pestis biovar Microtus str. 91001 plasmid pPCP1, complete sequence
Sequence:
TGTAACGAACGGTGCAATAGTGATCCACACCCAACGCCTGAAATCAGATC
AGGGGGTAATCTGCTCTCCTGATTCAGGAGAGTTTATGGTCACTTTTGAG
...
1st entry:
MDC020656.85 has size 2802
GAGGGGTTTAGTTCCTCATACTCGCAAAGCAAAGATACATAAATTTAGAA...
2nd entry:
MDC013284.379 has size 5173
TATCGTTTCCTCTGAGTAGAATATCGTTATAACAAGATTTTTTTTTTCCT...
3rd entry:
MDC018185.241 has size 23761
AAAACGAGGAAAATCCATCTTGATGAACAGGAGATGCGGAGGAAAAAAAT...
BioSeqIO.parse()¶
The method Bio.SeqIO.parse is used to parse some sequence data into a SeqRecord iterator. In particular, the basic syntax is:
SeqRecordIterator = Bio.SeqIO.parse(filename, file_format)
where filename is typically an open handle to a file and file_format is a lower case string describing the file format. Possible options include fasta, fastq-illumina, abi, ace, clustal… all the options are available here.
Example: Let’s read the first 10 entries in the .fasta file contigs82.fasta printing off the length of the sequence and the first 50 bases of each sequence followed by “…”.
[11]:
from Bio import SeqIO
cnt = 0
for seq_record in SeqIO.parse("file_samples/contigs82.fasta", "fasta"):
if(cnt == 10):
break
print("Seq {} has length {}".format(seq_record.id, len(seq_record)))
print(seq_record.seq[:50]+"...")
print("")
cnt += 1
Seq MDC020656.85 has length 2802
GAGGGGTTTAGTTCCTCATACTCGCAAAGCAAAGATACATAAATTTAGAA...
Seq MDC001115.177 has length 3118
TGAATGGTGAAAATTAGCCAGAAGATCTTCTCCACACATGACATATGCAT...
Seq MDC013284.379 has length 5173
TATCGTTTCCTCTGAGTAGAATATCGTTATAACAAGATTTTTTTTTTCCT...
Seq MDC018185.243 has length 22724
CCATTAGTGACCCCCAATGCGGATTAACCAAGCACGGTCAAGATAACCAA...
Seq MDC018185.241 has length 23761
AAAACGAGGAAAATCCATCTTGATGAACAGGAGATGCGGAGGAAAAAAAT...
Seq MDC004527.213 has length 3551
CTTGTATGTTGAAGCTTTGTGAGTGGAGCATATAGGTTGAGGTAGTGTTC...
Seq MDC003661.174 has length 3334
AGTAAGGTTGTAGAATTCAATTTCCACGGAACTCCAGCACAGCTTAGGCA...
Seq MDC012176.157 has length 2236
ATAGTCACTGACAGCCGGTGACAGTTCGACAACAATAAGTTCAGGATGTT...
Seq MDC001204.812 has length 5804
TAATGTCCGAAAAAGATGAAAATGTAGTTTGCATGAAGAAGGAGCTGTCC...
Seq MDC001204.810 has length 9798
ATGCTGCTGACATATTCCAATCGACTACACGTCACATCCGTTGCTATTAT...
Note that Bio.SeqIO.parse returns an iterator, therefore it is possible to manually fetch one SeqRecord after the other with the next(iterator) method.
Example: Let’s read the first 3 entries of the .fasta file contigs82.fasta printing off the length of the sequence and the first 50 bases of each sequence followed by “…”.
[12]:
from Bio import SeqIO
seqIterator = SeqIO.parse("file_samples/contigs82.fasta", "fasta")
labels = ["1st","2nd","3rd"]
for l in labels:
seqRec = next(seqIterator)
print(l, "entry:")
print(seqRec.id, " has size ", len(seqRec.seq))
print(seqRec.seq[:50]+"...")
print("")
1st entry:
MDC020656.85 has size 2802
GAGGGGTTTAGTTCCTCATACTCGCAAAGCAAAGATACATAAATTTAGAA...
2nd entry:
MDC001115.177 has size 3118
TGAATGGTGAAAATTAGCCAGAAGATCTTCTCCACACATGACATATGCAT...
3rd entry:
MDC013284.379 has size 5173
TATCGTTTCCTCTGAGTAGAATATCGTTATAACAAGATTTTTTTTTTCCT...
Sequences as dictionaries¶
The module Bio.SeqIO also has three different ways to allow random access to elements:
Bio.SeqIO.to_dict(file_handle/iterator): builds a dictionary of all the SeqRecords keeping them in memory and allowing modifications to the records. This potentially uses a lot of memory but is very fast;Bio.SeqIO.index(filename,file_type): builds a sort of read-only dictionary, parses the elements into SeqRecords on demand (i.e. it returns an iterator!). This method is slower, but more memory efficient;Bio.SeqIO.index_db(indexName.idx,filenames, file_format): builds a read-only dictionary, but stores ids and offsets on a SQLite3 database. It is slower but uses less memory.
The input of Bio.SeqIO.to_dict(file_handle/iterator) is a open file handler or the iterator to SeqRecords (like the output of Bio.SeqIO.parse()).
Example: Let’s read all the .fasta file contigs82.fasta in memory printing off the entry corresponding to contig “MDC019140.399”.
[13]:
from Bio import SeqIO
seqDict = SeqIO.to_dict(SeqIO.parse("file_samples/contigs82.fasta", "fasta"))
print(list(seqDict.keys())[0:5])
print("")
print("Number of sequences: ", len(seqDict))
print("")
mySeq = seqDict["MDC019140.399"]
print("Description:", mySeq.description)
print("")
print(mySeq)
['MDC020656.85', 'MDC001115.177', 'MDC013284.379', 'MDC018185.243', 'MDC018185.241']
Number of sequences: 82
Description: MDC019140.399
ID: MDC019140.399
Name: MDC019140.399
Description: MDC019140.399
Number of features: 0
Seq('GACGGGCGGGGAGGGTTTGGTTTTTTTTGGTTTTTAAAAAATTCAGGTTTNNAA...TTT')
The input of Bio.SeqIO.index(filename,file_type) is the file name to read sequences from and the file type (like fasta, genebank,…).
Example: Let’s read all the .fasta file contigs82.fasta in memory (as an index) printing off the entry corresponding to contig “MDC019140.399”.
[32]:
from Bio import SeqIO
seqDict = SeqIO.index("file_samples/contigs82.fasta", "fasta")
print("SeqDict is an iterator:")
print(seqDict.keys())
print("")
print(list(seqDict.keys()))
print("")
print("Number of sequences: ", len(seqDict))
print("")
mySeq = seqDict["MDC019140.399"]
print("Description:", mySeq.description)
print("")
print(mySeq)
SeqDict is an iterator:
KeysView(SeqIO.index('file_samples/contigs82.fasta', 'fasta', alphabet=None, key_function=None))
['MDC020656.85', 'MDC001115.177', 'MDC013284.379', 'MDC018185.243', 'MDC018185.241', 'MDC004527.213', 'MDC003661.174', 'MDC012176.157', 'MDC001204.812', 'MDC001204.810', 'MDC004389.256', 'MDC024257.15', 'MDC018297.229', 'MDC001802.364', 'MDC016621.241', 'MDC014057.243', 'MDC021015.302', 'MDC018185.242', 'MDC051782.000', 'MDC017187.314', 'MDC017187.311', 'MDC012865.410', 'MDC000427.83', 'MDC017187.319', 'MDC017187.318', 'MDC004081.319', 'MDC021913.275', 'MDC015147.205', 'MDC000038.355', 'MDC016032.95', 'MDC052568.000', 'MDC008119.414', 'MDC026201.7', 'MDC003995.601', 'MDC009211.561', 'MDC009211.567', 'MDC054294.001', 'MDC004364.265', 'MDC002360.219', 'MDC003408.117', 'MDC015155.172', 'MDC053310.000', 'MDC019140.398', 'MDC019140.399', 'MDC011390.337', 'MDC007154.375', 'MDC006346.716', 'MDC010588.505', 'MDC002519.240', 'MDC031322.5', 'MDC010588.502', 'MDC006346.711', 'MDC011551.182', 'MDC002717.156', 'MDC006346.719', 'MDC007838.447', 'MDC007018.186', 'MDC017873.233', 'MDC016296.138', 'MDC019067.226', 'MDC036568.1', 'MDC014019.318', 'MDC007995.528', 'MDC026961.60', 'MDC013443.168', 'MDC022800.298', 'MDC021558.159', 'MDC002479.192', 'MDC010751.301', 'MDC000219.190', 'MDC020963.161', 'MDC020963.162', 'MDC051637.000', 'MDC005174.220', 'MDC040033.7', 'MDC019674.147', 'MDC010450.877', 'MDC007097.457', 'MDC016278.70', 'MDC013723.254', 'MDC002838.179', 'MDC009771.217']
Number of sequences: 82
Description: MDC019140.399
ID: MDC019140.399
Name: MDC019140.399
Description: MDC019140.399
Number of features: 0
Seq('GACGGGCGGGGAGGGTTTGGTTTTTTTTGGTTTTTAAAAAATTCAGGTTTNNAA...TTT')
The input of Bio.SeqIO.index_db(indexName.idx,filenames, file_format) is the name of the (SQLite3) index to store (.idx), the file (or files) to index and the format of those files like fasta, genebank,…
Example: Let’s read all the .fasta file contigs82.fasta in memory (as an index) printing off the entry corresponding to contig “MDC019140.399”.
[15]:
from Bio import SeqIO
seqDict = SeqIO.index_db("file_samples/ctgs.idx","file_samples/contigs82.fasta", "fasta")
print("SeqDict is an iterator:")
print(seqDict.keys())
print("")
print(list(seqDict.keys()))
print("")
print("Number of sequences: ", len(seqDict))
print("")
mySeq = seqDict["MDC019140.399"]
print("Description:", mySeq.description)
print("")
print(mySeq)
SeqDict is an iterator:
KeysView(SeqIO.index_db('file_samples/ctgs.idx', filenames=['file_samples/contigs82.fasta'], format='fasta', key_function=None))
['MDC020656.85', 'MDC001115.177', 'MDC013284.379', 'MDC018185.243', 'MDC018185.241', 'MDC004527.213', 'MDC003661.174', 'MDC012176.157', 'MDC001204.812', 'MDC001204.810', 'MDC004389.256', 'MDC024257.15', 'MDC018297.229', 'MDC001802.364', 'MDC016621.241', 'MDC014057.243', 'MDC021015.302', 'MDC018185.242', 'MDC051782.000', 'MDC017187.314', 'MDC017187.311', 'MDC012865.410', 'MDC000427.83', 'MDC017187.319', 'MDC017187.318', 'MDC004081.319', 'MDC021913.275', 'MDC015147.205', 'MDC000038.355', 'MDC016032.95', 'MDC052568.000', 'MDC008119.414', 'MDC026201.7', 'MDC003995.601', 'MDC009211.561', 'MDC009211.567', 'MDC054294.001', 'MDC004364.265', 'MDC002360.219', 'MDC003408.117', 'MDC015155.172', 'MDC053310.000', 'MDC019140.398', 'MDC019140.399', 'MDC011390.337', 'MDC007154.375', 'MDC006346.716', 'MDC010588.505', 'MDC002519.240', 'MDC031322.5', 'MDC010588.502', 'MDC006346.711', 'MDC011551.182', 'MDC002717.156', 'MDC006346.719', 'MDC007838.447', 'MDC007018.186', 'MDC017873.233', 'MDC016296.138', 'MDC019067.226', 'MDC036568.1', 'MDC014019.318', 'MDC007995.528', 'MDC026961.60', 'MDC013443.168', 'MDC022800.298', 'MDC021558.159', 'MDC002479.192', 'MDC010751.301', 'MDC000219.190', 'MDC020963.161', 'MDC020963.162', 'MDC051637.000', 'MDC005174.220', 'MDC040033.7', 'MDC019674.147', 'MDC010450.877', 'MDC007097.457', 'MDC016278.70', 'MDC013723.254', 'MDC002838.179', 'MDC009771.217']
Number of sequences: 82
Description: MDC019140.399
ID: MDC019140.399
Name: MDC019140.399
Description: MDC019140.399
Number of features: 0
Seq('GACGGGCGGGGAGGGTTTGGTTTTTTTTGGTTTTTAAAAAATTCAGGTTTNNAA...TTT')
Note that a file ctgs.idx has been created to store ids and offsets.
Writing sequence files¶
SeqRecords can be written out to files by using
N = Bio.SeqIO.write(records,out_filename, file_format)
where records is a list of the SeqRecords to write, out_filename is the string with the filename to write and file_format is the format of the file to write. N is the number of sequences written.
WARNING: If you write a file that is already present, SeqIO.write will just rewrite it without telling you.
Example: Write three protein records to file then read the file and print the three sequences.
[16]:
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
rec1 = SeqRecord(Seq("MMYQQGCFAGGTVLRLAKDLAENNRGARVLVVCSEITAVTFRGPSETHLDSMVGQALFGD" \
+"GAGAVIVGSDPDLSVERPLYELVWTGATLLPDSEGAIDGHLREVGLTFHLLKDVPGLISK" \
+"NIEKSLKEAFTPLGISDWNSTFWIAHPGGPAILDQVEAKLGLKEEKMRATREVLSEYGNM" \
+"SSAC"),
id="gi|14150838|gb|AAK54648.1|AF376133_1",
description="chalcone synthase [Cucumis sativus]")
rec2 = SeqRecord(Seq("YPDYYFRITNREHKAELKEKFQRMCDKSMIKKRYMYLTEEILKENPSMCEYMAPSLDARQ" \
+"DMVVVEIPKLGKEAAVKAIKEWGQ"),
id="gi|13919613|gb|AAK33142.1|",
description="chalcone synthase [Fragaria vesca subsp. bracteata]")
rec3 = SeqRecord(Seq("MVTVEEFRRAQCAEGPATVMAIGTATPSNCVDQSTYPDYYFRITNSEHKVELKEKFKRMC" \
+"EKSMIKKRYMHLTEEILKENPNICAYMAPSLDARQDIVVVEVPKLGKEAAQKAIKEWGQP" \
+"KSKITHLVFCTTSGVDMPGCDYQLTKLLGLRPSVKRFMMYQQGCFAGGTVLRMAKDLAEN" \
+"NKGARVLVVCSEITAVTFRGPNDTHLDSLVGQALFGDGAAAVIIGSDPIPEVERPLFELV" \
+"SAAQTLLPDSEGAIDGHLREVGLTFHLLKDVPGLISKNIEKSLVEAFQPLGISDWNSLFW" \
+"IAHPGGPAILDQVELKLGLKQEKLKATRKVLSNYGNMSSACVLFILDEMRKASAKEGLGT" \
+"TGEGLEWGVLFGFGPGLTVETVVLHSVAT"),
id="gi|13925890|gb|AAK49457.1|",
description="chalcone synthase [Nicotiana tabacum]")
my_records = [rec1, rec2, rec3]
print(rec1)
seqWritten = SeqIO.write(my_records, "file_samples/my_proteins.fa", "fasta")
print(seqWritten, "sequences written!")
print("")
print("Reading file")
seqIT = SeqIO.parse("file_samples/my_proteins.fa", "fasta")
cnt = 1
for s in seqIT:
print("Sequence ", cnt, "(", s.id, ")")
print(s.seq)
print("")
cnt += 1
ID: gi|14150838|gb|AAK54648.1|AF376133_1
Name: <unknown name>
Description: chalcone synthase [Cucumis sativus]
Number of features: 0
Seq('MMYQQGCFAGGTVLRLAKDLAENNRGARVLVVCSEITAVTFRGPSETHLDSMVG...SAC')
3 sequences written!
Reading file
Sequence 1 ( gi|14150838|gb|AAK54648.1|AF376133_1 )
MMYQQGCFAGGTVLRLAKDLAENNRGARVLVVCSEITAVTFRGPSETHLDSMVGQALFGDGAGAVIVGSDPDLSVERPLYELVWTGATLLPDSEGAIDGHLREVGLTFHLLKDVPGLISKNIEKSLKEAFTPLGISDWNSTFWIAHPGGPAILDQVEAKLGLKEEKMRATREVLSEYGNMSSAC
Sequence 2 ( gi|13919613|gb|AAK33142.1| )
YPDYYFRITNREHKAELKEKFQRMCDKSMIKKRYMYLTEEILKENPSMCEYMAPSLDARQDMVVVEIPKLGKEAAVKAIKEWGQ
Sequence 3 ( gi|13925890|gb|AAK49457.1| )
MVTVEEFRRAQCAEGPATVMAIGTATPSNCVDQSTYPDYYFRITNSEHKVELKEKFKRMCEKSMIKKRYMHLTEEILKENPNICAYMAPSLDARQDIVVVEVPKLGKEAAQKAIKEWGQPKSKITHLVFCTTSGVDMPGCDYQLTKLLGLRPSVKRFMMYQQGCFAGGTVLRMAKDLAENNKGARVLVVCSEITAVTFRGPNDTHLDSLVGQALFGDGAAAVIIGSDPIPEVERPLFELVSAAQTLLPDSEGAIDGHLREVGLTFHLLKDVPGLISKNIEKSLVEAFQPLGISDWNSLFWIAHPGGPAILDQVELKLGLKQEKLKATRKVLSNYGNMSSACVLFILDEMRKASAKEGLGTTGEGLEWGVLFGFGPGLTVETVVLHSVAT
Multiple sequence alignment¶
Multiple Sequence Alignments, as the name says, are a collection of multiple sequences which have been aligned together – usually with the insertion of gap characters, and addition of leading or trailing gaps – such that all the sequence strings have the same length.
Such an alignment can be regarded as a matrix of letters, in biopython each row is a SeqRecord object. These alignments are stored in an object MultipleSeqAlignment
Parsing multiple sequence alignments¶
The function Bio.AlignIO.parse() returns an iterator of MultipleSeqAlignment objects. In the frequent case that we have to deal with a single alignment we will have to use the Bio.AlignIO.read() function.
The basic syntax of the two functions:
Bio.AlignIO.parse(file_handle, alignment_format)Bio.AlignIO.read(file_handle, alignment_format)where file_handle is the handler to the opened file, while the alignment_format is a lower case string with the alignment format (e.g. fasta, clustal, stockholm, mauve, phylip,…). Check here for all possible formats.
When more than one multiple alignment has to be read we will have to use the parse function, for single entries, we would use the function read.
Example: Load and visualize the seed alignment of the Piwi (PF02171) family stored in the pfam (stockholm) format. Information on the format can be found here. The file is available here: PF02171_seed.sth.
[17]:
from Bio import AlignIO
alignments = AlignIO.read("file_samples/PF02171_seed.sth", "stockholm")
print(alignments)
Alignment with 16 rows and 395 columns
YLFFILDK-NSPEP-YGSIKRVCNTMLGVPSQCAISKHILQS--...QDV AGO1_SCHPO/500-799
FILCILPERKTSDI-YGPWKKICLTEEGIHTQCICPIKI-----...FTK AGO6_ARATH/541-851
FILCVLPDKKNSDL-YGPWKKKNLTEFGIVTQCMAPTRQPND--...FMK AGO4_ARATH/577-885
CIIVVLQS-KNSDI-YMTVKEQSDIVHGIMSQCVLMKNVSRP--...HVK TAG76_CAEEL/660-966
LIVVVLPG--KTPI-YAEVKRVGDTVLGIATQCVQAKNAIRT--...HLV O16720_CAEEL/566-867
TFVFIITD-DSITT-LHQRYKMIEKDTKMIVQDMKLSKALSV--...LWN O62275_CAEEL/594-924
DILVGIAR-EKKPD-VHDILKYFEESIGLQTIQLCQQTVDKMMG...NYK YQ53_CAEEL/650-977
TIVFGIIA-EKRPD-MHDILKYFEEKLGQQTIQISSETADKFMR...NYK NRDE3_CAEEL/673-1001
MLVVMLAD-DNKTR-YDSLKKYLCVECPIPNQCVNLRTLAGKSK...SLH Q17567_CAEEL/397-708
IVMVVMRS-PNEEK-YSCIKKRTCVDRPVPSQVVTLKVIAPRQQ...SIN AUB_DROME/555-852
LILCLVPN-DNAER-YSSIKKRGYVDRAVPTQVVTLKTTKNRSL...NLH PIWI_DROME/538-829
IVVCLLSS-NRKDK-YDAIKKYLCTDCPTPSQCVVARTLGKQQT...SIH PIWL1_HUMAN/555-847
GIMLVLPE-YNTPL-YYKLKSYLINS--IPSQFMRYDILSNRNL...VNR PIWI_ARCFU/110-406
CFALIIGKEKYKDNDYYEILKKQLFDLKIISQNILWENWRKDDK...NWK Y1321_METJA/426-699
LVIVFLEEYPKVDP-YKSFLLYDFVKRELLKKMIPSQVILNRTL...GIE O67434_AQUAE/419-694
LLLAILPD-NNGSL-YGDLKRICETELGLISQCCLTKHVFKI--...YLE AGO10_ARATH/625-946
The code above prints a summary of the information, but each Bio.Align.MultipleSeqAlignment is composed of several alignment records (SeqRecord) that we can access with all their information looping through the object. Each SeqRecord contains several information like the ID, Name, Description, Number of features, start, end and sequence.
Example:
Load the seed alignment of the Piwi (PF02171) family stored in the pfam (stockholm) format PF02171_seed.sth. For each record print the description, start and the end point, the sequence and the external dbxrefs (if any).
[18]:
from Bio import AlignIO
alignments = AlignIO.read("file_samples/PF02171_seed.sth", "stockholm")
for align in alignments:
start = align.annotations["start"]
end = align.annotations["end"]
seq = align.seq
desc = align.description
dbref = ",".join([x for x in align.dbxrefs])
print("{} S:{} E:{}".format(desc, start, end))
if(len(dbref) > 0):
print(dbref)
print("{}".format(seq))
print("")
AGO1_SCHPO/500-799 S:500 E:799
YLFFILDK-NSPEP-YGSIKRVCNTMLGVPSQCAISKHILQS---------KPQYCANLGMKINVKVGGIN-CSLIPKSNP----LGNVPTL---------ILGGDVYHPGVGA----------TGVSIASIVASVD-LNGCKYTAVSRSQPRHQEVIEG-MKD------------IVVYLLQGFRAMTKQ-QPQRIIYFRDGTSEGQFLSVINDELSQIKEACH-------SLSPKYN--PKILVCTTQKRHHARFFIKNKSDG----------------------DRNGNPLPGTII---EKHVTHPYQYDFYLISHPSLQGVSVPVHYTVLHDEIQMPPDQF-QTL------CYNLCYVYARAT----SAVSLVPPVYYAHLVSNLARYQDV
AGO6_ARATH/541-851 S:541 E:851
FILCILPERKTSDI-YGPWKKICLTEEGIHTQCICPIKI------------SDQYLTNVLLKINSKLGGIN-SLLGIEYSYNIPLINKIPTL---------ILGMDVSHGPPGR---------ADVPSVAAVVGSKCWPLISRYRAAVRTQSPRLEMIDSLFQPIENTE--KGDNGIMNELFVEFYRTSRARKPKQIIIFRDGVSESQFEQVLKIEVDQIIKAYQ-------RLGESDV--PKFTVIVAQKNHHTKLFQAKGPE---------------------------NVPAGTVV---DTKIVHPTNYDFYMCAHAGKIGTSRPAHYHVLLDEIGFSPDDL-QNL------IHSLSYVNQRST----TATSIVAPVRYAHLAAAQVAQFTK
AGO4_ARATH/577-885 S:577 E:885
FILCVLPDKKNSDL-YGPWKKKNLTEFGIVTQCMAPTRQPND-----------QYLTNLLLKINAKLGGLN-SMLSVERTPAFTVISKVPTI---------ILGMDVSHGSPGQ---------SDVPSIAAVVSSREWPLISKYRASVRTQPSKAEMIESLVKKNGT-----EDDGIIKELLVDFYTSSNKRKPEHIIIFRDGVSESQFNQVLNIELDQIIEACK-------LLDANWN--PKFLLLVAQKNHHTKFFQPTSPE---------------------------NVPPGTII---DNKICHPKNNDFYLCAHAGMIGTTRPTHYHVLYDEIGFSADEL-QEL------VHSLSYVYQRST----SAISVVAPICYAHLAAAQLGTFMK
TAG76_CAEEL/660-966 S:660 E:966
CIIVVLQS-KNSDI-YMTVKEQSDIVHGIMSQCVLMKNVSRP---------TPATCANIVLKLNMKMGGIN--SRIVADKITNKYLVDQPTM---------VVGIDVTHPTQAEM-------RMNMPSVAAIVANVD-LLPQSYGANVKVQKKCRESVVY-LLD------------AIRERIITFYRHTKQ-KPARIIVYRDGVSEGQFSEVLREEIQSIRTACL-------AIAEDFR--PPITYIVVQKRHHARIFCKYQNDM---------------------VGKAKNVPPGTTV---DTGIVSPEGFDFYLCSHYGVQGTSRPARYHVLLDECKFTADEI-QSI------TYGMCHTYGRCT----RSVSIPTPVYYADLVATRARCHVK
O16720_CAEEL/566-867 S:566 E:867
LIVVVLPG--KTPI-YAEVKRVGDTVLGIATQCVQAKNAIRT---------TPQTLSNLCLKMNVKLGGVN-SILLPNVRPR---IFNEPVI---------FLGCDITHPAAGD---------TRKPSIAAVVGSMD-AHPSRYAATVRVQQHRQEIITD-LTY------------MVRELLVQFYRNTRF-KPARIVVYRDGVSEGQLFNVLQYELRAIREACV-------MLESGYQ--PGITFIAVQKRHHTRLFAADKADQ---------------------VGKAFNIPPGTTV---DVGITHPTEFDFFLCSHAGIQGTSRPSHYHVLWDDNDLTADEL-QQL------TYQMCHTYVRCT----RSVSIPAPAYYAHLVAFRARYHLV
O62275_CAEEL/594-924 S:594 E:924
TFVFIITD-DSITT-LHQRYKMIEKDTKMIVQDMKLSKALSV--IN---AGKRLTLENVINKTNVKLGGSN--YVFVDAKKQL-----DSHL---------IIGVGISAPPAGTKYAM-ENKGVLNPNVIGYAYNA--QHNQEFSGDFVLNSASQDTLAP-IED------------IVMHSLNEYQKFHDGGLPRRVIVYRTGTSEGNHGSIMAYEIPLARAAMR-------DFSPDIQ----LVYIVVSKDHSFRFFKPDLASLASRPQATSSTASRHSAMPAAPKAWDLNIAPGILV---DSIVTNPACKQFFLNSHITLQGTAKTPLYTVLADDAKVSMTAL-EDI------TYKLCHLHQIVG----LPTSLPTPLYVANEYAKRGRNLWN
YQ53_CAEEL/650-977 S:650 E:977
DILVGIAR-EKKPD-VHDILKYFEESIGLQTIQLCQQTVDKMMGG----QGGRQTIDNVMRKFNLKCGGTNFFVEIPNAVRGKAVCSNNETLRKKLLEHVQFIGFEISHGASRTLFDRSRSQMDGEPSVVGVSYSLT---NSTQLGGFTYLQTQKEYKLQKLDE------------FFPKCVRSYKEHSKT-LPTRIVIYRVGAGEGNFNRVKE-EVEEMRRTFD-------KIQPGYR--PHLVVIIAQRASHARVFPSCISGN---------------------RATDQNIPSGTCV---ENVLTSYGYDEFILSSQTPLIGTVRPCKYTILVNDAKWSKNEL-MHL------TYFRAFGHQVSY----QPPSVPDVLYAAENLAKRGRNNYK
NRDE3_CAEEL/673-1001 S:673 E:1001
TIVFGIIA-EKRPD-MHDILKYFEEKLGQQTIQISSETADKFMRD----HGGKQTIDNVIRKLNPKCGGTNFLIDVPESVGHRVVCNNSAEMRAKLYAKTQFIGFEMSHTGARTRFDIQKVMFDGDPTVVGVAYSL--KHSAQLGGFSYFQESRLHKLTN-LQE------------KMQICLNAYEQSSSY-LPETVVVYRVGSGEGDYPQIVN-EVNEMKLAAR-------KKKHGYN--PKFLVICTQRNSHIRVFPEHINERG--------------------KSMEQNVKSGTCV---DVPGASHGYEEFILCCQTPLIGTVKPTKYTIIVNDCRWSKNEI-MNV------TYHLAFAHQVSY----APPAIPNVSYAAQNLAKRGHNNYK
Q17567_CAEEL/397-708 S:397 E:708
MLVVMLAD-DNKTR-YDSLKKYLCVECPIPNQCVNLRTLAGKSKDGGENKNLGSIVLKIVLQMICKTGGA---LWKVNIPL-------KSTM---------IVGYDLYHDSTLK-----------GKTVGACVSTTS-NDFTQFYSQTRPHENPTQLGNN-LTH------------FVRKSLKQYYDNNDKTLPSRLILYRDGAGDGQIPYIKNTEVKLVRDACDAVTDKAAELSNKVQEKIKLAFIIVTKRVNMRILKQGSSS-----------------------KSAINPQPGTVV---DTTVTRPERMDFYLVPQFVNQGTVTPVSYNIIHDDTGLGPDKH-QQL------AFKLCHLYYNWQ----GTVRVPAPCQYAHKLAFLTAQSLH
AUB_DROME/555-852 S:555 E:852
IVMVVMRS-PNEEK-YSCIKKRTCVDRPVPSQVVTLKVIAPRQQKP---TGLMSIATKVVIQMNAKLMGA---PWQVVIPL-------HGLM---------TVGFDVCHSPKNK-----------NKSYGAFVATMDQKESFRYFSTVNEHIKGQELSEQ-MSV------------NMACALRSYQEQHRS-LPERILFFRDGVGDGQLYQVVNSEVNTLKDRLDEI---YKSAGKQEG--CRMTFIIVSKRINSRYFT-----------------------------GHRNPVPGTVV---DDVITLPERYDFFLVSQAVRIGTVSPTSYNVISDNMGLNADKL-QML------SYKMTHMYYNYS----GTIRVPAVCHYAHKLAFLVAESIN
PIWI_DROME/538-829 S:538 E:829
LILCLVPN-DNAER-YSSIKKRGYVDRAVPTQVVTLKTTKNRSL--------MSIATKIAIQLNCKLGYT---PWMIELPL-------SGLM---------TIGFDIAKSTRDR-----------KRAYGALIASMDLQQNSTYFSTV-TECSAFDVLANTLWP------------MIAKALRQYQHEHRK-LPSRIVFYRDGVSSGSLKQLFEFEVKDIIEKLKTE---YARVQLSP---PQLAYIVVTRSMNTRFFLN-----------------------------GQNPPPGTIV---DDVITLPERYDFYLVSQQVRQGTVSPTSYNVLYSSMGLSPEKM-QKL------TYKMCHLYYNWS----GTTRVPAVCQYAKKLATLVGTNLH
PIWL1_HUMAN/555-847 S:555 E:847
IVVCLLSS-NRKDK-YDAIKKYLCTDCPTPSQCVVARTLGKQQT-------VMAIATKIALQMNCKMGGE---LWRVDIPL-------KLVM---------IVGIDCYHDMTAG-----------RRSIAGFVASIN-EGMTRWFSRCIFQDRGQELVDG-LKV------------CLQAALRAW-NSCNEYMPSRIIVYRDGVGDGQLKTLVNYEVPQFLDCLK-------SIGRGYN--PRLTVIVVKKRVNTRFFAQSGGR-------------------------LQNPLPGTVI---DVEVTRPEWYDFFIVSQAVRSGSVSPTHYNVIYDNSGLKPDHI-QRL------TYKLCHIYYNWP----GVIRVPAPCQYAHKLAFLVGQSIH
PIWI_ARCFU/110-406 S:110 E:406
PDB; 2W42 B; 110-406;,PDB; 1YTU B; 110-406;,PDB; 2BGG B; 110-406;,PDB; 1W9H A; 110-406;,PDB; 2BGG A; 110-406;,PDB; 1YTU A; 110-406;,PDB; 2W42 A; 110-406;
GIMLVLPE-YNTPL-YYKLKSYLINS--IPSQFMRYDILSNRNL--------TFYVDNLLVQFVSKLGGK---PWILNVDPEK--------------------GSDIIIGTGAT--------RIDNVNLFCFAMVFK-KDGTMLWNEISPIVTSSEYLTY-LKS------------TIKKVVYGFKKSNPDWDVEKLTLHVSG----KRPKMKDGETKILKETVE-------ELKKQEMVSRDVKYAILHLNETHPFWVMGDPN------------------------NRFHPYEGTKVKLSSKRYLLTLLQPYLKRNGLEMVTPIKPLSVEIVSDN--WTSEEYYHNVHEILDEIYYLSKMNWRGF----RSRNLPVTVNYPKLVAGIIANVNR
Y1321_METJA/426-699 S:426 E:699
CFALIIGKEKYKDNDYYEILKKQLFDLKIISQNILWENWRKDDK--------GYMTNNLLIQIMGKLGIK---YFILDSKTPYDY----------------IMGLDTGLGIFGN------------HRVGGCTVVYDSEGKIRRIQPIETPAPGERLHLP----------------YVIEYLEN--KANIDMENKNILFLRDG-------FIQNSERNDLKEISK-------ELN------SNIEVISIRKNNKYKVFTSDYRI------------------------GSVFGNDGIFLPHKTPFGSNPVKLSTWLRFNCGNEEGLK---IN----------ESI-MQL------LYDLTKMNYSALYGEGRYLRIPAPIHYADKFVKALGKNWK
O67434_AQUAE/419-694 S:419 E:694
PDB; 1YVU A; 419-694;,PDB; 2F8S A; 419-694;,PDB; 2F8T A; 419-694;,PDB; 2F8S B; 419-694;,PDB; 2NUB A; 419-694;,PDB; 2F8T B; 419-694;
LVIVFLEEYPKVDP-YKSFLLYDFVKRELLKKMIPSQVILNRTLKN---ENLKFVLLNVAEQVLAKTGNIP--YKLKEIEGKVDA----------------FVGIDISRITRDG----------KTVNAVAFTKIFNSKGELVRYYLTSYPAFGEKLTEK----------------AIGDVFSLLEKLGF-KKGSKIVVHRDG-------RLYRDEVAAFK-----------KYGELYG--YSLELLEIIKRNNPRFFSNEKFI------------------------------KGYFYKLSEDSVILATYNQVY-------EGTHQPIKVRKVYGE--LPVEVL-CSQ------ILSLTLMNYSSF----QPIKLPATVHYSDKITKLMLRGIE
AGO10_ARATH/625-946 S:625 E:946
LLLAILPD-NNGSL-YGDLKRICETELGLISQCCLTKHVFKI---------SKQYLANVSLKINVKMGGRN-TVLVDAISCRIPLVSDIPTI---------IFGADVTHPENGE---------ESSPSIAAVVASQDWPEVTKYAGLVCAQAHRQELIQDLYKTWQDPVRGTVSGGMIRDLLISFRKATGQ-KPLRIIFYRDGVSEGQFYQVLLYELDAIRKACA-------SLEPNYQ--PPVTFIVVQKRHHTRLFANNHRDKN-------------------STDRSGNILPGTVV---DTKICHPTEFDFYLCSHAGIQGTSRPAHYHVLWDENNFTADGI-QSL------TNNLCYTYARCT----RSVSIVPPAYYAHLAAFRARFYLE
Writing multiple sequence alignments¶
Biopython provides a function Bio.AlignIO.write() to write alignments to file. The basic syntax is:
N = Bio.AlignIO.write(alignments,outfile,file_format)
where alignments are a MultipleSeqAlignment object with the alignments to write to the output file with name outfile that has format file_format (a low case string with the file format). N is the number of entries written to the file.
Example: Let’s create some multiple sequence alignments and store them in phylip format. The output file is present here my_malign.phy. Finally, read and print the content of the file.
[33]:
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Align import MultipleSeqAlignment
from Bio import AlignIO
align1 = MultipleSeqAlignment([
SeqRecord(Seq("ACTGCTAGCTAG"), id="Alpha"),
SeqRecord(Seq("ACT-CTAGCTAG"), id="Beta"),
SeqRecord(Seq("ACTGCTAGDTAG"), id="Gamma"),
])
align2 = MultipleSeqAlignment([
SeqRecord(Seq("GTCAGC-AG"), id="Delta"),
SeqRecord(Seq("GACAGCTAG"), id="Epsilon"),
SeqRecord(Seq("GTCAGCTAG"), id="Zeta"),
])
align3 = MultipleSeqAlignment([
SeqRecord(Seq("ACTAGTACAGCTG"), id="Eta"),
SeqRecord(Seq("ACTAGTACAGCT-"), id="Theta"),
SeqRecord(Seq("-CTACTACAGGTG"), id="Iota"),
])
my_alignments = [align1, align2, align3]
N = AlignIO.write(my_alignments, "file_samples/my_malign.phy", "phylip")
print("{} entries written to the file".format(N))
print("")
alignments = AlignIO.parse("file_samples/my_malign.phy", "phylip")
for align in alignments:
print(align)
3 entries written to the file
Alignment with 3 rows and 12 columns
ACTGCTAGCTAG Alpha
ACT-CTAGCTAG Beta
ACTGCTAGDTAG Gamma
Alignment with 3 rows and 9 columns
GTCAGC-AG Delta
GACAGCTAG Epsilon
GTCAGCTAG Zeta
Alignment with 3 rows and 13 columns
ACTAGTACAGCTG Eta
ACTAGTACAGCT- Theta
-CTACTACAGGTG Iota
The content of the file is reported in the following screenshot:
Note that it is also possible to convert one format into the other (provided that all information needed for the second format is available) by using the function:
Bio.AlignIO.convert(input_file, input_file_format, output_file, output_file_format)
basically by passing the input file name and format and output file name and format.
Ex:
Bio.AlignIO.convert("PF05371_seed.sth", "stockholm", "PF05371_seed.aln", "clustal")
converts a stockholm file into a clustal.
Manipulating alignments¶
It is possible to slice alignments using the [] operator applied on a SeqRecord. In particular:
SeqRecord[i,j]returns the jth character of alignment i as a string;SeqRecord[:,j]returns all the jth characters of the multiple alignment as a string;SeqRecord[:,i:j]returns a MultipleSeqAlignment with the sub-alignments going for i to j (excluded)SeqRecord[a:b,i:j]similar to 3. but for alignments going from a to b (excluded) only
One can also combine different portions of the alignment by slicing and adding the slices together with
SeqRecord[:,i:j] + SeqRecord[:,t:k]
Example: Load the seed alignment of the Piwi (PF02171) family stored in the pfam (stockholm) format PF02171_seed.sth. For each record print the description, the first 20 bases and the final 20 bases of the sequence.
[20]:
from Bio import AlignIO
alignments = AlignIO.read("file_samples/PF02171_seed.sth", "stockholm")
edited_aligns = alignments[:,0:20] + alignments[:,-20:]
for align in edited_aligns:
print(align.description, "\t", align.seq)
AGO1_SCHPO/500-799 YLFFILDK-NSPEP-YGSIKLVPPVYYAHLVSNLARYQDV
AGO6_ARATH/541-851 FILCILPERKTSDI-YGPWKIVAPVRYAHLAAAQVAQFTK
AGO4_ARATH/577-885 FILCVLPDKKNSDL-YGPWKVVAPICYAHLAAAQLGTFMK
TAG76_CAEEL/660-966 CIIVVLQS-KNSDI-YMTVKIPTPVYYADLVATRARCHVK
O16720_CAEEL/566-867 LIVVVLPG--KTPI-YAEVKIPAPAYYAHLVAFRARYHLV
O62275_CAEEL/594-924 TFVFIITD-DSITT-LHQRYLPTPLYVANEYAKRGRNLWN
YQ53_CAEEL/650-977 DILVGIAR-EKKPD-VHDILVPDVLYAAENLAKRGRNNYK
NRDE3_CAEEL/673-1001 TIVFGIIA-EKRPD-MHDILIPNVSYAAQNLAKRGHNNYK
Q17567_CAEEL/397-708 MLVVMLAD-DNKTR-YDSLKVPAPCQYAHKLAFLTAQSLH
AUB_DROME/555-852 IVMVVMRS-PNEEK-YSCIKVPAVCHYAHKLAFLVAESIN
PIWI_DROME/538-829 LILCLVPN-DNAER-YSSIKVPAVCQYAKKLATLVGTNLH
PIWL1_HUMAN/555-847 IVVCLLSS-NRKDK-YDAIKVPAPCQYAHKLAFLVGQSIH
PIWI_ARCFU/110-406 GIMLVLPE-YNTPL-YYKLKLPVTVNYPKLVAGIIANVNR
Y1321_METJA/426-699 CFALIIGKEKYKDNDYYEILIPAPIHYADKFVKALGKNWK
O67434_AQUAE/419-694 LVIVFLEEYPKVDP-YKSFLLPATVHYSDKITKLMLRGIE
AGO10_ARATH/625-946 LLLAILPD-NNGSL-YGDLKIVPPAYYAHLAAFRARFYLE
Example: Convert the seed alignment of the Piwi (PF02171) family stored in the pfam (stockholm) format PF02171_seed.sth into phylip format. Print some stats on the data.
[21]:
from Bio import AlignIO
alignments = AlignIO.read("file_samples/PF02171_seed.sth", "stockholm")
out = AlignIO.convert("file_samples/PF02171_seed.sth",
"stockholm",
"file_samples/PF02171_seed.aln",
"clustal")
print("N. of seq: {}\nLen of seq: {}".format(
len(alignments),
len(alignments[0])))
print("{} multiple alignments converted to phylip".format(out))
N. of seq: 16
Len of seq: 395
1 multiple alignments converted to phylip
Biopython’s pairwise2 alignment¶
Biopython supports running some classic multiple alignment tools like clustal, MUSCLE but these require to be installed in your system first.
Biopython has its own module to make pairwise alignment. It provides two algorithms: Smith-Waterman for local alignment and Needleman-Wunsch for global alignment. These methods are implemented in two Biopython functions of the Bio.pairwise2 module:
pairwise2.align.globalxx() and pairwise2.align.localxx().
The basic syntax of the two methods is the same:
aligns = pairwise2.align.globalxx(seq1,seq2)
aligns = pairwise2.align.localxx(seq1,seq2)
where seq1 and seq2 are two str objects. These methods return a list of alignments (at least one) that have the same optimal score. Each alignment is represented as tuples with the following 5 elements in order:
The alignment of the first sequence;
The alignment of the second sequence;
The alignment score;
The start of the alignment (for global alignments this is always 0);
The end of the alignment (for global alignments this is always the length of the alignment).
The xx in globalxx or localxx encodes the penalties and scores for gaps and matches (and mismatches) of the alignment. The first letter is the score for a match the second letter is the penalty for a gap:
Match parameters can be:
x: means that a match scores 1 a mismatch 0;m: the match and mismatch score are passed as additional params after the sequence (es.aligns = pairwise2.align.globalmx(seq1,seq2, 1, -1)to set 1 as match score and -1 as mismatch penalty.
Gap parameters can be:
x: gap penalty is 0;s: same gap open and gap extend penalties for the 2 sequences (passed as additional params after seqs).d: different gap open and gap extend penalties for the 2 seqs (additional params after the seqs).
Example:
Let’s perform the alignment of the two sequences “ACCGTTATATAGGCCA” and “ACGTACTAGTATAGGCCA”
[22]:
from Bio import pairwise2
from Bio import SeqIO
alignments = pairwise2.align.globalxx("ACCGTTATATAGGCCA",
"ACGTACTAGTATAGGCCA")
for i in range(len(alignments)):
print(alignments[i])
print("")
print("Looping through aligns")
for align in alignments:
print(align[0])
print(align[1])
print("Score: {}, Start: {}, End: {}".format(align[2],
align[3],
align[4]))
print("")
alignments = pairwise2.align.globalms("ACCGTTATATAGGCCA",
"ACGTACTAGTATAGGCCA",
1,-1,-0.5,-0.2)
print("")
print("Match: 1, Mismatch: -1, Gap open: -0.5, Gap extend: -0.2")
for align in alignments:
print(align[0])
print(align[1])
print("Score: {}, Start: {}, End: {}".format(align[2],
align[3],
align[4]))
print("")
Alignment(seqA='ACCGT--TA-TATAGGCCA', seqB='A-CGTACTAGTATAGGCCA', score=15.0, start=0, end=19)
Alignment(seqA='ACCGT--TA-TATAGGCCA', seqB='AC-GTACTAGTATAGGCCA', score=15.0, start=0, end=19)
Looping through aligns
ACCGT--TA-TATAGGCCA
A-CGTACTAGTATAGGCCA
Score: 15.0, Start: 0, End: 19
ACCGT--TA-TATAGGCCA
AC-GTACTAGTATAGGCCA
Score: 15.0, Start: 0, End: 19
Match: 1, Mismatch: -1, Gap open: -0.5, Gap extend: -0.2
ACCGT--TA-TATAGGCCA
A-CGTACTAGTATAGGCCA
Score: 13.3, Start: 0, End: 19
ACCGT--TA-TATAGGCCA
AC-GTACTAGTATAGGCCA
Score: 13.3, Start: 0, End: 19
It is also possible to specify a substitution matrix like the BLOSUM to improve the alignment of protein sequences. Substitution matrices like the blosum62 are present in Biopython and before using it we need to import it with from Bio.SubsMat.MatrixInfo import blosum62.
You can find all the substitution matrices available here.
Example: Align the alpha and beta subunits of the human hemoglobin protein stored in hem_alpha.fasta and hem_beta.fasta with globalxx and with a blosum62 substitution matrix and gap open -10 and gap extension -0.5.
[31]:
from Bio import pairwise2
from Bio import SeqIO
from Bio.pairwise2 import format_alignment
from Bio.SubsMat.MatrixInfo import blosum62
seq1 = SeqIO.read("file_samples/hem_alpha.fasta", "fasta")
seq2 = SeqIO.read("file_samples/hem_beta.fasta", "fasta")
alignments = pairwise2.align.globalxx(seq1.seq,seq2.seq)
print(len(alignments), "optimal alignments")
align = alignments[0]
print(align[0])
print(align[1])
print("Score: {}, Start: {}, End: {}".format(align[2],align[3],align[4]))
print("")
alignments = pairwise2.align.globalds(seq1.seq, seq2.seq, blosum62, -10, -0.5)
print(len(alignments), "optimal alignments")
align = alignments[0]
print(align[0])
print(align[1])
print("Score: {}, Start: {}, End: {}".format(align[2],align[3],align[4]))
80 optimal alignments
MV-LSPADKTNV---K-A--A-WGKVGAHAG---EY-GA-EALE-RMFLSF----PTTK-TY--FPHFDL-SH-G--S---AQVK-G------HGKKV--A--DA-LTNAVAHVD-DMPNALS----A-LSD-LHAH--KLR-VDPV-NFKL-LSHCL---LVT--LAAHLPA----EFTPA-VH-ASLDKFLAS---VSTV------LTS--KYR-
MVHL-----T--PEEKSAVTALWGKV-----NVDE-VG-GEAL-GR--L--LVVYP---WT-QRF--F--ES-FGDLSTPDA-V-MGNPKVKAHGKKVLGAFSD-GL----AH--LD--N-L-KGTFATLS-EL--HCDKL-HVDP-ENF--RL---LGNVLV-CVL-AH---HFGKEFTP-PV-QA------A-YQKV--VAGVANAL--AHKY-H
Score: 72.0, Start: 0, End: 217
2 optimal alignments
MV-LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-DLS-----HGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR
MVHLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH
Score: 292.5, Start: 0, End: 149
Exercises¶
Write a python function that reads a genebank file given in input and prints off the following information:
Identifier, name and description;
The first 100 characters of the sequence;
Number of external references (dbxrefs) and ids of the external refs.
The name of the organism (hint: check the annotations dictionary at the key “organism”)
Retrieve and print all (if any) associated publications (hint: annotation dictionary, key:”references”)
Retrieve and print all the locations of “CDS” features of the sequence (hint: check the features )
Hint: go back and check the details of the SeqRecord object.
Test the program downloading some files from genebank like this or this
Show/Hide Solution
Write a python program that loads a pfam file (stockholm format .sth) and reports for each record of the alignment:
the id of the entry
the start and end points
the number of gaps and the % of gaps on the total length of the alignment
the number of external database references (dbxrefs), and the first 3 external references comma separated (hint: use join).
Print these information to the screen. Finally, write this information in a tab separated file (.tsv) having the following format: #ID\tstart\tend\tnum_gaps\tpercentage_gaps\tdbxrefs.
You can test the program using the TP53 family file PF00870_seed.sth.
Show/Hide Solution
Given the sequence of the Spike protein in an isolate of the Sars-Cov-2 in human and in pangolin in fasta, read and store the sequences from the fasta files and align them with
pairwise2.align.globalxxand check the percentage of identity between the two. Repeat the same analysis with the complete genome of the isolate from Wuhan wuhan and from bat. Do not forget to translate them or you might use too much memory for your machine!!! Note that these are fasta files of the genomic sequence, therefore you should use biopython to translate them into proteins. To solve this exercise implement the following functions:
readSingleFasta(filename): reads the fasta and returns a SeqRecord;alignSequences(s1,s2): gets the two sequence records and aligns them returning the alignment;getPercentageIdentity(s1,s2):gets two aligned sequences and returns the percentage of identity between the two;printAlignDetails(alignments, num_entries = 1, ends_size = 10): that gets the alignments and prints the firstnum_entriesplotting the alignment of the initial/finalends_sizebases, the percentage of identity between the two sequences, the alignment score, the start and end point.
Show/Hide Solution
Given a multiple sequence alignment stored in “phylip” format, write three methods: readAlignment that reads the input file and prints the number of sequences present, printAlignments(alignments) that prints the alignments to the screen and computeConsensus(alignments,minFrequency) that creates the consensus of all the alignments. MinFrequency is the minimum frequency (that has to be > 0.5) to keep a base in the consensus. “?” is considered as the consensus if frequency < minFrequency for all possible bases.
Ex. if alignments are:
ATC-G
AAC-G
AAG-G
ATCGT
computeConsensus(alignments,0.6) is:
A?C-G
Test the script with the file alpha-globin.phy.
Show/Hide Solution
Load the contigs present in the filtered_contigs.fasta file and translate each DNA sequence into the corresponding protein. Count the number of stop codons (i.e. *) for each sequence and print them to the user (e.g. MDC020656.85 51). Finally, write the translated proteins in another .fasta file (e.g. filtered_contigs_translated.fasta).
Show/Hide Solution
Write the following three functions:
countMatches(s1,s2)that takes two sequences aligned with pairwise2 local or global of the same length and returns how many elements match;countMismatches(s1,s2)that takes two sequences aligned with pairwise2 local or global of the same length and returns how many elements are different (i.e. they are not gaps but the character is different);countGapOpens(s1,s2)that takes two sequences aligned with pairwise2 local or global of the same length and returns the number of gap opened in the alignment;countGapExtensions(s1,s2)that takes two sequences aligned with pairwise2 local or global of the same length and returns the number of gap extensions in the alignmentgetScore(s1,s2, matchScore, mismatchPenalty, gapOpenPenalty, gapExtensionPenalty)and returns the score of the alignment of s1 and s2 (aligned with pairwise2 as before) given the scores and penalties in input.
Finally, align the sequences of the Interleukin-12 chain A (let’s call it s1) IL12A.fasta and B IL12B.fasta (let’s call it s2) with the following parameters:
pairwise2.align.globalxx(s1,s2)
pairwise2.align.globalms(s1,s2,,1,-0.1,-1,-0.1)
pairwise2.align.globalxs(s1, s2,1,-0.5,-5,-0.5)
pairwise2.align.globalxd(s1, s2,1,-0.5,-5,-0.5,-5,-5)
and check the score as computed from pairwise2 and from your functions (use the first of all the alignments to check). Note the effect of changing parameters.
Show/Hide Solution
Practical 11¶
In this practical we will will see some other functionalities of Biopython.
Biopython¶
From the Biopython tutorial: The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology. The goal of Biopython is to make it as easy as possible to use Python for bioinformatics by creating high-quality, reusable modules and classes. Biopython features include parsers for various Bioinformatics file formats (BLAST, Clustalw, FASTA, Genbank,…), access to online services (NCBI, Expasy,…), interfaces to common and not-so-common programs (Clustalw, DSSP, MSMS…), a standard sequence class, various clustering modules, a KD tree data structure etc. and even some documentation :-).
In this practical we will see some features of Biopython but refer to biopython documentation to discover all its features, recipes etc.
These notes are largely based on the tutorial that is available here.
BLAST¶
Blast (Basic logical alignment search tool) is a well known tool to find similarities between biological sequences. It compares DNA or protein sequences and calculates the statistical significance of the matches found.
The typical interaction with BLAST sees the user submit some sequences to the tool to get an alignment and then the hits are parsed to obtain information on the matches. Both these steps can be performed from within Biopython. Although it is possible to interact directly with a local installation of BLAST, in this practical we will work with the tool made available by NCBI (available here). Note that this might require a lot more computational time due to the delays of the network and traffic limitations.
The function qblast¶
The online version of blast can be accessed through the Bio.Blast.NCBIWWW.qblast() function.
It’s basic syntax is the following (first import from Bio.Blast import NCBIWWW):
result_handle = Bio.Blast.NCBIWWW.qblast(blast_program, database, query_str)
where blast_program is the program to perform the alignment. The options are blastn, blastp, blastx, tblast or tblastx. database is the database to search against and query_str is a string containing the query to search against the database. The query can be a sequence or a fasta file entry or an identifier like a GI number (NCIBI’s sequence identification number). Among the others, some optional parameters are the output format (format_type that by default is “XML” which is
the most stable output format but results can be stored also as text with “Text”). It is also possible to specify an expectation value cut-off to filter out alignments expect (the e-value threshold, default value is 10.0).
Some databases to search against are reported below:
The query string can be obtained in different ways, for example it is possible to load sequences from a fasta file with:
from Bio.Blast import NCBIWWW
fasta_string = open("myfile.fasta").read()
result_handle = NCBIWWW.qblast("blastn", "nt", fasta_string)
or we can give a SeqRecord:
from Bio.Blast import NCBIWWW
from Bio import SeqIO
record = SeqIO.read("myfile.fasta", format="fasta")
result_handle = NCBIWWW.qblast("blastn", "nt", record.seq)
It is also possible to specify some optional parameters in the entrez_query for example we can limit the search to specific organisms with: entrez_query='"Malus Domestica" [Organism]'.
Example: Let’s align the first 100 bases of the first entry of the file contigs82.fasta to the Malus Domestica genome.
NOTE: this can take several minutes.
[1]:
from Bio.Blast import NCBIWWW
from Bio import SeqIO
records = SeqIO.parse("file_samples/contigs82.fasta", format="fasta")
rec = next(records)
seq = rec.seq[0:100]
print("Aligning {} [{}] to Malus Dom.".format(rec.id,
seq[0:10]+"..."+seq[90:101]))
result_handle = NCBIWWW.qblast("blastn", "nt",
seq,
entrez_query='"Malus Domestica" [Organism]'
)
Aligning MDC020656.85 [GAGGGGTTTA...TTGGCAGCAA] to Malus Dom.
Note that the previous code does not output anything, it just returns a result_handle. We need to parse it to get some results.
Parsing qblast output¶
Once the qblast call returns, it gives the results in a handle object result_handle that we can parse or we can write to disk to avoid having to rerun the query other times. If we expect to get one alignment only, we can use the method read otherwise (if we have multiple query sequences) we should use the method parse:
blast_record = NCBIXML.read(result_handle)
or
blast_records = NCBIXML.parse(result_handle)
Note that to use these methods we first need to import the NCBIXML module with from Bio.Blast import NCBIXML.
These methods are analogous to what seen in the case of SeqIO and AlignIO. In the case of multiple entries we can loop through them with:
blast_records = NCBIXML.parse(result_handle)
for record in blast_records:
#do something with it...
or we can retrieve one record at a time with record = next(blast_records).
Saving results to file¶
To save the results present in the result_handle we can simply write them to file. In case we have only one entry we can read it and write it to file:
out_f = open("my_blast_result.xml", "w")
out_f.write(result_handle.read())
out_f.close
result_handle.close()
If we have more than one entry we need to loop through all the entries and save them in the file:
out_f = open("my_blast_result.xml", "w")
for entry in result_handle.parse():
out_f.write(entry)
out_f.close
result_handle.close()
Example:
Let’s BLAST the galactosidase alpha (gi number: 2717) against the human database on NCBI and save the results to file. (Note that it can take several seconds/minutes to run!).
[2]:
from Bio.Blast import NCBIWWW
result_handle = NCBIWWW.qblast("blastn", "nt", "2717")
with open("file_samples/blast_res.xml","w") as out_f:
out_f.write(result_handle.read())
result_handle.close()
Open a blast .XML file¶
A BLAST output file can be read by opening the file to get the handler and then parse it with the method parse seen above:
from Bio.Blast import NCBIXML
result_handle = open("my_blast.xml")
blast_records = NCBIXML.parse(result_handle)
This will end up in a handle to the blast results.
The BLAST record class¶
The Bio.Blast.Record.Blast class holds the results of the alignment. In particular it is composed of the following three information:
query: the identifier of the query (a string).
Descriptions : a list of Description objects. Each
Descriptionholds the following information:Description.title: a string with the title of the hit;Description.score: a float with the score of the alignment;Description.num_alignments: an int with the number of alignments with the same subject;Description.e: a float with the e-value of the alignment.
Alignments : a list of Alignment objects. Each
Alignmentholds the following information:Alignment.title: a string with the title of the hit (identical toDescription.title);Alignment.length: an int with the length of the alignment;Alignment.hsps: a list of HSP objects (High Scoring Pair). EachHSPhas the following info:HSP.score: the BLAST score of the hitHSP.bits: the bits score of the hit (x: on average 2^x pairs to find such a good hit by chance)HSP.expect: the evalue of the hitHSP.num_alignments: the number of alignments for the same subjectHSP.identities: the number of identities between query and subjectHSP.positives: the number of identical bases/aminos or having similar chemical propertiesHSP.gaps: the number of gaps between query and subjectHSP.strand: a tuple with (query,subject) strandsHSP.frame: a tuple with the frame shiftsHSP.query/HSP.sbjct: query/subject sequenceHSP.query_start/HSP.sbjct_start:query/subject start pointHSP.match: the match sequence (basically “|” for matches and spaces for mismatches)HSP.align_length: the alignment length.
More information on the BLAST record can be found here.
Example:
Let’s blast the serum albumin sequence (gi number 23307792) on the human genome and report all the information reported by BLAST. (warning: it might take a while to run!)
[3]:
from Bio.Blast import NCBIWWW
from Bio.Blast import NCBIXML
result_handle = NCBIWWW.qblast("blastn", "nt", "23307792",
entrez_query='"Homo Sapiens" [Organism]'
)
for res in NCBIXML.parse(result_handle):
for d in res.descriptions:
print("TITLE:{}\nSCORE:{}\nN.ALIGN:{}\nE-VAL:{}".format(
d.title,d.score, d.num_alignments,d.e))
for a in res.alignments:
print("Align Title:{}\nAlign Len: {}".format(a.title, a.length))
for h in a.hsps:
s = h.score
b = h.bits
e = h.expect
n = h.num_alignments
i = h.identities
p = h.positives
g = h.gaps
st = h.strand
f = h.frame
q = h.query
sb = h.sbjct
qs = h.query_start
ss = h.sbjct_start
qe = h.query_end
se = h.sbjct_end
m = h.match
al = h.align_length
print("Score: {} Bits: {} E-val: {}".format(s,b,e))
print("N.aligns:{} Ident:{} Pos.:{} Gaps:{} Align len:{}".format(
n,i,p,g,al))
print("Strand: {} Frame: {}".format(st,f))
print("Query:", q, " start:", qs, " end:", qe)
print("Match:",m)
print("Subjc:",sb, " start:", ss, " end:", se)
result_handle.close()
TITLE:gi|23307792|gb|AF542069.1| Homo sapiens serum albumin (HSA) mRNA, complete cds
SCORE:4352.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|1519245814|ref|NM_000477.7| Homo sapiens albumin (ALB), mRNA
SCORE:4305.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|28591|emb|V00495.1| H.sapiens mRNA for serum albumin
SCORE:4253.0
N.ALIGN:2
E-VAL:0.0
TITLE:gi|7770116|gb|AF119840.1|AF119840 Homo sapiens PRO0903 mRNA, complete cds
SCORE:4062.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|25058738|gb|BC039235.1| Homo sapiens albumin, mRNA (cDNA clone IMAGE:4768004), containing frame-shift errors
SCORE:4056.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|23243417|gb|BC036003.1| Homo sapiens albumin, mRNA (cDNA clone MGC:32850 IMAGE:4724105), complete cds
SCORE:4052.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|158258946|dbj|AK292755.1| Homo sapiens cDNA FLJ78413 complete cds, highly similar to Homo sapiens albumin, mRNA
SCORE:4036.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|28589|emb|V00494.1| Human messenger RNA for serum albumin (HSA)
SCORE:4033.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|21706455|gb|BC034023.1| Homo sapiens albumin, mRNA (cDNA clone MGC:22784 IMAGE:4734617), complete cds
SCORE:4029.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|51476389|emb|CR749331.1| Homo sapiens mRNA; cDNA DKFZp779N1935 (from clone DKFZp779N1935)
SCORE:4027.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|21706470|gb|BC034026.1| Homo sapiens cDNA clone IMAGE:4734794, containing frame-shift errors
SCORE:4010.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|194391079|dbj|AK298437.1| Homo sapiens cDNA FLJ54371 complete cds, highly similar to Serum albumin precursor
SCORE:3994.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|408407943|gb|AF130077.2| Homo sapiens clone FLB9714 PRO2619 mRNA, complete cds
SCORE:3937.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|62113340|gb|AY960291.1| Homo sapiens serum albumin mRNA, complete cds
SCORE:3907.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|49176516|gb|AY550967.1| Homo sapiens cell growth inhibiting protein 42 mRNA, complete cds
SCORE:3848.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|115607206|gb|DQ986150.1| Homo sapiens serum albumin mRNA, complete cds
SCORE:3733.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|164692402|dbj|AK314794.1| Homo sapiens cDNA, FLJ95666, highly similar to Homo sapiens albumin (ALB), mRNA
SCORE:3676.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|52001696|gb|AY728024.1| Homo sapiens serum albumin precursor, mRNA, complete cds
SCORE:3630.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|6013426|gb|AF190168.1|AF190168 Homo sapiens serum albumin precursor, mRNA, complete cds
SCORE:3615.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|332356379|gb|HQ537426.1| Homo sapiens albumin mRNA, partial cds
SCORE:3471.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|194391111|dbj|AK298461.1| Homo sapiens cDNA FLJ50830 complete cds, highly similar to Serum albumin precursor
SCORE:3084.0
N.ALIGN:2
E-VAL:0.0
TITLE:gi|763428|gb|U22961.1|HSU22961 Human mRNA clone with similarity to L-glycerol-3-phosphate:NAD oxidoreductase and albumin gene sequences
SCORE:2748.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|27692692|gb|BC041789.1| Homo sapiens albumin, mRNA (cDNA clone MGC:32888 IMAGE:4766983), complete cds
SCORE:2620.0
N.ALIGN:2
E-VAL:0.0
TITLE:gi|164694201|dbj|AK308044.1| Homo sapiens cDNA, FLJ97992
SCORE:2536.0
N.ALIGN:2
E-VAL:0.0
TITLE:gi|7770216|gb|AF119890.1|AF119890 Homo sapiens PRO2675 mRNA, complete cds
SCORE:2488.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|47118014|gb|AY544124.1| Homo sapiens growth-inhibiting protein 20 mRNA, complete cds
SCORE:2453.0
N.ALIGN:2
E-VAL:0.0
TITLE:gi|7959790|gb|AF116645.1|AF116645 Homo sapiens PRO1708 mRNA, complete cds
SCORE:2003.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|6650825|gb|AF118090.1|AF118090 Homo sapiens PRO2044 mRNA, complete cds
SCORE:1983.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|23241674|gb|BC035969.1| Homo sapiens albumin, mRNA (cDNA clone MGC:32581 IMAGE:4714468), complete cds
SCORE:1767.0
N.ALIGN:2
E-VAL:0.0
TITLE:gi|15679995|gb|BC014308.1|BC014308 Homo sapiens, clone IMAGE:3934797, mRNA, partial cds
SCORE:1571.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|37181745|gb|AY358313.1| Homo sapiens DNA66677 ALB (UNQ696) mRNA, partial cds
SCORE:1018.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|6642751|gb|AF113014.1|AF113014 Homo sapiens clone FLB3512 mRNA sequence
SCORE:618.0
N.ALIGN:1
E-VAL:1.28079e-155
TITLE:gi|219842221|ref|NG_009291.1| Homo sapiens albumin (ALB), RefSeqGene on chromosome 4
SCORE:581.0
N.ALIGN:15
E-VAL:2.64223e-145
TITLE:gi|152112963|gb|EF649953.1| Homo sapiens albumin (ALB) gene, complete cds
SCORE:581.0
N.ALIGN:15
E-VAL:2.64223e-145
TITLE:gi|19387810|gb|AC108157.3| Homo sapiens BAC clone RP11-580P21 from 4, complete sequence
SCORE:581.0
N.ALIGN:16
E-VAL:2.64223e-145
TITLE:gi|178343|gb|M12523.1|HUMALBGC Human serum albumin (ALB) gene, complete cds
SCORE:581.0
N.ALIGN:15
E-VAL:2.64223e-145
TITLE:gi|1036032687|gb|AH007061.2| Homo sapiens chromosome 4 serum albumin (ALB) gene, partial cds; and serum albumin-alphafetoprotein intergenic spacer, partial sequence
SCORE:579.0
N.ALIGN:1
E-VAL:9.2223e-145
TITLE:gi|408407822|gb|AF116616.2| Homo sapiens PRO0998 mRNA, complete cds
SCORE:577.0
N.ALIGN:1
E-VAL:3.2189e-144
TITLE:gi|338858118|gb|AH002596.2|SEG_HUMALB Homo sapiens albumin (ALB) gene, partial cds
SCORE:573.0
N.ALIGN:2
E-VAL:3.92142e-143
TITLE:gi|1122817323|gb|DQ145726.2| Homo sapiens ARNT-interacting protein 2 (AINP2) mRNA, complete cds
SCORE:404.0
N.ALIGN:1
E-VAL:1.56446e-97
TITLE:gi|32428|emb|X51365.1| Homo sapiens mRNA for albumin (clone pHA19)
SCORE:232.0
N.ALIGN:1
E-VAL:7.60363e-51
TITLE:gi|1338686512|ref|NG_056261.1| Homo sapiens albumin (ALB) 5' regulatory region (LOC111832671) on chromosome 4
SCORE:221.0
N.ALIGN:1
E-VAL:1.37477e-47
TITLE:gi|7959920|gb|AF116711.1|AF116711 Homo sapiens PRO2646 mRNA, complete cds
SCORE:216.0
N.ALIGN:1
E-VAL:1.67481e-46
TITLE:gi|35452|emb|X51363.1| Homo sapiens mRNA for albumin (clones pHA1, pHA12)
SCORE:208.0
N.ALIGN:1
E-VAL:2.48564e-44
TITLE:gi|35453|emb|X51364.1| Homo sapiens mRNA for albumin (clones pHA8, pHA25)
SCORE:198.0
N.ALIGN:1
E-VAL:1.28759e-41
TITLE:gi|7959874|gb|AF116688.1|AF116688 Homo sapiens PRO2133 mRNA, complete cds
SCORE:123.0
N.ALIGN:1
E-VAL:5.47982e-21
TITLE:gi|546032|gb|S69192.1| albumin {exon 8} [human, analbuminemia patient ROMA, Genomic Mutant, 60 nt]
SCORE:111.0
N.ALIGN:1
E-VAL:9.90775e-18
TITLE:gi|547231|gb|S70799.1| serum albumin=alloalbumin {Bazzano variant} [human, Genomic Mutant, 57 nt]
SCORE:102.0
N.ALIGN:1
E-VAL:1.47044e-15
TITLE:gi|1370486375|ref|XM_017007844.2| PREDICTED: Homo sapiens afamin (AFM), transcript variant X3, mRNA
SCORE:60.0
N.ALIGN:1
E-VAL:0.000369554
TITLE:gi|1370486374|ref|XM_017007843.2| PREDICTED: Homo sapiens afamin (AFM), transcript variant X2, mRNA
SCORE:60.0
N.ALIGN:1
E-VAL:0.000369554
Align Title:gi|23307792|gb|AF542069.1| Homo sapiens serum albumin (HSA) mRNA, complete cds
Align Len: 2176
Score: 4352.0 Bits: 3925.42 E-val: 0.0
N.aligns:None Ident:2176 Pos.:2176 Gaps:0 Align len:2176
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAATAGAGTGGTACAGCACTGTTATTTTTCAAAGATGTGTTGCTATCCTGAAAATTCTGTAGGTTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTTCGGTAGAGGATTTCTAGTTTCTGTGGGC start: 1 end: 2176
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAATAGAGTGGTACAGCACTGTTATTTTTCAAAGATGTGTTGCTATCCTGAAAATTCTGTAGGTTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTTCGGTAGAGGATTTCTAGTTTCTGTGGGC start: 1 end: 2176
Align Title:gi|1519245814|ref|NM_000477.7| Homo sapiens albumin (ALB), mRNA
Align Len: 2285
Score: 4305.0 Bits: 3883.04 E-val: 0.0
N.aligns:None Ident:2168 Pos.:2168 Gaps:1 Align len:2177
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAATAGAGTGGTACAGCACTGTTATTTTTCAAAGATGTGTTGCTATCCTGAAAATTCTGTAGGTTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTTCGGTAGAGGATTTCTAGTTTC-TGTGGGC start: 1 end: 2176
Match: ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAATAGAGTGGTACAGCACTGTTATTTTTCAAAGATGTGTTGCTATCCTGAAAATTCTGTAGGTTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTTCGGTAGAGGATTTCTAGTTTCTTGTGGGC start: 9 end: 2185
Align Title:gi|28591|emb|V00495.1| H.sapiens mRNA for serum albumin
Align Len: 2251
Score: 4253.0 Bits: 3836.15 E-val: 0.0
N.aligns:None Ident:2159 Pos.:2159 Gaps:4 Align len:2177
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATC-ACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAATAGAGTGGTACAGCACTGTTATTTTTCAAAGATGTGTTGCTATCCTGAAAATTCTGTAGGTTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTTCGGTAGAGGATTTCTAGTTTCTGTGGGC start: 1 end: 2176
Match: ||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| |||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TCTCTTCTGTCAACCCCACGC--CTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTAGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAATGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTGGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAGGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAACTGTGAGCTTTTTAAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACAAAATGCTGCACAGAGTCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCTACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTG-TTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAATAGAGTGGTACAGCACTGTTATTTTTCAAAGATGTGTTGCTATCCTGAAAATTCTGTAGGTTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTTCGGTAGAGGATTTCTAGTTTCTGTGGGC start: 45 end: 2218
Score: 103.0 Bits: 94.1598 E-val: 1.47044e-15
N.aligns:None Ident:56 Pos.:56 Gaps:2 Align len:58
Strand: ('Plus', 'Minus') Frame: (1, -1)
Query: TGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCT start: 489 end: 546
Match: ||||| |||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TGACA--GAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCT start: 56 end: 1
Align Title:gi|7770116|gb|AF119840.1|AF119840 Homo sapiens PRO0903 mRNA, complete cds
Align Len: 2720
Score: 4062.0 Bits: 3663.93 E-val: 0.0
N.aligns:None Ident:2043 Pos.:2043 Gaps:0 Align len:2051
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA start: 1 end: 2051
Match: ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA start: 649 end: 2699
Align Title:gi|25058738|gb|BC039235.1| Homo sapiens albumin, mRNA (cDNA clone IMAGE:4768004), containing frame-shift errors
Align Len: 2085
Score: 4056.0 Bits: 3658.52 E-val: 0.0
N.aligns:None Ident:2042 Pos.:2042 Gaps:1 Align len:2050
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGT-AAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCT start: 1 end: 2049
Match: ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCT start: 7 end: 2056
Align Title:gi|23243417|gb|BC036003.1| Homo sapiens albumin, mRNA (cDNA clone MGC:32850 IMAGE:4724105), complete cds
Align Len: 2087
Score: 4052.0 Bits: 3654.91 E-val: 0.0
N.aligns:None Ident:2041 Pos.:2041 Gaps:0 Align len:2051
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA start: 1 end: 2051
Match: ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGTCCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCGAA start: 9 end: 2059
Align Title:gi|158258946|dbj|AK292755.1| Homo sapiens cDNA FLJ78413 complete cds, highly similar to Homo sapiens albumin, mRNA
Align Len: 2054
Score: 4036.0 Bits: 3640.48 E-val: 0.0
N.aligns:None Ident:2037 Pos.:2037 Gaps:3 Align len:2049
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCT start: 1 end: 2049
Match: ||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAA---AATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTTGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCT start: 9 end: 2054
Align Title:gi|28589|emb|V00494.1| Human messenger RNA for serum albumin (HSA)
Align Len: 2055
Score: 4033.0 Bits: 3637.78 E-val: 0.0
N.aligns:None Ident:2036 Pos.:2036 Gaps:0 Align len:2049
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCT start: 1 end: 2049
Match: ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGGGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCTTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTGTTAGTTCGTTACACCAAGAAAGTACCCGAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCTGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCT start: 7 end: 2055
Align Title:gi|21706455|gb|BC034023.1| Homo sapiens albumin, mRNA (cDNA clone MGC:22784 IMAGE:4734617), complete cds
Align Len: 2068
Score: 4029.0 Bits: 3634.17 E-val: 0.0
N.aligns:None Ident:2028 Pos.:2028 Gaps:0 Align len:2037
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAA start: 1 end: 2037
Match: ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACGTTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAACAAAAAA start: 9 end: 2045
Align Title:gi|51476389|emb|CR749331.1| Homo sapiens mRNA; cDNA DKFZp779N1935 (from clone DKFZp779N1935)
Align Len: 2075
Score: 4027.0 Bits: 3632.37 E-val: 0.0
N.aligns:None Ident:2036 Pos.:2036 Gaps:0 Align len:2051
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA start: 1 end: 2051
Match: ||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCATACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCCTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGCGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAGAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAGCTGCACTTGTTGAGCTTGTGAAACACAGGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATTACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCCAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA start: 8 end: 2058
Align Title:gi|21706470|gb|BC034026.1| Homo sapiens cDNA clone IMAGE:4734794, containing frame-shift errors
Align Len: 2059
Score: 4010.0 Bits: 3617.04 E-val: 0.0
N.aligns:None Ident:2025 Pos.:2025 Gaps:1 Align len:2037
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAA start: 1 end: 2037
Match: ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| || ||||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAA-TTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCTTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAAAAAAAAAAAAA start: 7 end: 2042
Align Title:gi|194391079|dbj|AK298437.1| Homo sapiens cDNA FLJ54371 complete cds, highly similar to Serum albumin precursor
Align Len: 2082
Score: 3994.0 Bits: 3602.61 E-val: 0.0
N.aligns:None Ident:2040 Pos.:2040 Gaps:27 Align len:2076
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCAC---------------------------ACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCT start: 1 end: 2049
Match: ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACTATTTATTTTTTTCTTCCCTTGCCCAGACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGGAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGGATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCT start: 7 end: 2082
Align Title:gi|408407943|gb|AF130077.2| Homo sapiens clone FLB9714 PRO2619 mRNA, complete cds
Align Len: 2560
Score: 3937.0 Bits: 3551.22 E-val: 0.0
N.aligns:None Ident:1982 Pos.:1982 Gaps:0 Align len:1991
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: CTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA start: 61 end: 2051
Match: || || |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: CTGTTACTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCACGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA start: 477 end: 2467
Align Title:gi|62113340|gb|AY960291.1| Homo sapiens serum albumin mRNA, complete cds
Align Len: 1981
Score: 3907.0 Bits: 3524.17 E-val: 0.0
N.aligns:None Ident:1970 Pos.:1970 Gaps:0 Align len:1981
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: CTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAA start: 2 end: 1982
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: CTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGGGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGGAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTGTCTATCCGTGTTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACGGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAA start: 1 end: 1981
Align Title:gi|49176516|gb|AY550967.1| Homo sapiens cell growth inhibiting protein 42 mRNA, complete cds
Align Len: 1939
Score: 3848.0 Bits: 3470.97 E-val: 0.0
N.aligns:None Ident:1933 Pos.:1933 Gaps:0 Align len:1939
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCA start: 27 end: 1965
Match: |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCA start: 1 end: 1939
Align Title:gi|115607206|gb|DQ986150.1| Homo sapiens serum albumin mRNA, complete cds
Align Len: 1884
Score: 3733.0 Bits: 3367.27 E-val: 0.0
N.aligns:None Ident:1877 Pos.:1877 Gaps:0 Align len:1884
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: CCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGA start: 23 end: 1906
Match: |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: CCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGA start: 1 end: 1884
Align Title:gi|164692402|dbj|AK314794.1| Homo sapiens cDNA, FLJ95666, highly similar to Homo sapiens albumin (ALB), mRNA
Align Len: 1871
Score: 3676.0 Bits: 3315.88 E-val: 0.0
N.aligns:None Ident:1853 Pos.:1853 Gaps:0 Align len:1863
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAA start: 1 end: 1863
Match: ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCCTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTTTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAATAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAA start: 9 end: 1871
Align Title:gi|52001696|gb|AY728024.1| Homo sapiens serum albumin precursor, mRNA, complete cds
Align Len: 1842
Score: 3630.0 Bits: 3274.4 E-val: 0.0
N.aligns:None Ident:1824 Pos.:1824 Gaps:0 Align len:1830
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: ATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAA start: 34 end: 1863
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||
Subjc: ATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAA start: 7 end: 1836
Align Title:gi|6013426|gb|AF190168.1|AF190168 Homo sapiens serum albumin precursor, mRNA, complete cds
Align Len: 1830
Score: 3615.0 Bits: 3260.88 E-val: 0.0
N.aligns:None Ident:1821 Pos.:1821 Gaps:0 Align len:1830
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: ATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAA start: 34 end: 1863
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||
Subjc: ATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGTAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACCTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGGAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAA start: 1 end: 1830
Align Title:gi|332356379|gb|HQ537426.1| Homo sapiens albumin mRNA, partial cds
Align Len: 1758
Score: 3471.0 Bits: 3131.03 E-val: 0.0
N.aligns:None Ident:1749 Pos.:1749 Gaps:0 Align len:1758
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: GATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAA start: 106 end: 1863
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||
Subjc: GATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCGTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGGGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAGAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAA start: 1 end: 1758
Align Title:gi|194391111|dbj|AK298461.1| Homo sapiens cDNA FLJ50830 complete cds, highly similar to Serum albumin precursor
Align Len: 1799
Score: 3084.0 Bits: 2782.08 E-val: 0.0
N.aligns:None Ident:1551 Pos.:1551 Gaps:0 Align len:1557
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: AATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCT start: 493 end: 2049
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: AATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGGGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCT start: 243 end: 1799
Score: 472.0 Bits: 426.881 E-val: 5.45568e-116
N.aligns:None Ident:239 Pos.:239 Gaps:0 Align len:241
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAG start: 1 end: 241
Match: ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAG start: 9 end: 249
Align Title:gi|763428|gb|U22961.1|HSU22961 Human mRNA clone with similarity to L-glycerol-3-phosphate:NAD oxidoreductase and albumin gene sequences
Align Len: 3239
Score: 2748.0 Bits: 2479.12 E-val: 0.0
N.aligns:None Ident:1386 Pos.:1386 Gaps:0 Align len:1394
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: CTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAA start: 7 end: 1400
Match: ||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: CTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGGGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCTTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAA start: 1846 end: 3239
Align Title:gi|27692692|gb|BC041789.1| Homo sapiens albumin, mRNA (cDNA clone MGC:32888 IMAGE:4766983), complete cds
Align Len: 1510
Score: 2620.0 Bits: 2363.7 E-val: 0.0
N.aligns:None Ident:1327 Pos.:1327 Gaps:1 Align len:1337
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: AAAAATTTGG-AGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA start: 716 end: 2051
Match: ||| |||||| |||| | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||
Subjc: AAAGATTTGGGAGAAGAAAATTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCGGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCGAA start: 147 end: 1483
Score: 329.0 Bits: 297.94 E-val: 6.65812e-77
N.aligns:None Ident:166 Pos.:166 Gaps:0 Align len:167
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGC start: 1 end: 167
Match: ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGC start: 9 end: 175
Align Title:gi|164694201|dbj|AK308044.1| Homo sapiens cDNA, FLJ97992
Align Len: 1544
Score: 2536.0 Bits: 2287.96 E-val: 0.0
N.aligns:None Ident:1279 Pos.:1279 Gaps:1 Align len:1285
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACC-AAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAA start: 378 end: 1661
Match: |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| || |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTTCCCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAA start: 260 end: 1544
Score: 506.0 Bits: 457.539 E-val: 3.22174e-125
N.aligns:None Ident:256 Pos.:256 Gaps:0 Align len:258
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAA start: 1 end: 258
Match: ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAA start: 9 end: 266
Align Title:gi|7770216|gb|AF119890.1|AF119890 Homo sapiens PRO2675 mRNA, complete cds
Align Len: 1618
Score: 2488.0 Bits: 2244.68 E-val: 0.0
N.aligns:None Ident:1247 Pos.:1247 Gaps:0 Align len:1249
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: AGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA start: 803 end: 2051
Match: |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: AGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA start: 350 end: 1598
Align Title:gi|47118014|gb|AY544124.1| Homo sapiens growth-inhibiting protein 20 mRNA, complete cds
Align Len: 1363
Score: 2453.0 Bits: 2213.12 E-val: 0.0
N.aligns:None Ident:1242 Pos.:1242 Gaps:1 Align len:1251
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: AAAAATTTGG-AGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCA start: 716 end: 1965
Match: ||| |||||| |||| | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: AAAGATTTGGGAGAAGAAAATTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCGGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCA start: 113 end: 1363
Score: 282.0 Bits: 255.561 E-val: 2.03854e-64
N.aligns:None Ident:141 Pos.:141 Gaps:0 Align len:141
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGC start: 27 end: 167
Match: |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGC start: 1 end: 141
Align Title:gi|7959790|gb|AF116645.1|AF116645 Homo sapiens PRO1708 mRNA, complete cds
Align Len: 1251
Score: 2003.0 Bits: 1807.36 E-val: 0.0
N.aligns:None Ident:1006 Pos.:1006 Gaps:0 Align len:1009
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAA start: 1029 end: 2037
Match: |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGCGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAA start: 234 end: 1242
Align Title:gi|6650825|gb|AF118090.1|AF118090 Homo sapiens PRO2044 mRNA, complete cds
Align Len: 1759
Score: 1983.0 Bits: 1789.33 E-val: 0.0
N.aligns:None Ident:996 Pos.:996 Gaps:0 Align len:999
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: CAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA start: 1053 end: 2051
Match: |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: CAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA start: 692 end: 1690
Align Title:gi|23241674|gb|BC035969.1| Homo sapiens albumin, mRNA (cDNA clone MGC:32581 IMAGE:4714468), complete cds
Align Len: 1449
Score: 1767.0 Bits: 1594.56 E-val: 0.0
N.aligns:None Ident:888 Pos.:888 Gaps:0 Align len:891
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: ATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA start: 1161 end: 2051
Match: |||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: ATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA start: 530 end: 1420
Score: 1048.0 Bits: 946.252 E-val: 0.0
N.aligns:None Ident:527 Pos.:527 Gaps:0 Align len:529
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAA start: 1 end: 529
Match: ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAA start: 9 end: 537
Align Title:gi|15679995|gb|BC014308.1|BC014308 Homo sapiens, clone IMAGE:3934797, mRNA, partial cds
Align Len: 823
Score: 1571.0 Bits: 1417.83 E-val: 0.0
N.aligns:None Ident:790 Pos.:790 Gaps:0 Align len:793
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: AGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA start: 1259 end: 2051
Match: |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||
Subjc: AGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCCAA start: 4 end: 796
Align Title:gi|37181745|gb|AY358313.1| Homo sapiens DNA66677 ALB (UNQ696) mRNA, partial cds
Align Len: 524
Score: 1018.0 Bits: 919.201 E-val: 0.0
N.aligns:None Ident:517 Pos.:517 Gaps:0 Align len:523
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: AACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCC start: 12 end: 534
Match: ||||||| || || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: AACCCCANANGCTTTGGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCC start: 2 end: 524
Align Title:gi|6642751|gb|AF113014.1|AF113014 Homo sapiens clone FLB3512 mRNA sequence
Align Len: 1476
Score: 618.0 Bits: 558.527 E-val: 1.28079e-155
N.aligns:None Ident:312 Pos.:312 Gaps:0 Align len:314
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: AAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA start: 1738 end: 2051
Match: ||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: AAAGCTGCTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA start: 1153 end: 1466
Align Title:gi|219842221|ref|NG_009291.1| Homo sapiens albumin (ALB), RefSeqGene on chromosome 4
Align Len: 24158
Score: 581.0 Bits: 525.165 E-val: 2.64223e-145
N.aligns:None Ident:294 Pos.:294 Gaps:1 Align len:295
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAATAGAGTGGTACAGCACTGTTATTTTTCAAAGATGTGTTGCTATCCTGAAAATTCTGTAGGTTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTTCGGTAGAGGATTTCTAGTTTC-TGTGGGC start: 1883 end: 2176
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||
Subjc: TCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAATAGAGTGGTACAGCACTGTTATTTTTCAAAGATGTGTTGCTATCCTGAAAATTCTGTAGGTTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTTCGGTAGAGGATTTCTAGTTTCTTGTGGGC start: 21834 end: 22128
Score: 449.0 Bits: 406.143 E-val: 1.78347e-109
N.aligns:None Ident:226 Pos.:226 Gaps:0 Align len:227
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAAC start: 1459 end: 1685
Match: || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TAGCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAAC start: 18831 end: 19057
Score: 436.0 Bits: 394.421 E-val: 3.22459e-106
N.aligns:None Ident:218 Pos.:218 Gaps:0 Align len:218
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: GGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGT start: 876 end: 1093
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGT start: 14165 end: 14382
Score: 425.0 Bits: 384.502 E-val: 5.83019e-103
N.aligns:None Ident:214 Pos.:214 Gaps:0 Align len:215
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: CATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATA start: 304 end: 518
Match: |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||
Subjc: CATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAGTA start: 9340 end: 9554
Score: 278.0 Bits: 251.955 E-val: 2.48344e-63
N.aligns:None Ident:139 Pos.:139 Gaps:0 Align len:139
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: GCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTAT start: 1323 end: 1461
Match: |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTAT start: 18277 end: 18415
Score: 264.0 Bits: 239.331 E-val: 1.56722e-59
N.aligns:None Ident:132 Pos.:132 Gaps:0 Align len:132
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: GTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTT start: 172 end: 303
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTT start: 7376 end: 7507
Score: 264.0 Bits: 239.331 E-val: 1.56722e-59
N.aligns:None Ident:132 Pos.:132 Gaps:0 Align len:132
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: GGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGG start: 746 end: 877
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGG start: 12741 end: 12872
Score: 264.0 Bits: 239.331 E-val: 1.56722e-59
N.aligns:None Ident:138 Pos.:138 Gaps:0 Align len:142
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: AAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGG start: 1678 end: 1819
Match: |||| | ||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: AAACTCAGTGCACTTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGG start: 20245 end: 20386
Score: 261.0 Bits: 236.626 E-val: 1.90927e-58
N.aligns:None Ident:132 Pos.:132 Gaps:0 Align len:133
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: GTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTG start: 1092 end: 1224
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTG start: 15781 end: 15913
Score: 256.0 Bits: 232.118 E-val: 2.32597e-57
N.aligns:None Ident:131 Pos.:131 Gaps:0 Align len:133
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: ATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAG start: 516 end: 648
Match: |||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||
Subjc: ATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAG start: 10101 end: 10233
Score: 221.0 Bits: 200.559 E-val: 1.37477e-47
N.aligns:None Ident:115 Pos.:115 Gaps:0 Align len:118
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGA start: 1 end: 118
Match: ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACGTAAGA start: 5041 end: 5158
Score: 200.0 Bits: 181.623 E-val: 3.68902e-42
N.aligns:None Ident:100 Pos.:100 Gaps:0 Align len:100
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: GTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCG start: 1224 end: 1323
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCG start: 17001 end: 17100
Score: 197.0 Bits: 178.918 E-val: 4.49414e-41
N.aligns:None Ident:100 Pos.:100 Gaps:0 Align len:101
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: AGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGG start: 647 end: 747
Match: ||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: AGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGG start: 11056 end: 11156
Score: 135.0 Bits: 123.014 E-val: 3.0308e-24
N.aligns:None Ident:69 Pos.:69 Gaps:0 Align len:70
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: AGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAG start: 1817 end: 1886
Match: ||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||
Subjc: AGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAG start: 20998 end: 21067
Score: 117.0 Bits: 106.783 E-val: 2.33008e-19
N.aligns:None Ident:60 Pos.:60 Gaps:0 Align len:61
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: CACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTT start: 110 end: 170
Match: || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: CAGACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTT start: 5859 end: 5919
Align Title:gi|152112963|gb|EF649953.1| Homo sapiens albumin (ALB) gene, complete cds
Align Len: 21070
Score: 581.0 Bits: 525.165 E-val: 2.64223e-145
N.aligns:None Ident:294 Pos.:294 Gaps:1 Align len:295
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAATAGAGTGGTACAGCACTGTTATTTTTCAAAGATGTGTTGCTATCCTGAAAATTCTGTAGGTTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTTCGGTAGAGGATTTCTAGTTTC-TGTGGGC start: 1883 end: 2176
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||
Subjc: TCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAATAGAGTGGTACAGCACTGTTATTTTTCAAAGATGTGTTGCTATCCTGAAAATTCTGTAGGTTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTTCGGTAGAGGATTTCTAGTTTCTTGTGGGC start: 18784 end: 19078
Score: 449.0 Bits: 406.143 E-val: 1.78347e-109
N.aligns:None Ident:226 Pos.:226 Gaps:0 Align len:227
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAAC start: 1459 end: 1685
Match: || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TAGCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAAC start: 15781 end: 16007
Score: 436.0 Bits: 394.421 E-val: 3.22459e-106
N.aligns:None Ident:218 Pos.:218 Gaps:0 Align len:218
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: GGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGT start: 876 end: 1093
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGT start: 11115 end: 11332
Score: 425.0 Bits: 384.502 E-val: 5.83019e-103
N.aligns:None Ident:214 Pos.:214 Gaps:0 Align len:215
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: CATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATA start: 304 end: 518
Match: |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||
Subjc: CATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAGTA start: 6290 end: 6504
Score: 278.0 Bits: 251.955 E-val: 2.48344e-63
N.aligns:None Ident:139 Pos.:139 Gaps:0 Align len:139
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: GCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTAT start: 1323 end: 1461
Match: |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTAT start: 15227 end: 15365
Score: 264.0 Bits: 239.331 E-val: 1.56722e-59
N.aligns:None Ident:132 Pos.:132 Gaps:0 Align len:132
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: GTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTT start: 172 end: 303
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTT start: 4326 end: 4457
Score: 264.0 Bits: 239.331 E-val: 1.56722e-59
N.aligns:None Ident:132 Pos.:132 Gaps:0 Align len:132
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: GGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGG start: 746 end: 877
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGG start: 9691 end: 9822
Score: 264.0 Bits: 239.331 E-val: 1.56722e-59
N.aligns:None Ident:138 Pos.:138 Gaps:0 Align len:142
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: AAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGG start: 1678 end: 1819
Match: |||| | ||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: AAACTCAGTGCACTTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGG start: 17195 end: 17336
Score: 261.0 Bits: 236.626 E-val: 1.90927e-58
N.aligns:None Ident:132 Pos.:132 Gaps:0 Align len:133
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: GTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTG start: 1092 end: 1224
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTG start: 12731 end: 12863
Score: 256.0 Bits: 232.118 E-val: 2.32597e-57
N.aligns:None Ident:131 Pos.:131 Gaps:0 Align len:133
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: ATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAG start: 516 end: 648
Match: |||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||
Subjc: ATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAG start: 7051 end: 7183
Score: 221.0 Bits: 200.559 E-val: 1.37477e-47
N.aligns:None Ident:115 Pos.:115 Gaps:0 Align len:118
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGA start: 1 end: 118
Match: ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACGTAAGA start: 1991 end: 2108
Score: 200.0 Bits: 181.623 E-val: 3.68902e-42
N.aligns:None Ident:100 Pos.:100 Gaps:0 Align len:100
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: GTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCG start: 1224 end: 1323
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCG start: 13951 end: 14050
Score: 197.0 Bits: 178.918 E-val: 4.49414e-41
N.aligns:None Ident:100 Pos.:100 Gaps:0 Align len:101
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: AGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGG start: 647 end: 747
Match: ||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: AGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGG start: 8006 end: 8106
Score: 135.0 Bits: 123.014 E-val: 3.0308e-24
N.aligns:None Ident:69 Pos.:69 Gaps:0 Align len:70
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: AGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAG start: 1817 end: 1886
Match: ||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||
Subjc: AGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAG start: 17948 end: 18017
Score: 117.0 Bits: 106.783 E-val: 2.33008e-19
N.aligns:None Ident:60 Pos.:60 Gaps:0 Align len:61
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: CACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTT start: 110 end: 170
Match: || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: CAGACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTT start: 2809 end: 2869
Align Title:gi|19387810|gb|AC108157.3| Homo sapiens BAC clone RP11-580P21 from 4, complete sequence
Align Len: 167001
Score: 581.0 Bits: 525.165 E-val: 2.64223e-145
N.aligns:None Ident:294 Pos.:294 Gaps:1 Align len:295
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAATAGAGTGGTACAGCACTGTTATTTTTCAAAGATGTGTTGCTATCCTGAAAATTCTGTAGGTTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTTCGGTAGAGGATTTCTAGTTTC-TGTGGGC start: 1883 end: 2176
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||
Subjc: TCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAATAGAGTGGTACAGCACTGTTATTTTTCAAAGATGTGTTGCTATCCTGAAAATTCTGTAGGTTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTTCGGTAGAGGATTTCTAGTTTCTTGTGGGC start: 86936 end: 87230
Score: 449.0 Bits: 406.143 E-val: 1.78347e-109
N.aligns:None Ident:226 Pos.:226 Gaps:0 Align len:227
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAAC start: 1459 end: 1685
Match: || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TAGCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAAC start: 83933 end: 84159
Score: 436.0 Bits: 394.421 E-val: 3.22459e-106
N.aligns:None Ident:218 Pos.:218 Gaps:0 Align len:218
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: GGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGT start: 876 end: 1093
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGT start: 79267 end: 79484
Score: 425.0 Bits: 384.502 E-val: 5.83019e-103
N.aligns:None Ident:214 Pos.:214 Gaps:0 Align len:215
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: CATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATA start: 304 end: 518
Match: |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||
Subjc: CATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAGTA start: 74442 end: 74656
Score: 278.0 Bits: 251.955 E-val: 2.48344e-63
N.aligns:None Ident:139 Pos.:139 Gaps:0 Align len:139
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: GCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTAT start: 1323 end: 1461
Match: |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTAT start: 83379 end: 83517
Score: 264.0 Bits: 239.331 E-val: 1.56722e-59
N.aligns:None Ident:132 Pos.:132 Gaps:0 Align len:132
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: GTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTT start: 172 end: 303
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTT start: 72478 end: 72609
Score: 264.0 Bits: 239.331 E-val: 1.56722e-59
N.aligns:None Ident:132 Pos.:132 Gaps:0 Align len:132
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: GGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGG start: 746 end: 877
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGG start: 77843 end: 77974
Score: 264.0 Bits: 239.331 E-val: 1.56722e-59
N.aligns:None Ident:138 Pos.:138 Gaps:0 Align len:142
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: AAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGG start: 1678 end: 1819
Match: |||| | ||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: AAACTCAGTGCACTTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGG start: 85347 end: 85488
Score: 261.0 Bits: 236.626 E-val: 1.90927e-58
N.aligns:None Ident:132 Pos.:132 Gaps:0 Align len:133
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: GTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTG start: 1092 end: 1224
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTG start: 80883 end: 81015
Score: 256.0 Bits: 232.118 E-val: 2.32597e-57
N.aligns:None Ident:131 Pos.:131 Gaps:0 Align len:133
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: ATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAG start: 516 end: 648
Match: |||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||
Subjc: ATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAG start: 75203 end: 75335
Score: 221.0 Bits: 200.559 E-val: 1.37477e-47
N.aligns:None Ident:115 Pos.:115 Gaps:0 Align len:118
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGA start: 1 end: 118
Match: ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACGTAAGA start: 70143 end: 70260
Score: 200.0 Bits: 181.623 E-val: 3.68902e-42
N.aligns:None Ident:100 Pos.:100 Gaps:0 Align len:100
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: GTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCG start: 1224 end: 1323
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCG start: 82103 end: 82202
Score: 197.0 Bits: 178.918 E-val: 4.49414e-41
N.aligns:None Ident:100 Pos.:100 Gaps:0 Align len:101
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: AGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGG start: 647 end: 747
Match: ||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: AGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGG start: 76158 end: 76258
Score: 135.0 Bits: 123.014 E-val: 3.0308e-24
N.aligns:None Ident:69 Pos.:69 Gaps:0 Align len:70
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: AGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAG start: 1817 end: 1886
Match: ||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||
Subjc: AGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAG start: 86100 end: 86169
Score: 117.0 Bits: 106.783 E-val: 2.33008e-19
N.aligns:None Ident:60 Pos.:60 Gaps:0 Align len:61
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: CACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTT start: 110 end: 170
Match: || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: CAGACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTT start: 70961 end: 71021
Score: 60.0 Bits: 55.3874 E-val: 0.000369554
N.aligns:None Ident:45 Pos.:45 Gaps:0 Align len:55
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: ATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAA start: 893 end: 947
Match: |||| ||| ||| |||||||| |||||||| ||| | || || |||||||||||
Subjc: ATATTTGTTCAAAACAAGATTCTATCTCCAGCAAAATCAAAGAGTGCTGTGAAAA start: 157736 end: 157790
Align Title:gi|178343|gb|M12523.1|HUMALBGC Human serum albumin (ALB) gene, complete cds
Align Len: 19002
Score: 581.0 Bits: 525.165 E-val: 2.64223e-145
N.aligns:None Ident:294 Pos.:294 Gaps:1 Align len:295
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAATAGAGTGGTACAGCACTGTTATTTTTCAAAGATGTGTTGCTATCCTGAAAATTCTGTAGGTTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTTCGGTAGAGGATTTCTAGTTTC-TGTGGGC start: 1883 end: 2176
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||
Subjc: TCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAATAGAGTGGTACAGCACTGTTATTTTTCAAAGATGTGTTGCTATCCTGAAAATTCTGTAGGTTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTTCGGTAGAGGATTTCTAGTTTCTTGTGGGC start: 18522 end: 18816
Score: 449.0 Bits: 406.143 E-val: 1.78347e-109
N.aligns:None Ident:226 Pos.:226 Gaps:0 Align len:227
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAAC start: 1459 end: 1685
Match: || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TAGCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAAC start: 15531 end: 15757
Score: 436.0 Bits: 394.421 E-val: 3.22459e-106
N.aligns:None Ident:218 Pos.:218 Gaps:0 Align len:218
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: GGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGT start: 876 end: 1093
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGT start: 10866 end: 11083
Score: 425.0 Bits: 384.502 E-val: 5.83019e-103
N.aligns:None Ident:214 Pos.:214 Gaps:0 Align len:215
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: CATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATA start: 304 end: 518
Match: |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||
Subjc: CATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAGTA start: 6041 end: 6255
Score: 278.0 Bits: 251.955 E-val: 2.48344e-63
N.aligns:None Ident:139 Pos.:139 Gaps:0 Align len:139
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: GCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTAT start: 1323 end: 1461
Match: |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTAT start: 14977 end: 15115
Score: 264.0 Bits: 239.331 E-val: 1.56722e-59
N.aligns:None Ident:132 Pos.:132 Gaps:0 Align len:132
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: GTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTT start: 172 end: 303
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTT start: 4077 end: 4208
Score: 264.0 Bits: 239.331 E-val: 1.56722e-59
N.aligns:None Ident:132 Pos.:132 Gaps:0 Align len:132
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: GGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGG start: 746 end: 877
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGG start: 9443 end: 9574
Score: 264.0 Bits: 239.331 E-val: 1.56722e-59
N.aligns:None Ident:138 Pos.:138 Gaps:0 Align len:142
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: AAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGG start: 1678 end: 1819
Match: |||| | ||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: AAACTCAGTGCACTTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGG start: 16933 end: 17074
Score: 261.0 Bits: 236.626 E-val: 1.90927e-58
N.aligns:None Ident:132 Pos.:132 Gaps:0 Align len:133
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: GTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTG start: 1092 end: 1224
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTG start: 12481 end: 12613
Score: 256.0 Bits: 232.118 E-val: 2.32597e-57
N.aligns:None Ident:131 Pos.:131 Gaps:0 Align len:133
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: ATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAG start: 516 end: 648
Match: |||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||
Subjc: ATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAG start: 6802 end: 6934
Score: 221.0 Bits: 200.559 E-val: 1.37477e-47
N.aligns:None Ident:115 Pos.:115 Gaps:0 Align len:118
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGA start: 1 end: 118
Match: ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACGTAAGA start: 1743 end: 1860
Score: 200.0 Bits: 181.623 E-val: 3.68902e-42
N.aligns:None Ident:100 Pos.:100 Gaps:0 Align len:100
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: GTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCG start: 1224 end: 1323
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCG start: 13701 end: 13800
Score: 197.0 Bits: 178.918 E-val: 4.49414e-41
N.aligns:None Ident:100 Pos.:100 Gaps:0 Align len:101
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: AGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGG start: 647 end: 747
Match: ||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: AGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGG start: 7757 end: 7857
Score: 135.0 Bits: 123.014 E-val: 3.0308e-24
N.aligns:None Ident:69 Pos.:69 Gaps:0 Align len:70
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: AGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAG start: 1817 end: 1886
Match: ||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||
Subjc: AGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAG start: 17686 end: 17755
Score: 117.0 Bits: 106.783 E-val: 2.33008e-19
N.aligns:None Ident:60 Pos.:60 Gaps:0 Align len:61
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: CACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTT start: 110 end: 170
Match: || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: CAGACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTT start: 2561 end: 2621
Align Title:gi|1036032687|gb|AH007061.2| Homo sapiens chromosome 4 serum albumin (ALB) gene, partial cds; and serum albumin-alphafetoprotein intergenic spacer, partial sequence
Align Len: 523
Score: 579.0 Bits: 523.362 E-val: 9.2223e-145
N.aligns:None Ident:293 Pos.:293 Gaps:1 Align len:294
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAATAGAGTGGTACAGCACTGTTATTTTTCAAAGATGTGTTGCTATCCTGAAAATTCTGTAGGTTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTTCGGTAGAGGATTTCTAGTTTCTGTGGGC start: 1883 end: 2176
Match: |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTT-CTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAATAGAGTGGTACAGCACTGTTATTTTTCAAAGATGTGTTGCTATCCTGAAAATTCTGTAGGTTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTTCGGTAGAGGATTTCTAGTTTCTGTGGGC start: 4 end: 296
Align Title:gi|408407822|gb|AF116616.2| Homo sapiens PRO0998 mRNA, complete cds
Align Len: 1649
Score: 577.0 Bits: 521.558 E-val: 3.2189e-144
N.aligns:None Ident:290 Pos.:290 Gaps:0 Align len:291
Strand: ('Plus', 'Minus') Frame: (1, -1)
Query: AGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA start: 1761 end: 2051
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: AGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA start: 317 end: 27
Align Title:gi|338858118|gb|AH002596.2|SEG_HUMALB Homo sapiens albumin (ALB) gene, partial cds
Align Len: 1863
Score: 573.0 Bits: 517.951 E-val: 3.92142e-143
N.aligns:None Ident:290 Pos.:290 Gaps:1 Align len:291
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: CCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAATAGAGTGGTACAGCACTGTTATTTTTCAAAGATGTGTTGCTATCCTGAAAATTCTGTAGGTTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTTCGGTAGAGGATTTCTAGTTTC-TGTGGGC start: 1887 end: 2176
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||
Subjc: CCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAATAGAGTGGTACAGCACTGTTATTTTTCAAAGATGTGTTGCTATCCTGAAAATTCTGTAGGTTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTTCGGTAGAGGATTTCTAGTTTCTTGTGGGC start: 1387 end: 1677
Score: 221.0 Bits: 200.559 E-val: 1.37477e-47
N.aligns:None Ident:115 Pos.:115 Gaps:0 Align len:118
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGA start: 1 end: 118
Match: ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACGTAAGA start: 1059 end: 1176
Align Title:gi|1122817323|gb|DQ145726.2| Homo sapiens ARNT-interacting protein 2 (AINP2) mRNA, complete cds
Align Len: 1054
Score: 404.0 Bits: 365.567 E-val: 1.56446e-97
N.aligns:None Ident:205 Pos.:205 Gaps:0 Align len:207
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: AGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA start: 1845 end: 2051
Match: ||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: AGCTGCCTTTGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGCCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA start: 836 end: 1042
Align Title:gi|32428|emb|X51365.1| Homo sapiens mRNA for albumin (clone pHA19)
Align Len: 117
Score: 232.0 Bits: 210.477 E-val: 7.60363e-51
N.aligns:None Ident:116 Pos.:116 Gaps:0 Align len:116
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: AGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGG start: 1925 end: 2040
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: AGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGG start: 2 end: 117
Align Title:gi|1338686512|ref|NG_056261.1| Homo sapiens albumin (ALB) 5' regulatory region (LOC111832671) on chromosome 4
Align Len: 6858
Score: 221.0 Bits: 200.559 E-val: 1.37477e-47
N.aligns:None Ident:115 Pos.:115 Gaps:0 Align len:118
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGA start: 1 end: 118
Match: ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACGTAAGA start: 6711 end: 6828
Align Title:gi|7959920|gb|AF116711.1|AF116711 Homo sapiens PRO2646 mRNA, complete cds
Align Len: 1160
Score: 216.0 Bits: 196.05 E-val: 1.67481e-46
N.aligns:None Ident:108 Pos.:108 Gaps:0 Align len:108
Strand: ('Plus', 'Minus') Frame: (1, -1)
Query: GGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCA start: 1248 end: 1355
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCA start: 274 end: 167
Align Title:gi|35452|emb|X51363.1| Homo sapiens mRNA for albumin (clones pHA1, pHA12)
Align Len: 104
Score: 208.0 Bits: 188.837 E-val: 2.48564e-44
N.aligns:None Ident:104 Pos.:104 Gaps:0 Align len:104
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCT start: 1946 end: 2049
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCT start: 1 end: 104
Align Title:gi|35453|emb|X51364.1| Homo sapiens mRNA for albumin (clones pHA8, pHA25)
Align Len: 99
Score: 198.0 Bits: 179.82 E-val: 1.28759e-41
N.aligns:None Ident:99 Pos.:99 Gaps:0 Align len:99
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAG start: 1946 end: 2044
Match: |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAG start: 1 end: 99
Align Title:gi|7959874|gb|AF116688.1|AF116688 Homo sapiens PRO2133 mRNA, complete cds
Align Len: 1247
Score: 123.0 Bits: 112.193 E-val: 5.47982e-21
N.aligns:None Ident:65 Pos.:65 Gaps:1 Align len:66
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: TTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTTCGGTAGAGGATTTCTAGTTTC-TGTGGGC start: 2112 end: 2176
Match: |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||
Subjc: TTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTTCGGTAGAGGATTTCTAGTTTCTTGTGGGC start: 1029 end: 1094
Align Title:gi|546032|gb|S69192.1| albumin {exon 8} [human, analbuminemia patient ROMA, Genomic Mutant, 60 nt]
Align Len: 60
Score: 111.0 Bits: 101.373 E-val: 9.90775e-18
N.aligns:None Ident:59 Pos.:59 Gaps:1 Align len:60
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: GCGGACCTTGCCAAGTATATCTGTGAAAA-TCAAGATTCGATCTCCAGTAAACTGAAGGA start: 877 end: 935
Match: ||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||
Subjc: GCGGACCTTGCCAAGTATATCTGTGAAAAATCAAGATTCGATCTCCAGTAAACTGAAGGA start: 1 end: 60
Align Title:gi|547231|gb|S70799.1| serum albumin=alloalbumin {Bazzano variant} [human, Genomic Mutant, 57 nt]
Align Len: 57
Score: 102.0 Bits: 93.2581 E-val: 1.47044e-15
N.aligns:None Ident:56 Pos.:56 Gaps:1 Align len:58
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: GAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAG start: 1798 end: 1855
Match: |||||| ||||||||||||||||||||||||||||||||||||||| |||||||||||
Subjc: GAGACC-GCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAG start: 1 end: 57
Align Title:gi|1370486375|ref|XM_017007844.2| PREDICTED: Homo sapiens afamin (AFM), transcript variant X3, mRNA
Align Len: 1404
Score: 60.0 Bits: 55.3874 E-val: 0.000369554
N.aligns:None Ident:45 Pos.:45 Gaps:0 Align len:55
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: ATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAA start: 893 end: 947
Match: |||| ||| ||| |||||||| |||||||| ||| | || || |||||||||||
Subjc: ATATTTGTTCAAAACAAGATTCTATCTCCAGCAAAATCAAAGAGTGCTGTGAAAA start: 891 end: 945
Align Title:gi|1370486374|ref|XM_017007843.2| PREDICTED: Homo sapiens afamin (AFM), transcript variant X2, mRNA
Align Len: 1395
Score: 60.0 Bits: 55.3874 E-val: 0.000369554
N.aligns:None Ident:45 Pos.:45 Gaps:0 Align len:55
Strand: ('Plus', 'Plus') Frame: (1, 1)
Query: ATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAA start: 893 end: 947
Match: |||| ||| ||| |||||||| |||||||| ||| | || || |||||||||||
Subjc: ATATTTGTTCAAAACAAGATTCTATCTCCAGCAAAATCAAAGAGTGCTGTGAAAA start: 891 end: 945
Example: Let’s align the first 100 bases of the first 5 entries of the file contigs82.fasta to the Malus Domestica genome, writing the results to a apple_first5.xml file. Sample output is here: apple_first5.xml. NOTE: this can take several minutes.
[4]:
from Bio.Blast import NCBIWWW
from Bio import SeqIO
rc = SeqIO.parse("file_samples/contigs82.fasta", format="fasta")
fasta_string = ""
ids2align =[]
for i in range(5):
entry = next(rc)
fasta_string +=">" + entry.id +"\n"+entry.seq +"\n"
ids2align.append(entry.id)
print("Aligning the following {} entries:\n\t{}".format(
len(ids2align),
"\n\t".join(ids2align)
))
result_handle = NCBIWWW.qblast("blastn", "nt",
fasta_string,
entrez_query='"Malus Domestica" [Organism]'
)
with open("file_samples/blast_res_apple.xml","w") as out_f:
out_f.write(result_handle.read())
print("Output written to \"blast_res_apple.xml\"")
Aligning the following 5 entries:
MDC020656.85
MDC001115.177
MDC013284.379
MDC018185.243
MDC018185.241
Output written to "blast_res_apple.xml"
Getting data from NCBI¶
Biopython provides a module (Bio.Entrez) to pull data off resources like PubMed or GenBank, and other repositories programmatically through Entrez.
There are some limitations (mostly taken care of directly by Biopython) that you should be aware of when you use NCBI’s services (e.g. they recommend not to run more than 3 requests per second on weekdays, …). Check here if you want to learn what these limitations are.
First of all we need to import the Entrez module with (from Bio import Entrez) and then we can start interacting with Entrez, then we should specify (optional) an email setting Entrez.email (this is optional but you get a warning if you do not specify it – the email would be used to notify the user in case of excessive usage).
In particular the module (complete info on Entrez module are here) provides, among the others, the following functions:
res_handle = Entrez.einfo(db)returns a summary of the Entez databases as a results handle.dbis an optional parameter specifying the resource of interest;res_handle = Entrez.esearch(db, term,id)returns all the entries indbhaving query matching the termterm. It is also possible to specify anidto get the information relative to that resource id;res_handle = Entrez.efetch(db, id, rettype, retmode)returns full record corresponding to the identifieridfrom the databasedbformatted inrettype(eg. gb, fasta,… complete list) and return moderetmode(eg. text);res_handle = Entrez.esummary(db, id)returns the summary of the entryidfrom the databasedbas a handle;result = Entrez.read(res_handle)reads the information on the XML handleres_handleand stores them in a dictionary, list or string, depending on the case.
Example:
Let’s get a list of all available databases in Entrez as a dictionary. Let’s then get a summary of the entries in ‘sra’.
[47]:
from Bio import Entrez
import datetime
Entrez.email = "my_email"
handle = Entrez.einfo()
res = Entrez.read(handle)
#print(res)
print("")
print("As a list:")
print(res['DbList'])
res = Entrez.read(Entrez.einfo(db = "sra"))
#uncomment to see all the information captured
#print(res)
#for el in res["DbInfo"].keys():
# print(el)
date = res["DbInfo"]["LastUpdate"]
dt = datetime.datetime.strptime(date, "%Y/%m/%d %H:%M")
print("")
print("Entries count: {:,}".format(int(res["DbInfo"]["Count"])))
print("LastUpdate: {}/{}/{} {}:{}".format(dt.day,
dt.month,
dt.year,
dt.hour,
dt.minute))
print("Description:", res["DbInfo"]["Description"])
As a list:
['pubmed', 'protein', 'nuccore', 'ipg', 'nucleotide', 'structure', 'sparcle', 'protfam', 'genome', 'annotinfo', 'assembly', 'bioproject', 'biosample', 'blastdbinfo', 'books', 'cdd', 'clinvar', 'gap', 'gapplus', 'grasp', 'dbvar', 'gene', 'gds', 'geoprofiles', 'homologene', 'medgen', 'mesh', 'ncbisearch', 'nlmcatalog', 'omim', 'orgtrack', 'pmc', 'popset', 'proteinclusters', 'pcassay', 'biosystems', 'pccompound', 'pcsubstance', 'seqannot', 'snp', 'sra', 'taxonomy', 'biocollections', 'gtr']
Entries count: 12,222,409
LastUpdate: 27/10/2020 4:39
Description: SRA Database
Note that effectively einfo returned a handler to an object that can be read by the read function that produces a dictionary. This dictionary had one key only “DbList” that is the list of available databases in the first case, while the key when db was specified is “DbInfo”.
Example: Fetch the latest 10 entries (retmax = 10) in pubmed that are related to the species “Pyrus Communis” and report the title of the publication.
[43]:
from Bio import Entrez
Entrez.email = "my_email"
handle = Entrez.esearch(db="pubmed", term="Pyrus communis", retmax = 10)
res = Entrez.read(handle)
for el in res.keys():
print(el , " : ", res[el])
print("")
for ids in res["IdList"]:
print("Results for id:", ids)
handle = Entrez.esummary(db="pubmed", id = ids)
res = Entrez.read(handle)
#uncomment to see all info
#print(res)
for r in res:
print(r["Title"])
print("{}, {}".format(r['FullJournalName'],r['SO']))
print("")
Count : 356
RetMax : 10
RetStart : 0
IdList : ['33038244', '32992651', '32990517', '32972020', '32942590', '32899287', '32894061', '32889351', '32882874', '32849839']
TranslationSet : [{'From': 'Pyrus', 'To': '"pyrus"[MeSH Terms] OR "pyrus"[All Fields]'}]
TranslationStack : [{'Term': '"pyrus"[MeSH Terms]', 'Field': 'MeSH Terms', 'Count': '1092', 'Explode': 'Y'}, {'Term': '"pyrus"[All Fields]', 'Field': 'All Fields', 'Count': '1573', 'Explode': 'N'}, 'OR', 'GROUP', {'Term': 'communis[All Fields]', 'Field': 'All Fields', 'Count': '6139', 'Explode': 'N'}, 'AND', 'GROUP']
QueryTranslation : ("pyrus"[MeSH Terms] OR "pyrus"[All Fields]) AND communis[All Fields]
Results for id: 33038244
From the roots to the stem: unveiling pear root colonization and infection pathways by Erwinia amylovora.
FEMS microbiology ecology, 2020 Oct 10;
Results for id: 32992651
Bioactive Compounds and Health-Promoting Properties of Pear (<i>Pyrus communis</i> L.) Fruits.
Molecules (Basel, Switzerland), 2020 Sep 27;25(19)
Results for id: 32990517
First report of <i>Phytophthora chlamydospora</i> causing postharvest fruit rot on apples and pears in the Netherlands.
Plant disease, 2020 Sep 29;
Results for id: 32972020
Organic Control of Pear Psylla in Pear with Trunk Injection.
Insects, 2020 Sep 22;11(9)
Results for id: 32942590
The Impact of Plant-Based Coatings in "ROCHA" Pear Preservation during Cold Storage: A Metabolomic Approach.
Foods (Basel, Switzerland), 2020 Sep 15;9(9)
Results for id: 32899287
Characterization of <i>PcLEA14</i>, a Group 5 Late Embryogenesis Abundant Protein Gene from Pear (<i>Pyrus communis</i>).
Plants (Basel, Switzerland), 2020 Sep 3;9(9)
Results for id: 32894061
Genome-wide identification of lysin motif containing protein family genes in eight rosaceae species, and expression analysis in response to pathogenic fungus Botryosphaeria dothidea in Chinese white pear.
BMC genomics, 2020 Sep 7;21(1):612
Results for id: 32889351
Elucidating the involvement of ethylene and oxidative stress during on- and off-tree ripening of two pear cultivars with different ripening patterns.
Plant physiology and biochemistry : PPB, 2020 Oct;155:842-850
Results for id: 32882874
Physicochemical Fingerprint of "Pera Rocha do Oeste". A PDO Pear Native from Portugal.
Foods (Basel, Switzerland), 2020 Sep 1;9(9)
Results for id: 32849839
RIGD: A Database for Intronless Genes in the Rosaceae.
Frontiers in genetics, 2020;11:868
Example: Retrieve genbank formatted information of the Malus x domestica MYB domain class transcription factor (MYB1) mRNA complete cds (nucleotide database id:HM122614.1). Parse it as a SeqRecord, printing only the sequence (remember previous practical’s SeqIO).
[7]:
from Bio import Entrez
from Bio import SeqIO
Entrez.email = "my_email"
handle = Entrez.efetch(db="nucleotide",
id = "HM122614.1",
rettype = "gb",
retmode="text")
my_seq = SeqIO.read(handle, format = "genbank")
print(handle.read())
print(my_seq)
print("")
print("SEQUENCE:")
print(my_seq.seq)
ID: HM122614.1
Name: HM122614
Description: Malus x domestica MYB domain class transcription factor (MYB1) mRNA, complete cds
Number of features: 3
/molecule_type=mRNA
/topology=linear
/data_file_division=HTC
/date=15-AUG-2010
/accessions=['HM122614']
/sequence_version=1
/keywords=['HTC']
/source=Malus domestica (apple)
/organism=Malus domestica
/taxonomy=['Eukaryota', 'Viridiplantae', 'Streptophyta', 'Embryophyta', 'Tracheophyta', 'Spermatophyta', 'Magnoliopsida', 'eudicotyledons', 'Gunneridae', 'Pentapetalae', 'rosids', 'fabids', 'Rosales', 'Rosaceae', 'Amygdaloideae', 'Maleae', 'Malus']
/references=[Reference(title='Transcription Factors in Apple', ...), Reference(title='The FruiTFul database; full length cDNAs of apple transcription factors', ...), Reference(title='Direct Submission', ...)]
Seq('TTTGGTCTGCTGGGTAGGTACTCATAAAAACAAACCAACCGAAGCCTCCGAACC...AAA')
SEQUENCE:
TTTGGTCTGCTGGGTAGGTACTCATAAAAACAAACCAACCGAAGCCTCCGAACCGACCACCAATGACGGCCCCAAACGGCGCCGTCCCCAAACAAGCCGACGACCGCCCCGGCACCGAGGCCGAGTTGAACGAGGGCGCAGTGCCCAACGGGAAAGTGAGGGGACCGTGGTCGCCCGAGGAGGACGCGGTGCTGAGCCGGCTCGTGAGCAACTTCGGGGCGAGGAATTGGAGCCTGATCGCCCGAGGAATTCCCGGACGGTCTGGGAAGTCGTGCCGGCTGAGGTGGTGTAATCAGCTTGACCCCTGCGTCAAGCGTAAACCCTTTTCTGAGGAAGAAGACCGTATTATAGTTTCAGCACATGCTATCCATGGGAACAAATGGGCAGTAATTGCAAAGCTTCTTCCAGGTAGAACAGATAACGGAATCAAGAACCATTGGAATTCTACACTAAGGCGCAAGTGCTTTGATAAAGGAAGGTTTAATACTGGACCTGGGGAAATGATGGAAGATGACACCTTTGACAGAAAAAATGCATCCTCAGAAGAAACCCTGTCAGTTGGGAATATCAGTTCATTCAAGACTCATGAAGGAAGAGAGGTCTTGATGGAAAATAGACCAAACCAGTTCGATGTAAGAAGTCATGCAAAGGAGGGCTCTGGCGCTGCCGAATCAAAGCACAATTCTACTCTTATTGCCGAGCCAAGAGACCATCCGACTCTCCAGTCCACCATTTGTTGTCCAGTGGCACGTGTTAGTGCATTTAGTGTTTATAACCGTCCAAGTGTTCCAGCAAATGCTTCATCGTTGTCAAGGACAGTCCCAAGTCATGGCCCTTTGGTCCCAATAACTAAACTAGATTTCGGCTTTGACAACTTCCTTGAAGGTGCATGCAATGAGCCTACGGTTCCTCAACGCTGTGGTCACGGTTGCTGTGATCGAATTGAGGGGCATTCTCAAAGCTCGTTGTTGGGGCCTGAGTTCGTTGAGTATGATGAGCCTCTCCCTTTCTCTAGCCACGAATTAATCTCCATTGCTACGGATTTGAACAAGATTGCATGGATTAAGGGTGGCCTTGAGAGTAATGGGATAAGGATGCCAGAGCACGTAGCAAGCCAGAGAGTCTTTCAAGCAGCTGCCACTACCTTGCAAATGGGGTTGCCAGCAAACACTCCGATGAATGACCATATGCGCTTTGAGGAAGGAAGAAACAAGTTGATGGGAATGATGACGGACGTGCTATCAACCCAGGTGCCTAGACAAACTTTTGCAATGCCAACTGAAGTTGAGGGATTGAGCTAGAACTCATGGCTGGTCTTCCTCAGTCTTCCGGGTGTTTCGGTTAATTTACAGCAGATTAAGTTGAAGTCTCCAGTTTCATTTAGAAGGCTTTTCACTTTTGACTTATCTCGTTTAAGAGGGCATTACATCAAAGATATATATGTAGGTACTTCTCTACCCCTTTTGTCATGAGCAAAGAAGCTGTTGACTAGTAAATGCTTTTATACAAGTGCTTTTATCTCAAATCCGAAAACATAATTGATAAAAAAAAAAAA
Getting data from ExPASy¶
Similarly to what done with Entrez, it is possible to pull data out of ExPASy (https://www.expasy.org/) through the Bio.ExPASy module. We will not cover this in detail. All information can be found here: Bio.ExPASy module.
As an example, we will see how to download a couple of SwissProt entries (the human, rhesus macaque and mouse P53 protein) and perform pairwise sequence alignment of Human vs Macaque and Human vs Mouse.
[8]:
from Bio import ExPASy
from Bio import SwissProt
from Bio import pairwise2
#the ids of the human, rhesus and mouse proteins
accessions = ["P04637", "P56424", "P02340"]
sequences = []
for accession in accessions:
handle = ExPASy.get_sprot_raw(accession)
record = SwissProt.read(handle)
print("Organism: {}".format(record.organism))
print(record.entry_name)
print(",".join(record.accessions))
print(record.keywords)
print(record.sequence[:30] + "...")
sequences.append(record.sequence)
print("\n\nPairwise sequence alignment of Human vs Rhesus P53:")
aligns = pairwise2.align.globalxx(sequences[0],sequences[1])
for al in aligns[0:3]:
print("Score {}:".format(al[2]))
print(al[0][0:50])
print(al[1][0:50])
print("\n\nPairwise sequence alignment of Human vs Mouse P53:")
aligns = pairwise2.align.globalxx(sequences[0],sequences[2])
for al in aligns[0:3]:
print("Score {}:".format(al[2]))
print(al[0][0:50])
print(al[1][0:50])
Organism: Homo sapiens (Human).
P53_HUMAN
P04637,Q15086,Q15087,Q15088,Q16535,Q16807,Q16808,Q16809,Q16810,Q16811,Q16848,Q2XN98,Q3LRW1,Q3LRW2,Q3LRW3,Q3LRW4,Q3LRW5,Q86UG1,Q8J016,Q99659,Q9BTM4,Q9HAQ8,Q9NP68,Q9NPJ2,Q9NZD0,Q9UBI2,Q9UQ61
['3D-structure', 'Acetylation', 'Activator', 'Alternative promoter usage', 'Alternative splicing', 'Apoptosis', 'Biological rhythms', 'Cell cycle', 'Cytoplasm', 'Cytoskeleton', 'Direct protein sequencing', 'Disease mutation', 'DNA-binding', 'Endoplasmic reticulum', 'Glycoprotein', 'Host-virus interaction', 'Isopeptide bond', 'Li-Fraumeni syndrome', 'Metal-binding', 'Methylation', 'Mitochondrion', 'Necrosis', 'Nucleus', 'Phosphoprotein', 'Polymorphism', 'Reference proteome', 'Repressor', 'Transcription', 'Transcription regulation', 'Tumor suppressor', 'Ubl conjugation', 'Zinc']
MEEPQSDPSVEPPLSQETFSDLWKLLPENN...
Organism: Macaca mulatta (Rhesus macaque).
P53_MACMU
P56424
['Acetylation', 'Activator', 'Apoptosis', 'Biological rhythms', 'Cell cycle', 'Cytoplasm', 'Cytoskeleton', 'DNA-binding', 'Endoplasmic reticulum', 'Isopeptide bond', 'Metal-binding', 'Methylation', 'Mitochondrion', 'Necrosis', 'Nucleus', 'Phosphoprotein', 'Reference proteome', 'Repressor', 'Transcription', 'Transcription regulation', 'Tumor suppressor', 'Ubl conjugation', 'Zinc']
MEEPQSDPSIEPPLSQETFSDLWKLLPENN...
Organism: Mus musculus (Mouse).
P53_MOUSE
P02340,Q9QUP3
['3D-structure', 'Acetylation', 'Activator', 'Apoptosis', 'Biological rhythms', 'Cell cycle', 'Cytoplasm', 'Cytoskeleton', 'Disease mutation', 'DNA-binding', 'Endoplasmic reticulum', 'Isopeptide bond', 'Metal-binding', 'Methylation', 'Mitochondrion', 'Necrosis', 'Nucleus', 'Phosphoprotein', 'Reference proteome', 'Repressor', 'Transcription', 'Transcription regulation', 'Tumor suppressor', 'Ubl conjugation', 'Zinc']
MTAMEESQSDISLELPLSQETFSGLWKLLP...
Pairwise sequence alignment of Human vs Rhesus P53:
Score 376.0:
MEEPQSDPSV-EPPLSQETFSDLWKLLPENNVLSPLPSQAM-DDLMLSPD
MEEPQSDPS-IEPPLSQETFSDLWKLLPENNVLSPLPSQA-VDDLMLSPD
Score 376.0:
MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAM-DDLMLSPDD
MEEPQSDPSIEPPLSQETFSDLWKLLPENNVLSPLPSQA-VDDLMLSPDD
Score 376.0:
MEEPQSDPSV-EPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDD
MEEPQSDPS-IEPPLSQETFSDLWKLLPENNVLSPLPSQAVDDLMLSPDD
Pairwise sequence alignment of Human vs Mouse P53:
Score 315.0:
M---EEP-QSDP-SV-EP-PLSQETFSD-LWKLLPENNVLSP---LPSQA
MTAMEE-SQSD-IS-LE-LPLSQETFS-GLWKLLP------PEDILPS--
Score 315.0:
---MEEP-QSDP-SV-EP-PLSQETFSD-LWKLLPENNVLSP---LPSQA
MTAMEE-SQSD-IS-LE-LPLSQETFS-GLWKLLP------PEDILPS--
Score 315.0:
M---EEPQSDP-SV-EP-PLSQETFSD-LWKLLPENNVLSP---LPSQA-
MTAMEESQSD-IS-LE-LPLSQETFS-GLWKLLP------PEDILPS--P
You can find here all the details on how to deal with the SwissProt records.
3D structure and PDB¶
Biopython can also deal with data coming from the Protein Data Bank database. It is a database of structural information of 3D shapes of proteins, nucleic acids, and complex assemblies. The database currently contains more than 157,000 total structures.
To deal with this kind of data we first need to import Biopython’s module Bio.PDB with from Bio.PDB import *. All the information on this module can be found here.
It is possible to download a structure directly from PDB by using a PDBList object that features a function called download_pdb_files having the basic syntax:
PDBList.download_pdb_files(pdb_codes, pdir, file_format)
that downloads the file_format formatted structures defined in the pdb_codes list of 4 symbols structure Ids from PDB, stores them in the directory pdir. The safer file_format to use is “mmCif”. The function will not download the structures more than once. If a file is already present in the specified directory, a message Structure exists will be displayed.
Example:
Let’s programmatically download two different structures of the DNA polymerase 3C2K and 3C2L
[9]:
from Bio.PDB import *
pdbl = PDBList()
structures = ["3C2K", "3C2L"]
el = pdbl.download_pdb_files(structures,
file_format = "mmCif",
pdir = "file_samples/")
Downloading PDB structure '3C2K'...
Downloading PDB structure '3C2L'...
Macromolecular Crystallographic Information Files (mmCif files .cif) is a paired collection of names (starting with “_”) and values.They also contain a description of the 3D placement of every crystalized atom of the structure. A detailed description of the format can be found here.
Once the structures are available locally, one can start parsing them to do something useful. Parsing can be done through the MMCIFParser object:
parser = MMCIFParser()
The parser object has several methods able to deal with structures. One of these is the get_structure that creates a PDB.Structure.Structure object with all the data present in the structure file.
The basic syntax is:
structure = parser.get_structure(pdb_code, filename)
where pdb_code is the PDB code of the structure contained in the file filename. The method returns a PDB.Structure.Structure that contains one or more models.
A Structure consists of a collection of one or more Model (different 3D conformations of the very same structure) that is a collection of Chain that is a collection of Residues that is a collection of Atoms. Look in the documentation to get the information on each of these classes. This is the diagram of a structure:
Given a Structure we can obtain iterators to models, chains, residues or atoms with:
Structure.get_models()
Structure.get_chains()
Structure.get_residues()
Structure.get_atoms()
For each model obtained with structure.get_models() function we can loop through its chains, residues and atoms. For atoms we can get the 3D coordinates with Atom.get_coord().
Example: Let’s loop through all the models, chain, residues and atoms of the DNA polymerase structure 3C2K. Print the 3D coordinates of each atom.
[10]:
from Bio.PDB import *
parser = MMCIFParser(QUIET=True) #To disable warnings
filename = "file_samples/3c2l.cif"
structure = parser.get_structure("3c2l", filename)
for model in structure.get_models():
print("model", model, "has {} chains".format(len(model)))
for chain in model:
print(" - chain ", chain, "has {} residues".format(len(chain)))
for residue in chain:
print (" - residue", residue.get_resname(), "has {} atoms".format(len(residue)))
for atom in residue:
x,y,z = atom.get_coord()
print(" - atom:", atom.get_name(), "x: {} y:{} z:{}".format(x,y,z))
model <Model id=0> has 4 chains
- chain <Chain id=T> has 41 residues
- residue DC has 16 atoms
- atom: O5' x: 30.740999221801758 y:-2.2209999561309814 z:16.618999481201172
- atom: C5' x: 31.167999267578125 y:-0.9599999785423279 z:16.062999725341797
- atom: C4' x: 29.996000289916992 y:-0.009999999776482582 z:15.932999610900879
- atom: O4' x: 28.96299934387207 y:-0.6069999933242798 z:15.107000350952148
- atom: C3' x: 29.320999145507812 y:0.38499999046325684 z:17.253000259399414
- atom: O3' x: 29.166000366210938 y:1.8140000104904175 z:17.327999114990234
- atom: C2' x: 27.96500015258789 y:-0.3019999861717224 z:17.187999725341797
- atom: C1' x: 27.701000213623047 y:-0.3490000069141388 z:15.692000389099121
- atom: N1 x: 26.76099967956543 y:-1.4010000228881836 z:15.24899959564209
- atom: C2 x: 25.65999984741211 y:-1.034000039100647 z:14.456999778747559
- atom: O2 x: 25.51300048828125 y:0.16200000047683716 z:14.140999794006348
- atom: N3 x: 24.78499984741211 y:-1.9910000562667847 z:14.057000160217285
- atom: C4 x: 24.97599983215332 y:-3.2660000324249268 z:14.414999961853027
- atom: N4 x: 24.086000442504883 y:-4.172999858856201 z:14.0
- atom: C5 x: 26.08799934387207 y:-3.6679999828338623 z:15.21399974822998
- atom: C6 x: 26.94700050354004 y:-2.7139999866485596 z:15.604000091552734
- residue DC has 19 atoms
- atom: P x: 28.641000747680664 y:2.5 z:18.69099998474121
- atom: OP1 x: 29.559999465942383 y:3.625 z:19.025999069213867
- atom: OP2 x: 28.385000228881836 y:1.4290000200271606 z:19.698999404907227
- atom: O5' x: 27.225000381469727 y:3.124000072479248 z:18.30299949645996
- atom: C5' x: 27.128999710083008 y:4.366000175476074 z:17.600000381469727
- atom: C4' x: 25.67799949645996 y:4.741000175476074 z:17.399999618530273
- atom: O4' x: 24.954999923706055 y:3.5789999961853027 z:16.92799949645996
- atom: C3' x: 24.93600082397461 y:5.171000003814697 z:18.663000106811523
- atom: O3' x: 23.81800079345703 y:5.980000019073486 z:18.29800033569336
- atom: C2' x: 24.413000106811523 y:3.8489999771118164 z:19.187999725341797
- atom: C1' x: 23.961999893188477 y:3.2190001010894775 z:17.882999420166016
- atom: N1 x: 23.832000732421875 y:1.7519999742507935 z:17.87299919128418
- atom: C2 x: 22.68899917602539 y:1.1799999475479126 z:17.298999786376953
- atom: O2 x: 21.812999725341797 y:1.9190000295639038 z:16.829999923706055
- atom: N3 x: 22.569000244140625 y:-0.16200000047683716 z:17.268999099731445
- atom: C4 x: 23.52899932861328 y:-0.9279999732971191 z:17.78700065612793
- atom: N4 x: 23.367000579833984 y:-2.252000093460083 z:17.738000869750977
- atom: C5 x: 24.697999954223633 y:-0.37400001287460327 z:18.3799991607666
- atom: C6 x: 24.808000564575195 y:0.9559999704360962 z:18.40399932861328
- residue DG has 22 atoms
- atom: P x: 23.493000030517578 y:7.309000015258789 z:19.131000518798828
- atom: OP1 x: 24.016000747680664 y:8.472999572753906 z:18.36199951171875
- atom: OP2 x: 23.934999465942383 y:7.0960001945495605 z:20.5310001373291
- atom: O5' x: 21.90399932861328 y:7.382999897003174 z:19.136999130249023
- atom: C5' x: 21.174999237060547 y:7.506999969482422 z:17.922000885009766
- atom: C4' x: 19.93899917602539 y:6.644999980926514 z:17.98200035095215
- atom: O4' x: 20.363000869750977 y:5.269000053405762 z:18.142000198364258
- atom: C3' x: 19.0310001373291 y:6.951000213623047 z:19.179000854492188
- atom: O3' x: 17.66200065612793 y:6.968999862670898 z:18.77199935913086
- atom: C2' x: 19.263999938964844 y:5.7769999504089355 z:20.11400032043457
- atom: C1' x: 19.552000045776367 y:4.665999889373779 z:19.12700080871582
- atom: N9 x: 20.26799964904785 y:3.5169999599456787 z:19.67300033569336
- atom: C8 x: 21.375 y:3.5269999504089355 z:20.490999221801758
- atom: N7 x: 21.760000228881836 y:2.3299999237060547 z:20.850000381469727
- atom: C5 x: 20.85700035095215 y:1.4789999723434448 z:20.225000381469727
- atom: C6 x: 20.763999938964844 y:0.06800000369548798 z:20.246999740600586
- atom: O6 x: 21.47800064086914 y:-0.7459999918937683 z:20.850000381469727
- atom: N1 x: 19.707000732421875 y:-0.382999986410141 z:19.465999603271484
- atom: C2 x: 18.85099983215332 y:0.4169999957084656 z:18.756000518798828
- atom: N2 x: 17.89900016784668 y:-0.20800000429153442 z:18.055999755859375
- atom: N3 x: 18.92099952697754 y:1.7330000400543213 z:18.733999252319336
- atom: C4 x: 19.940000534057617 y:2.194999933242798 z:19.485000610351562
- residue DA has 21 atoms
- atom: P x: 16.55500030517578 y:7.6579999923706055 z:19.7189998626709
- atom: OP1 x: 16.44099998474121 y:9.088000297546387 z:19.329999923706055
- atom: OP2 x: 16.868000030517578 y:7.307000160217285 z:21.135000228881836
- atom: O5' x: 15.189000129699707 y:6.940000057220459 z:19.316999435424805
- atom: C5' x: 14.980999946594238 y:6.421999931335449 z:18.000999450683594
- atom: C4' x: 13.972000122070312 y:5.296999931335449 z:18.041000366210938
- atom: O4' x: 14.60099983215332 y:4.105000019073486 z:18.56999969482422
- atom: C3' x: 12.777000427246094 y:5.566999912261963 z:18.947999954223633
- atom: O3' x: 11.604000091552734 y:4.940000057220459 z:18.440000534057617
- atom: C2' x: 13.196000099182129 y:4.954999923706055 z:20.273000717163086
- atom: C1' x: 14.07699966430664 y:3.7829999923706055 z:19.85700035095215
- atom: N9 x: 15.21399974822998 y:3.496999979019165 z:20.743000030517578
- atom: C8 x: 15.923999786376953 y:4.367000102996826 z:21.542999267578125
- atom: N7 x: 16.92300033569336 y:3.805999994277954 z:22.18000030517578
- atom: C5 x: 16.867000579833984 y:2.4760000705718994 z:21.781999588012695
- atom: C6 x: 17.660999298095703 y:1.3539999723434448 z:22.099000930786133
- atom: N6 x: 18.72599983215332 y:1.3949999809265137 z:22.900999069213867
- atom: N1 x: 17.31800079345703 y:0.1720000058412552 z:21.548999786376953
- atom: C2 x: 16.260000228881836 y:0.12600000202655792 z:20.73200035095215
- atom: N3 x: 15.449000358581543 y:1.1030000448226929 z:20.347999572753906
- atom: C4 x: 15.809000015258789 y:2.2679998874664307 z:20.913000106811523
- residue DC has 19 atoms
- atom: P x: 10.178999900817871 y:5.289999961853027 z:19.089000701904297
- atom: OP1 x: 9.128999710083008 y:5.105999946594238 z:18.054000854492188
- atom: OP2 x: 10.288999557495117 y:6.593999862670898 z:19.79800033569336
- atom: O5' x: 9.972999572753906 y:4.1579999923706055 z:20.18600082397461
- atom: C5' x: 9.642000198364258 y:2.8340001106262207 z:19.795000076293945
- atom: C4' x: 9.98900032043457 y:1.8619999885559082 z:20.893999099731445
- atom: O4' x: 11.369999885559082 y:1.9759999513626099 z:21.277000427246094
- atom: C3' x: 9.21500015258789 y:2.0450000762939453 z:22.19499969482422
- atom: O3' x: 8.050999641418457 y:1.2230000495910645 z:22.155000686645508
- atom: C2' x: 10.194000244140625 y:1.5709999799728394 z:23.26799964904785
- atom: C1' x: 11.472000122070312 y:1.246999979019165 z:22.483999252319336
- atom: N1 x: 12.76099967956543 y:1.5789999961853027 z:23.125999450683594
- atom: C2 x: 13.718000411987305 y:0.5619999766349792 z:23.277999877929688
- atom: O2 x: 13.458999633789062 y:-0.578000009059906 z:22.86400032043457
- atom: N3 x: 14.899999618530273 y:0.8500000238418579 z:23.868999481201172
- atom: C4 x: 15.147000312805176 y:2.0880000591278076 z:24.297000885009766
- atom: N4 x: 16.325000762939453 y:2.3239998817443848 z:24.8700008392334
- atom: C5 x: 14.196999549865723 y:3.1410000324249268 z:24.152000427246094
- atom: C6 x: 13.029999732971191 y:2.8459999561309814 z:23.56599998474121
- residue DC has 19 atoms
- atom: P x: 6.784999847412109 y:1.5880000591278076 z:23.06800079345703
- atom: OP1 x: 7.255000114440918 y:1.5880000591278076 z:24.479000091552734
- atom: OP2 x: 5.660999774932861 y:0.6949999928474426 z:22.66699981689453
- atom: O5' x: 6.434000015258789 y:3.0880000591278076 z:22.659000396728516
- atom: C5' x: 5.370999813079834 y:3.378000020980835 z:21.74799919128418
- atom: C4' x: 4.375999927520752 y:4.328000068664551 z:22.378000259399414
- atom: O4' x: 3.687000036239624 y:3.677000045776367 z:23.465999603271484
- atom: C3' x: 4.9770002365112305 y:5.60699987411499 z:22.972999572753906
- atom: O3' x: 4.706999778747559 y:6.71999979019165 z:22.107999801635742
- atom: C2' x: 4.288000106811523 y:5.76200008392334 z:24.326000213623047
- atom: C1' x: 3.2070000171661377 y:4.689000129699707 z:24.322999954223633
- atom: N1 x: 2.882999897003174 y:4.071000099182129 z:25.628000259399414
- atom: C2 x: 3.9179999828338623 y:3.555999994277954 z:26.45199966430664
- atom: O2 x: 5.10099983215332 y:3.6510000228881836 z:26.08799934387207
- atom: N3 x: 3.5899999141693115 y:2.9709999561309814 z:27.625
- atom: C4 x: 2.311000108718872 y:2.88700008392334 z:27.996999740600586
- atom: N4 x: 2.0390000343322754 y:2.2960000038146973 z:29.16200065612793
- atom: C5 x: 1.2519999742507935 y:3.4059998989105225 z:27.194000244140625
- atom: C6 x: 1.5789999961853027 y:3.9860000610351562 z:26.031999588012695
- residue DG has 22 atoms
- atom: P x: 5.339000225067139 y:8.164999961853027 z:22.430999755859375
- atom: OP1 x: 5.185999870300293 y:9.013999938964844 z:21.215999603271484
- atom: OP2 x: 6.695000171661377 y:7.960000038146973 z:23.01799964904785
- atom: O5' x: 4.388999938964844 y:8.75 z:23.570999145507812
- atom: C5' x: 2.9639999866485596 y:8.717000007629395 z:23.433000564575195
- atom: C4' x: 2.2890000343322754 y:8.987000465393066 z:24.761999130249023
- atom: O4' x: 2.5959999561309814 y:7.940000057220459 z:25.718000411987305
- atom: C3' x: 2.671999931335449 y:10.305999755859375 z:25.44499969482422
- atom: O3' x: 1.5190000534057617 y:10.883999824523926 z:26.075000762939453
- atom: C2' x: 3.6530001163482666 y:9.859000205993652 z:26.516000747680664
- atom: C1' x: 3.0190000534057617 y:8.543000221252441 z:26.93000030517578
- atom: N9 x: 3.871000051498413 y:7.5920000076293945 z:27.639999389648438
- atom: C8 x: 5.236999988555908 y:7.434000015258789 z:27.535999298095703
- atom: N7 x: 5.703999996185303 y:6.49399995803833 z:28.315000534057617
- atom: C5 x: 4.581999778747559 y:5.999000072479248 z:28.972000122070312
- atom: C6 x: 4.456999778747559 y:4.964000225067139 z:29.95199966430664
- atom: O6 x: 5.3429999351501465 y:4.252999782562256 z:30.444000244140625
- atom: N1 x: 3.134000062942505 y:4.795000076293945 z:30.350000381469727
- atom: C2 x: 2.063999891281128 y:5.514999866485596 z:29.8700008392334
- atom: N2 x: 0.8629999756813049 y:5.197000026702881 z:30.371000289916992
- atom: N3 x: 2.1649999618530273 y:6.474999904632568 z:28.964000701904297
- atom: C4 x: 3.443000078201294 y:6.664000034332275 z:28.562999725341797
- residue DC has 19 atoms
- atom: P x: 0.33799999952316284 y:11.519000053405762 z:25.18000030517578
- atom: OP1 x: 0.1550000011920929 y:10.725000381469727 z:23.934999465942383
- atom: OP2 x: 0.6060000061988831 y:12.97599983215332 z:25.08799934387207
- atom: O5' x: -0.9620000123977661 y:11.310999870300293 z:26.07699966430664
- atom: C5' x: -1.5479999780654907 y:10.01099967956543 z:26.243999481201172
- atom: C4' x: -2.0759999752044678 y:9.840999603271484 z:27.652999877929688
- atom: O4' x: -1.0989999771118164 y:9.121000289916992 z:28.450000762939453
- atom: C3' x: -2.3559999465942383 y:11.156999588012695 z:28.393999099731445
- atom: O3' x: -3.6589999198913574 y:11.140999794006348 z:28.993000030517578
- atom: C2' x: -1.2630000114440918 y:11.21500015258789 z:29.448999404907227
- atom: C1' x: -1.0080000162124634 y:9.743000030517578 z:29.716999053955078
- atom: N1 x: 0.3089999854564667 y:9.418000221252441 z:30.30299949645996
- atom: C2 x: 0.3610000014305115 y:8.574000358581543 z:31.42300033569336
- atom: O2 x: -0.6980000138282776 y:8.114999771118164 z:31.885000228881836
- atom: N3 x: 1.565000057220459 y:8.277999877929688 z:31.972000122070312
- atom: C4 x: 2.681999921798706 y:8.782999992370605 z:31.444000244140625
- atom: N4 x: 3.8420000076293945 y:8.456999778747559 z:32.00699996948242
- atom: C5 x: 2.6589999198913574 y:9.640000343322754 z:30.309999465942383
- atom: C6 x: 1.4630000591278076 y:9.928999900817871 z:29.774999618530273
- residue DG has 22 atoms
- atom: P x: -4.367000102996826 y:12.529000282287598 z:29.423999786376953
- atom: OP1 x: -5.24399995803833 y:12.972000122070312 z:28.31399917602539
- atom: OP2 x: -3.3519999980926514 y:13.472999572753906 z:29.975000381469727
- atom: O5' x: -5.328999996185303 y:12.105999946594238 z:30.618999481201172
- atom: C5' x: -5.7230000495910645 y:10.743000030517578 z:30.81599998474121
- atom: C4' x: -5.9730000495910645 y:10.482000350952148 z:32.2859992980957
- atom: O4' x: -4.754000186920166 y:10.02400016784668 z:32.917999267578125
- atom: C3' x: -6.394000053405762 y:11.713000297546387 z:33.08300018310547
- atom: O3' x: -7.164999961853027 y:11.305000305175781 z:34.207000732421875
- atom: C2' x: -5.059999942779541 y:12.281000137329102 z:33.53200149536133
- atom: C1' x: -4.284999847412109 y:11.005999565124512 z:33.8380012512207
- atom: N9 x: -2.8359999656677246 y:11.102999687194824 z:33.691001892089844
- atom: C8 x: -2.1500000953674316 y:11.842000007629395 z:32.762001037597656
- atom: N7 x: -0.8539999723434448 y:11.725000381469727 z:32.86600112915039
- atom: C5 x: -0.6690000295639038 y:10.854999542236328 z:33.930999755859375
- atom: C6 x: 0.5249999761581421 y:10.35200023651123 z:34.5099983215332
- atom: O6 x: 1.6929999589920044 y:10.571999549865723 z:34.17399978637695
- atom: N1 x: 0.25699999928474426 y:9.508999824523926 z:35.584999084472656
- atom: C2 x: -0.9919999837875366 y:9.182999610900879 z:36.04100036621094
- atom: N2 x: -1.0390000343322754 y:8.371000289916992 z:37.106998443603516
- atom: N3 x: -2.114000082015991 y:9.626999855041504 z:35.5
- atom: C4 x: -1.8799999952316284 y:10.461000442504883 z:34.457000732421875
- residue DC has 19 atoms
- atom: P x: -7.857999801635742 y:12.404000282287598 z:35.13100051879883
- atom: OP1 x: -9.21500015258789 y:11.907999992370605 z:35.45399856567383
- atom: OP2 x: -7.696000099182129 y:13.723999977111816 z:34.48099899291992
- atom: O5' x: -6.958000183105469 y:12.425999641418457 z:36.45100021362305
- atom: C5' x: -7.033999919891357 y:11.376999855041504 z:37.417999267578125
- atom: C4' x: -5.870999813079834 y:11.456999778747559 z:38.382999420166016
- atom: O4' x: -4.645999908447266 y:11.569000244140625 z:37.64799880981445
- atom: C3' x: -5.867000102996826 y:12.637999534606934 z:39.358001708984375
- atom: O3' x: -6.331999778747559 y:12.196000099182129 z:40.64400100708008
- atom: C2' x: -4.410999774932861 y:13.088000297546387 z:39.395999908447266
- atom: C1' x: -3.680999994277954 y:12.074999809265137 z:38.53200149536133
- atom: N1 x: -2.5789999961853027 y:12.61400032043457 z:37.72200012207031
- atom: C2 x: -1.2640000581741333 y:12.213000297546387 z:38.012001037597656
- atom: O2 x: -1.0640000104904175 y:11.440999984741211 z:38.959999084472656
- atom: N3 x: -0.24699999392032623 y:12.678999900817871 z:37.25299835205078
- atom: C4 x: -0.4959999918937683 y:13.519000053405762 z:36.24800109863281
- atom: N4 x: 0.5400000214576721 y:13.949999809265137 z:35.527000427246094
- atom: C5 x: -1.8209999799728394 y:13.954999923706055 z:35.93899917602539
- atom: C6 x: -2.822999954223633 y:13.482999801635742 z:36.69499969482422
- residue DA has 21 atoms
- atom: P x: -6.264999866485596 y:13.177000045776367 z:41.92599868774414
- atom: OP1 x: -7.065999984741211 y:12.534000396728516 z:43.00299835205078
- atom: OP2 x: -6.591000080108643 y:14.555000305175781 z:41.50400161743164
- atom: O5' x: -4.739999771118164 y:13.109999656677246 z:42.375999450683594
- atom: C5' x: -4.144000053405762 y:11.85200023651123 z:42.70800018310547
- atom: C4' x: -2.9830000400543213 y:12.027999877929688 z:43.66400146484375
- atom: O4' x: -1.7519999742507935 y:12.300000190734863 z:42.95500183105469
- atom: C3' x: -3.1029999256134033 y:13.125 z:44.70899963378906
- atom: O3' x: -2.431999921798706 y:12.666999816894531 z:45.887001037597656
- atom: C2' x: -2.390000104904175 y:14.291999816894531 z:44.04800033569336
- atom: C1' x: -1.2949999570846558 y:13.611000061035156 z:43.23400115966797
- atom: N9 x: -0.9739999771118164 y:14.23900032043457 z:41.952999114990234
- atom: C8 x: -1.8300000429153442 y:14.854999542236328 z:41.07400131225586
- atom: N7 x: -1.25 y:15.282999992370605 z:39.97800064086914
- atom: C5 x: 0.07800000160932541 y:14.930999755859375 z:40.14799880981445
- atom: C6 x: 1.2029999494552612 y:15.083999633789062 z:39.32500076293945
- atom: N6 x: 1.1610000133514404 y:15.645000457763672 z:38.11600112915039
- atom: N1 x: 2.38700008392334 y:14.62600040435791 z:39.78900146484375
- atom: C2 x: 2.4230000972747803 y:14.048999786376953 z:40.99599838256836
- atom: N3 x: 1.430999994277954 y:13.84000015258789 z:41.85900115966797
- atom: C4 x: 0.26899999380111694 y:14.305000305175781 z:41.36800003051758
- residue DT has 20 atoms
- atom: P x: -2.188999891281128 y:13.661999702453613 z:47.132999420166016
- atom: OP1 x: -2.315999984741211 y:12.843000411987305 z:48.37300109863281
- atom: OP2 x: -2.986999988555908 y:14.913000106811523 z:47.0
- atom: O5' x: -0.6570000052452087 y:14.04800033569336 z:46.965999603271484
- atom: C5' x: 0.3330000042915344 y:13.050999641418457 z:46.792999267578125
- atom: C4' x: 1.6670000553131104 y:13.706999778747559 z:46.54499816894531
- atom: O4' x: 1.6430000066757202 y:14.303999900817871 z:45.2239990234375
- atom: C3' x: 1.9980000257492065 y:14.854999542236328 z:47.505001068115234
- atom: O3' x: 3.4089999198913574 y:14.859000205993652 z:47.75600051879883
- atom: C2' x: 1.628999948501587 y:16.091999053955078 z:46.70199966430664
- atom: C1' x: 2.1050000190734863 y:15.644000053405762 z:45.33000183105469
- atom: N1 x: 1.6460000276565552 y:16.400999069213867 z:44.13199996948242
- atom: C2 x: 2.572999954223633 y:16.636999130249023 z:43.12900161743164
- atom: O2 x: 3.7309999465942383 y:16.2810001373291 z:43.194000244140625
- atom: N3 x: 2.0889999866485596 y:17.312999725341797 z:42.03900146484375
- atom: C4 x: 0.8059999942779541 y:17.77199935913086 z:41.84700012207031
- atom: O4 x: 0.5199999809265137 y:18.349000930786133 z:40.797000885009766
- atom: C5 x: -0.11999999731779099 y:17.506999969482422 z:42.948001861572266
- atom: C7 x: -1.534999966621399 y:17.979000091552734 z:42.840999603271484
- atom: C6 x: 0.3440000116825104 y:16.844999313354492 z:44.018001556396484
- residue DC has 19 atoms
- atom: P x: 3.9679999351501465 y:15.352999687194824 z:49.18199920654297
- atom: OP1 x: 4.440999984741211 y:14.140000343322754 z:49.9010009765625
- atom: OP2 x: 2.9700000286102295 y:16.26300048828125 z:49.823001861572266
- atom: O5' x: 5.254000186920166 y:16.208999633789062 z:48.83000183105469
- atom: C5' x: 6.129000186920166 y:15.824000358581543 z:47.78900146484375
- atom: C4' x: 6.697999954223633 y:17.05900001525879 z:47.137001037597656
- atom: O4' x: 5.788000106811523 y:17.520000457763672 z:46.10200119018555
- atom: C3' x: 6.85699987411499 y:18.238000869750977 z:48.10900115966797
- atom: O3' x: 8.050000190734863 y:18.95199966430664 z:47.797000885009766
- atom: C2' x: 5.665999889373779 y:19.121000289916992 z:47.775001525878906
- atom: C1' x: 5.61899995803833 y:18.917999267578125 z:46.27199935913086
- atom: N1 x: 4.400000095367432 y:19.339000701904297 z:45.55400085449219
- atom: C2 x: 4.5269999504089355 y:19.80699920654297 z:44.236000061035156
- atom: O2 x: 5.656000137329102 y:19.850000381469727 z:43.71200180053711
- atom: N3 x: 3.4189999103546143 y:20.195999145507812 z:43.56399917602539
- atom: C4 x: 2.2239999771118164 y:20.1200008392334 z:44.14899826049805
- atom: N4 x: 1.159999966621399 y:20.499000549316406 z:43.44300079345703
- atom: C5 x: 2.065999984741211 y:19.648000717163086 z:45.48500061035156
- atom: C6 x: 3.1689999103546143 y:19.274999618530273 z:46.145999908447266
- residue DA has 21 atoms
- atom: P x: 9.348999977111816 y:18.784000396728516 z:48.71699905395508
- atom: OP1 x: 9.670999526977539 y:17.33099937438965 z:48.79199981689453
- atom: OP2 x: 9.105999946594238 y:19.55500030517578 z:49.965999603271484
- atom: O5' x: 10.47599983215332 y:19.483999252319336 z:47.83599853515625
- atom: C5' x: 10.871000289916992 y:18.892000198364258 z:46.59400177001953
- atom: C4' x: 11.45199966430664 y:19.92099952697754 z:45.64799880981445
- atom: O4' x: 10.427000045776367 y:20.615999221801758 z:44.90599822998047
- atom: C3' x: 12.335000038146973 y:21.007999420166016 z:46.249000549316406
- atom: O3' x: 13.369999885559082 y:21.326000213623047 z:45.31800079345703
- atom: C2' x: 11.381999969482422 y:22.177000045776367 z:46.426998138427734
- atom: C1' x: 10.312000274658203 y:21.95800018310547 z:45.35599899291992
- atom: N9 x: 8.944000244140625 y:22.131000518798828 z:45.83399963378906
- atom: C8 x: 8.444000244140625 y:21.815000534057617 z:47.073001861572266
- atom: N7 x: 7.1620001792907715 y:22.04400062561035 z:47.196998596191406
- atom: C5 x: 6.795000076293945 y:22.551000595092773 z:45.95899963378906
- atom: C6 x: 5.565000057220459 y:22.979999542236328 z:45.452999114990234
- atom: N6 x: 4.434999942779541 y:22.95800018310547 z:46.16299819946289
- atom: N1 x: 5.5329999923706055 y:23.437000274658203 z:44.18199920654297
- atom: C2 x: 6.673999786376953 y:23.458999633789062 z:43.481998443603516
- atom: N3 x: 7.896999835968018 y:23.07699966430664 z:43.85300064086914
- atom: C4 x: 7.885000228881836 y:22.624000549316406 z:45.11600112915039
- residue DG has 22 atoms
- atom: P x: 14.439000129699707 y:22.465999603271484 z:45.67100143432617
- atom: OP1 x: 15.732000350952148 y:22.033000946044922 z:45.07500076293945
- atom: OP2 x: 14.36400032043457 y:22.801000595092773 z:47.12300109863281
- atom: O5' x: 13.901000022888184 y:23.725000381469727 z:44.86199951171875
- atom: C5' x: 13.479999542236328 y:23.606000900268555 z:43.500999450683594
- atom: C4' x: 12.72700023651123 y:24.849000930786133 z:43.0880012512207
- atom: O4' x: 11.375 y:24.797000885009766 z:43.606998443603516
- atom: C3' x: 13.336999893188477 y:26.138999938964844 z:43.637001037597656
- atom: O3' x: 13.461999893188477 y:27.09600067138672 z:42.59199905395508
- atom: C2' x: 12.329000473022461 y:26.611000061035156 z:44.67499923706055
- atom: C1' x: 11.03499984741211 y:26.066999435424805 z:44.11199951171875
- atom: N9 x: 9.951000213623047 y:25.892000198364258 z:45.073001861572266
- atom: C8 x: 10.029000282287598 y:25.426000595092773 z:46.36800003051758
- atom: N7 x: 8.871000289916992 y:25.405000686645508 z:46.97800064086914
- atom: C5 x: 7.974999904632568 y:25.875999450683594 z:46.02299880981445
- atom: C6 x: 6.565999984741211 y:26.079999923706055 z:46.090999603271484
- atom: O6 x: 5.789000034332275 y:25.85099983215332 z:47.0369987487793
- atom: N1 x: 6.070000171661377 y:26.593000411987305 z:44.902000427246094
- atom: C2 x: 6.811999797821045 y:26.860000610351562 z:43.779998779296875
- atom: N2 x: 6.139999866485596 y:27.356000900268555 z:42.720001220703125
- atom: N3 x: 8.112000465393066 y:26.660999298095703 z:43.69499969482422
- atom: C4 x: 8.626999855041504 y:26.17799949645996 z:44.845001220703125
- residue DC has 19 atoms
- atom: P x: 14.321999549865723 y:28.42799949645996 z:42.8380012512207
- atom: OP1 x: 15.064000129699707 y:28.68000030517578 z:41.57600021362305
- atom: OP2 x: 15.067000389099121 y:28.295000076293945 z:44.112998962402344
- atom: O5' x: 13.229000091552734 y:29.56800079345703 z:43.03499984741211
- atom: C5' x: 12.413000106811523 y:29.974000930786133 z:41.94300079345703
- atom: C4' x: 11.097000122070312 y:30.51300048828125 z:42.446998596191406
- atom: O4' x: 10.517000198364258 y:29.645000457763672 z:43.43600082397461
- atom: C3' x: 11.199999809265137 y:31.851999282836914 z:43.159000396728516
- atom: O3' x: 11.206000328063965 y:32.849998474121094 z:42.15399932861328
- atom: C2' x: 9.986000061035156 y:31.849000930786133 z:44.07699966430664
- atom: C1' x: 9.475000381469727 y:30.405000686645508 z:44.016998291015625
- atom: N1 x: 9.112000465393066 y:29.808000564575195 z:45.314998626708984
- atom: C2 x: 7.763000011444092 y:29.753999710083008 z:45.65299987792969
- atom: O2 x: 6.926000118255615 y:30.17300033569336 z:44.83599853515625
- atom: N3 x: 7.3979997634887695 y:29.2450008392334 z:46.8489990234375
- atom: C4 x: 8.324999809265137 y:28.78700065612793 z:47.6870002746582
- atom: N4 x: 7.909999847412109 y:28.29199981689453 z:48.85599899291992
- atom: C5 x: 9.71399974822998 y:28.812999725341797 z:47.36399841308594
- atom: C6 x: 10.059000015258789 y:29.32699966430664 z:46.17900085449219
- residue MN has 1 atoms
- atom: MN x: 23.54800033569336 y:1.0 z:22.975000381469727
- residue HOH has 1 atoms
- atom: O x: -0.03799999877810478 y:22.62299919128418 z:45.85499954223633
- residue HOH has 1 atoms
- atom: O x: -0.2680000066757202 y:6.394999980926514 z:26.27400016784668
- residue HOH has 1 atoms
- atom: O x: -2.617000102996826 y:17.14299964904785 z:38.38199996948242
- residue HOH has 1 atoms
- atom: O x: -2.8450000286102295 y:9.204000473022461 z:40.37200164794922
- residue HOH has 1 atoms
- atom: O x: -4.395999908447266 y:15.696999549865723 z:41.887001037597656
- residue HOH has 1 atoms
- atom: O x: 8.746000289916992 y:3.684000015258789 z:24.974000930786133
- residue HOH has 1 atoms
- atom: O x: 20.542999267578125 y:3.009999990463257 z:24.375
- residue HOH has 1 atoms
- atom: O x: -6.396999835968018 y:10.779000282287598 z:28.01799964904785
- residue HOH has 1 atoms
- atom: O x: -9.277000427246094 y:15.675000190734863 z:35.47200012207031
- residue HOH has 1 atoms
- atom: O x: 6.900000095367432 y:24.628000259399414 z:49.99599838256836
- residue HOH has 1 atoms
- atom: O x: 30.777999877929688 y:4.184000015258789 z:16.06800079345703
- residue HOH has 1 atoms
- atom: O x: 14.788999557495117 y:20.408000946044922 z:42.99700164794922
- residue HOH has 1 atoms
- atom: O x: -2.247999906539917 y:17.725000381469727 z:46.025001525878906
- residue HOH has 1 atoms
- atom: O x: 25.37700080871582 y:2.634999990463257 z:22.086999893188477
- residue HOH has 1 atoms
- atom: O x: 24.393999099731445 y:-1.1100000143051147 z:22.084999084472656
- residue HOH has 1 atoms
- atom: O x: 5.159999847412109 y:11.8100004196167 z:48.76900100708008
- residue HOH has 1 atoms
- atom: O x: -1.069000005722046 y:4.329999923706055 z:24.06399917602539
- residue HOH has 1 atoms
- atom: O x: -0.26600000262260437 y:7.039999961853027 z:23.948999404907227
- residue HOH has 1 atoms
- atom: O x: 7.377999782562256 y:9.512999534606934 z:17.650999069213867
- residue HOH has 1 atoms
- atom: O x: 9.468000411987305 y:9.222999572753906 z:19.29199981689453
- residue HOH has 1 atoms
- atom: O x: 10.92199993133545 y:19.01799964904785 z:41.494998931884766
- residue HOH has 1 atoms
- atom: O x: -5.491000175476074 y:14.925999641418457 z:35.11899948120117
- residue HOH has 1 atoms
- atom: O x: -8.88599967956543 y:16.402999877929688 z:38.94599914550781
- residue HOH has 1 atoms
- atom: O x: -9.723999977111816 y:17.750999450683594 z:33.974998474121094
- chain <Chain id=P> has 18 residues
- residue DG has 19 atoms
- atom: O5' x: -2.617000102996826 y:29.32900047302246 z:49.946998596191406
- atom: C5' x: -3.3010001182556152 y:30.40399932861328 z:49.26599884033203
- atom: C4' x: -2.434000015258789 y:30.941999435424805 z:48.154998779296875
- atom: O4' x: -1.0850000381469727 y:30.972999572753906 z:48.6510009765625
- atom: C3' x: -2.38700008392334 y:30.049999237060547 z:46.91699981689453
- atom: O3' x: -3.3589999675750732 y:30.52400016784668 z:45.96099853515625
- atom: C2' x: -0.9549999833106995 y:30.20599937438965 z:46.415000915527344
- atom: C1' x: -0.17599999904632568 y:30.812999725341797 z:47.584999084472656
- atom: N9 x: 0.9449999928474426 y:30.017000198364258 z:48.07699966430664
- atom: C8 x: 0.9980000257492065 y:29.2549991607666 z:49.22100067138672
- atom: N7 x: 2.1589999198913574 y:28.683000564575195 z:49.40299987792969
- atom: C5 x: 2.9100000858306885 y:29.089000701904297 z:48.3129997253418
- atom: C6 x: 4.244999885559082 y:28.812999725341797 z:47.972999572753906
- atom: O6 x: 5.076000213623047 y:28.15399932861328 z:48.59700012207031
- atom: N1 x: 4.5980000495910645 y:29.413999557495117 z:46.77299880981445
- atom: C2 x: 3.7769999504089355 y:30.197999954223633 z:46.01499938964844
- atom: N2 x: 4.291999816894531 y:30.69099998474121 z:44.88600158691406
- atom: N3 x: 2.5409998893737793 y:30.482999801635742 z:46.33399963378906
- atom: C4 x: 2.1710000038146973 y:29.89900016784668 z:47.481998443603516
- residue DC has 19 atoms
- atom: P x: -3.7049999237060547 y:29.652999877929688 z:44.64699935913086
- atom: OP1 x: -4.730999946594238 y:30.423999786376953 z:43.893001556396484
- atom: OP2 x: -3.9800000190734863 y:28.243000030517578 z:45.04199981689453
- atom: O5' x: -2.365999937057495 y:29.698999404907227 z:43.7859992980957
- atom: C5' x: -1.8380000591278076 y:30.945999145507812 z:43.33399963378906
- atom: C4' x: -0.75 y:30.716999053955078 z:42.310001373291016
- atom: O4' x: 0.4480000138282776 y:30.246000289916992 z:42.97100067138672
- atom: C3' x: -1.0950000286102295 y:29.672000885009766 z:41.250999450683594
- atom: O3' x: -0.6209999918937683 y:30.075000762939453 z:39.96699905395508
- atom: C2' x: -0.3880000114440918 y:28.417999267578125 z:41.731998443603516
- atom: C1' x: 0.8130000233650208 y:28.95599937438965 z:42.499000549316406
- atom: N1 x: 1.187000036239624 y:28.141000747680664 z:43.66999816894531
- atom: C2 x: 2.503999948501587 y:27.666000366210938 z:43.784000396728516
- atom: O2 x: 3.3299999237060547 y:27.927000045776367 z:42.89099884033203
- atom: N3 x: 2.8429999351501465 y:26.937000274658203 z:44.86800003051758
- atom: C4 x: 1.9320000410079956 y:26.677000045776367 z:45.81399917602539
- atom: N4 x: 2.319999933242798 y:25.972000122070312 z:46.88399887084961
- atom: C5 x: 0.5879999995231628 y:27.132999420166016 z:45.71099853515625
- atom: C6 x: 0.2630000114440918 y:27.854000091552734 z:44.63600158691406
- residue DT has 20 atoms
- atom: P x: -0.828000009059906 y:29.101999282836914 z:38.70800018310547
- atom: OP1 x: -0.8669999837875366 y:29.930999755859375 z:37.46799850463867
- atom: OP2 x: -1.9559999704360962 y:28.173999786376953 z:39.0099983215332
- atom: O5' x: 0.5260000228881836 y:28.270999908447266 z:38.683998107910156
- atom: C5' x: 1.777999997138977 y:28.93600082397461 z:38.53799819946289
- atom: C4' x: 2.8570001125335693 y:27.93600082397461 z:38.20399856567383
- atom: O4' x: 3.250999927520752 y:27.259000778198242 z:39.422000885009766
- atom: C3' x: 2.3949999809265137 y:26.836000442504883 z:37.24700164794922
- atom: O3' x: 3.496999979019165 y:26.400999069213867 z:36.444000244140625
- atom: C2' x: 1.9589999914169312 y:25.736000061035156 z:38.19599914550781
- atom: C1' x: 3.0169999599456787 y:25.868000030517578 z:39.27899932861328
- atom: N1 x: 2.696000099182129 y:25.316999435424805 z:40.617000579833984
- atom: C2 x: 3.7639999389648438 y:24.950000762939453 z:41.40399932861328
- atom: O2 x: 4.928999900817871 y:25.084999084472656 z:41.055999755859375
- atom: N3 x: 3.421999931335449 y:24.41900062561035 z:42.61800003051758
- atom: C4 x: 2.1570000648498535 y:24.222000122070312 z:43.119998931884766
- atom: O4 x: 2.010999917984009 y:23.68400001525879 z:44.21900177001953
- atom: C5 x: 1.0809999704360962 y:24.665000915527344 z:42.263999938964844
- atom: C7 x: -0.328000009059906 y:24.54599952697754 z:42.757999420166016
- atom: C6 x: 1.3980000019073486 y:25.173999786376953 z:41.064998626708984
- residue DG has 22 atoms
- atom: P x: 3.2839999198913574 y:26.125 z:34.874000549316406
- atom: OP1 x: 2.9730000495910645 y:27.427000045776367 z:34.23400115966797
- atom: OP2 x: 2.3570001125335693 y:24.972999572753906 z:34.70800018310547
- atom: O5' x: 4.7270002365112305 y:25.694000244140625 z:34.374000549316406
- atom: C5' x: 5.872000217437744 y:26.429000854492188 z:34.78499984741211
- atom: C4' x: 6.8429999351501465 y:25.516000747680664 z:35.494998931884766
- atom: O4' x: 6.228000164031982 y:24.899999618530273 z:36.65399932861328
- atom: C3' x: 7.355000019073486 y:24.358999252319336 z:34.64799880981445
- atom: O3' x: 8.71399974822998 y:24.148000717163086 z:35.01499938964844
- atom: C2' x: 6.465000152587891 y:23.198999404907227 z:35.07500076293945
- atom: C1' x: 6.324999809265137 y:23.479999542236328 z:36.55500030517578
- atom: N9 x: 5.156000137329102 y:22.92099952697754 z:37.22999954223633
- atom: C8 x: 3.8529999256134033 y:22.968000411987305 z:36.803001403808594
- atom: N7 x: 3.006999969482422 y:22.51300048828125 z:37.68600082397461
- atom: C5 x: 3.7990000247955322 y:22.11199951171875 z:38.75199890136719
- atom: C6 x: 3.437000036239624 y:21.558000564575195 z:40.00899887084961
- atom: O6 x: 2.309999942779541 y:21.3439998626709 z:40.45800018310547
- atom: N1 x: 4.552999973297119 y:21.260000228881836 z:40.77899932861328
- atom: C2 x: 5.854000091552734 y:21.476999282836914 z:40.400001525878906
- atom: N2 x: 6.788000106811523 y:21.107999801635742 z:41.284000396728516
- atom: N3 x: 6.209000110626221 y:22.014999389648438 z:39.24100112915039
- atom: C4 x: 5.132999897003174 y:22.309999465942383 z:38.47100067138672
- residue DA has 21 atoms
- atom: P x: 9.545999526977539 y:22.961999893188477 z:34.34600067138672
- atom: OP1 x: 10.937999725341797 y:23.468000411987305 z:34.21900177001953
- atom: OP2 x: 8.817999839782715 y:22.490999221801758 z:33.14099884033203
- atom: O5' x: 9.5 y:21.81399917602539 z:35.448001861572266
- atom: C5' x: 10.081000328063965 y:22.02400016784668 z:36.736000061035156
- atom: C4' x: 10.329000473022461 y:20.70199966430664 z:37.426998138427734
- atom: O4' x: 9.138999938964844 y:20.261999130249023 z:38.12099838256836
- atom: C3' x: 10.741000175476074 y:19.54400062561035 z:36.52299880981445
- atom: O3' x: 11.741999626159668 y:18.784000396728516 z:37.20500183105469
- atom: C2' x: 9.444000244140625 y:18.773000717163086 z:36.327999114990234
- atom: C1' x: 8.732000350952148 y:18.981000900268555 z:37.65599822998047
- atom: N9 x: 7.264999866485596 y:18.985000610351562 z:37.60900115966797
- atom: C8 x: 6.453999996185303 y:19.448999404907227 z:36.606998443603516
- atom: N7 x: 5.175000190734863 y:19.384000778198242 z:36.88800048828125
- atom: C5 x: 5.138000011444092 y:18.83099937438965 z:38.15700149536133
- atom: C6 x: 4.072999954223633 y:18.517000198364258 z:39.018001556396484
- atom: N6 x: 2.7899999618530273 y:18.732999801635742 z:38.7239990234375
- atom: N1 x: 4.375 y:17.97100067138672 z:40.21099853515625
- atom: C2 x: 5.659999847412109 y:17.757999420166016 z:40.50899887084961
- atom: N3 x: 6.749000072479248 y:18.011999130249023 z:39.78799819946289
- atom: C4 x: 6.415999889373779 y:18.558000564575195 z:38.606998443603516
- residue DT has 20 atoms
- atom: P x: 12.317000389099121 y:17.43600082397461 z:36.55500030517578
- atom: OP1 x: 13.734999656677246 y:17.33300018310547 z:36.98099899291992
- atom: OP2 x: 11.979999542236328 y:17.409000396728516 z:35.11199951171875
- atom: O5' x: 11.479000091552734 y:16.302000045776367 z:37.290000915527344
- atom: C5' x: 11.32800006866455 y:16.334999084472656 z:38.70600128173828
- atom: C4' x: 10.307000160217285 y:15.317999839782715 z:39.159000396728516
- atom: O4' x: 8.970999717712402 y:15.774999618530273 z:38.867000579833984
- atom: C3' x: 10.42199993133545 y:13.913000106811523 z:38.55099868774414
- atom: O3' x: 10.61299991607666 y:12.967000007629395 z:39.61199951171875
- atom: C2' x: 9.071999549865723 y:13.696999549865723 z:37.87799835205078
- atom: C1' x: 8.182999610900879 y:14.621000289916992 z:38.68199920654297
- atom: N1 x: 6.90500020980835 y:15.03499984741211 z:38.07099914550781
- atom: C2 x: 5.755000114440918 y:14.852999687194824 z:38.80699920654297
- atom: O2 x: 5.739999771118164 y:14.33899974822998 z:39.91299819946289
- atom: N3 x: 4.610000133514404 y:15.300000190734863 z:38.196998596191406
- atom: C4 x: 4.497000217437744 y:15.899999618530273 z:36.95600128173828
- atom: O4 x: 3.3940000534057617 y:16.273000717163086 z:36.55699920654297
- atom: C5 x: 5.741000175476074 y:16.042999267578125 z:36.229000091552734
- atom: C7 x: 5.723999977111816 y:16.673999786376953 z:34.87300109863281
- atom: C6 x: 6.864999771118164 y:15.604000091552734 z:36.8129997253418
- residue DG has 22 atoms
- atom: P x: 11.225000381469727 y:11.51099967956543 z:39.29899978637695
- atom: OP1 x: 12.70300006866455 y:11.628000259399414 z:39.255001068115234
- atom: OP2 x: 10.50100040435791 y:10.935999870300293 z:38.132999420166016
- atom: O5' x: 10.819999694824219 y:10.654000282287598 z:40.57899856567383
- atom: C5' x: 10.031000137329102 y:11.215999603271484 z:41.62900161743164
- atom: C4' x: 8.626999855041504 y:10.654999732971191 z:41.597999572753906
- atom: O4' x: 7.829999923706055 y:11.324000358581543 z:40.608001708984375
- atom: C3' x: 8.498000144958496 y:9.168999671936035 z:41.27399826049805
- atom: O3' x: 8.227999687194824 y:8.444999694824219 z:42.47800064086914
- atom: C2' x: 7.328999996185303 y:9.090999603271484 z:40.29499816894531
- atom: C1' x: 6.724999904632568 y:10.484000205993652 z:40.34600067138672
- atom: N9 x: 6.067999839782715 y:10.968999862670898 z:39.12699890136719
- atom: C8 x: 6.690000057220459 y:11.46500015258789 z:38.00699996948242
- atom: N7 x: 5.853000164031982 y:11.904000282287598 z:37.10599899291992
- atom: C5 x: 4.598999977111816 y:11.670999526977539 z:37.6510009765625
- atom: C6 x: 3.306999921798706 y:11.958000183105469 z:37.13800048828125
- atom: O6 x: 2.999000072479248 y:12.503999710083008 z:36.073001861572266
- atom: N1 x: 2.312000036239624 y:11.548999786376953 z:38.00899887084961
- atom: C2 x: 2.5190000534057617 y:10.954000473022461 z:39.215999603271484
- atom: N2 x: 1.4140000343322754 y:10.656999588012695 z:39.900001525878906
- atom: N3 x: 3.7149999141693115 y:10.678999900817871 z:39.7130012512207
- atom: C4 x: 4.704999923706055 y:11.067999839782715 z:38.88600158691406
- residue DC has 19 atoms
- atom: P x: 8.17199993133545 y:6.841000080108643 z:42.446998596191406
- atom: OP1 x: 8.222999572753906 y:6.381999969482422 z:43.845001220703125
- atom: OP2 x: 9.154999732971191 y:6.321000099182129 z:41.47800064086914
- atom: O5' x: 6.704999923706055 y:6.544000148773193 z:41.90299987792969
- atom: C5' x: 5.586999893188477 y:6.679999828338623 z:42.770999908447266
- atom: C4' x: 4.313000202178955 y:6.329999923706055 z:42.04499816894531
- atom: O4' x: 4.117000102996826 y:7.260000228881836 z:40.965999603271484
- atom: C3' x: 4.315999984741211 y:4.946000099182129 z:41.40299987792969
- atom: O3' x: 3.621000051498413 y:4.050000190734863 z:42.27799987792969
- atom: C2' x: 3.617000102996826 y:5.1479997634887695 z:40.055999755859375
- atom: C1' x: 3.2750000953674316 y:6.645999908447266 z:40.01100158691406
- atom: N1 x: 3.4820001125335693 y:7.343999862670898 z:38.71900177001953
- atom: C2 x: 2.378000020980835 y:7.947999954223633 z:38.071998596191406
- atom: O2 x: 1.2549999952316284 y:7.870999813079834 z:38.58700180053711
- atom: N3 x: 2.571000099182129 y:8.600000381469727 z:36.9109992980957
- atom: C4 x: 3.7929999828338623 y:8.67300033569336 z:36.38600158691406
- atom: N4 x: 3.941999912261963 y:9.338000297546387 z:35.24399948120117
- atom: C5 x: 4.923999786376953 y:8.069000244140625 z:37.013999938964844
- atom: C6 x: 4.724999904632568 y:7.420000076293945 z:38.16299819946289
- residue DG has 22 atoms
- atom: P x: 3.5369999408721924 y:2.490000009536743 z:41.92900085449219
- atom: OP1 x: 3.2130000591278076 y:1.7960000038146973 z:43.191001892089844
- atom: OP2 x: 4.730999946594238 y:2.0999999046325684 z:41.15800094604492
- atom: O5' x: 2.25 y:2.365000009536743 z:41.00199890136719
- atom: C5' x: 0.9470000267028809 y:2.680999994277954 z:41.50899887084961
- atom: C4' x: -0.08699999749660492 y:2.5480000972747803 z:40.415000915527344
- atom: O4' x: 0.22200000286102295 y:3.51200008392334 z:39.380001068115234
- atom: C3' x: -0.08799999952316284 y:1.1829999685287476 z:39.724998474121094
- atom: O3' x: -1.4179999828338623 y:0.8140000104904175 z:39.356998443603516
- atom: C2' x: 0.7760000228881836 y:1.4210000038146973 z:38.50400161743164
- atom: C1' x: 0.375 y:2.8369998931884766 z:38.14500045776367
- atom: N9 x: 1.3359999656677246 y:3.5820000171661377 z:37.33599853515625
- atom: C8 x: 2.7079999446868896 y:3.490000009536743 z:37.36399841308594
- atom: N7 x: 3.2909998893737793 y:4.26800012588501 z:36.49399948120117
- atom: C5 x: 2.243000030517578 y:4.920000076293945 z:35.858001708984375
- atom: C6 x: 2.259000062942505 y:5.873000144958496 z:34.814998626708984
- atom: O6 x: 3.2360000610351562 y:6.339000225067139 z:34.21500015258789
- atom: N1 x: 0.9739999771118164 y:6.2789998054504395 z:34.470001220703125
- atom: C2 x: -0.17900000512599945 y:5.818999767303467 z:35.04999923706055
- atom: N2 x: -1.3250000476837158 y:6.327000141143799 z:34.58100128173828
- atom: N3 x: -0.20900000631809235 y:4.921999931335449 z:36.020999908447266
- atom: C4 x: 1.031999945640564 y:4.517000198364258 z:36.37200164794922
- residue DC has 19 atoms
- atom: P x: -1.694000005722046 y:-0.6140000224113464 z:38.65599822998047
- atom: OP1 x: -2.994999885559082 y:-1.1480000019073486 z:39.14899826049805
- atom: OP2 x: -0.46000000834465027 y:-1.430999994277954 z:38.821998596191406
- atom: O5' x: -1.8730000257492065 y:-0.24400000274181366 z:37.11000061035156
- atom: C5' x: -2.808000087738037 y:0.7670000195503235 z:36.698001861572266
- atom: C4' x: -2.8580000400543213 y:0.8840000033378601 z:35.1879997253418
- atom: O4' x: -1.7769999504089355 y:1.7239999771118164 z:34.69900131225586
- atom: C3' x: -2.756999969482422 y:-0.4309999942779541 z:34.39899826049805
- atom: O3' x: -3.569999933242798 y:-0.4269999861717224 z:33.20000076293945
- atom: C2' x: -1.312000036239624 y:-0.4320000112056732 z:33.9370002746582
- atom: C1' x: -1.125 y:1.0440000295639038 z:33.637001037597656
- atom: N1 x: 0.2680000066757202 y:1.524999976158142 z:33.55699920654297
- atom: C2 x: 0.5590000152587891 y:2.6029999256134033 z:32.71099853515625
- atom: O2 x: -0.36800000071525574 y:3.1510000228881836 z:32.09000015258789
- atom: N3 x: 1.8370000123977661 y:3.0220000743865967 z:32.59600067138672
- atom: C4 x: 2.8010001182556152 y:2.4200000762939453 z:33.29399871826172
- atom: N4 x: 4.046999931335449 y:2.8559999465942383 z:33.137001037597656
- atom: C5 x: 2.5299999713897705 y:1.3420000076293945 z:34.178001403808594
- atom: C6 x: 1.2660000324249268 y:0.9300000071525574 z:34.27899932861328
- residue MN has 1 atoms
- atom: MN x: -0.07199999690055847 y:21.77899932861328 z:37.319000244140625
- residue HOH has 1 atoms
- atom: O x: 6.046000003814697 y:3.1649999618530273 z:39.082000732421875
- residue HOH has 1 atoms
- atom: O x: 13.569999694824219 y:10.14799976348877 z:41.25299835205078
- residue HOH has 1 atoms
- atom: O x: -5.609000205993652 y:-0.41600000858306885 z:34.5
- residue HOH has 1 atoms
- atom: O x: 4.633999824523926 y:30.27400016784668 z:40.766998291015625
- residue HOH has 1 atoms
- atom: O x: -5.763999938964844 y:33.71799850463867 z:44.33599853515625
- residue HOH has 1 atoms
- atom: O x: 2.937000036239624 y:31.315000534057617 z:42.645999908447266
- residue HOH has 1 atoms
- atom: O x: 7.23199987411499 y:5.645999908447266 z:38.564998626708984
- chain <Chain id=D> has 9 residues
- residue DG has 23 atoms
- atom: OP3 x: 21.908000946044922 y:-5.788000106811523 z:31.12700080871582
- atom: P x: 22.32200050354004 y:-5.873000144958496 z:29.663000106811523
- atom: OP1 x: 23.104999542236328 y:-4.658999919891357 z:29.17799949645996
- atom: OP2 x: 22.988000869750977 y:-7.199999809265137 z:29.34600067138672
- atom: O5' x: 20.930999755859375 y:-5.881999969482422 z:28.815000534057617
- atom: C5' x: 19.81999969482422 y:-6.675000190734863 z:29.256000518798828
- atom: C4' x: 19.066999435424805 y:-7.238999843597412 z:28.073999404907227
- atom: O4' x: 18.231000900268555 y:-6.247000217437744 z:27.457000732421875
- atom: C3' x: 19.908000946044922 y:-7.807000160217285 z:26.941999435424805
- atom: O3' x: 19.149999618530273 y:-8.842000007629395 z:26.315000534057617
- atom: C2' x: 20.09000015258789 y:-6.60699987411499 z:26.030000686645508
- atom: C1' x: 18.798999786376953 y:-5.822999954223633 z:26.229999542236328
- atom: N9 x: 18.93199920654297 y:-4.373000144958496 z:26.301000595092773
- atom: C8 x: 19.9060001373291 y:-3.635999917984009 z:26.934999465942383
- atom: N7 x: 19.700000762939453 y:-2.3499999046325684 z:26.86199951171875
- atom: C5 x: 18.525999069213867 y:-2.2360000610351562 z:26.134000778198242
- atom: C6 x: 17.79400062561035 y:-1.0950000286102295 z:25.75200080871582
- atom: O6 x: 18.014999389648438 y:0.0860000029206276 z:26.02899932861328
- atom: N1 x: 16.68000030517578 y:-1.4359999895095825 z:24.983999252319336
- atom: C2 x: 16.304000854492188 y:-2.7179999351501465 z:24.660999298095703
- atom: N2 x: 15.206000328063965 y:-2.86299991607666 z:23.91699981689453
- atom: N3 x: 16.96299934387207 y:-3.7890000343322754 z:25.04400062561035
- atom: C4 x: 18.05699920654297 y:-3.4769999980926514 z:25.764999389648438
- residue DT has 20 atoms
- atom: P x: 19.722999572753906 y:-9.595000267028809 z:25.020999908447266
- atom: OP1 x: 19.643999099731445 y:-11.03600025177002 z:25.367000579833984
- atom: OP2 x: 21.0049991607666 y:-9.012999534606934 z:24.559999465942383
- atom: O5' x: 18.625999450683594 y:-9.286999702453613 z:23.91699981689453
- atom: C5' x: 17.94099998474121 y:-8.050000190734863 z:23.905000686645508
- atom: C4' x: 17.011999130249023 y:-7.999000072479248 z:22.722000122070312
- atom: O4' x: 16.64699935913086 y:-6.625 z:22.472999572753906
- atom: C3' x: 17.648000717163086 y:-8.508000373840332 z:21.43199920654297
- atom: O3' x: 16.665000915527344 y:-9.154999732971191 z:20.62299919128418
- atom: C2' x: 18.21299934387207 y:-7.251999855041504 z:20.790000915527344
- atom: C1' x: 17.34600067138672 y:-6.119999885559082 z:21.343000411987305
- atom: N1 x: 18.05500030517578 y:-4.886000156402588 z:21.767000198364258
- atom: C2 x: 17.41699981689453 y:-3.680999994277954 z:21.559999465942383
- atom: O2 x: 16.343000411987305 y:-3.5769999027252197 z:20.979000091552734
- atom: N3 x: 18.089000701904297 y:-2.5910000801086426 z:22.051000595092773
- atom: C4 x: 19.31100082397461 y:-2.578000068664551 z:22.687000274658203
- atom: O4 x: 19.77400016784668 y:-1.5240000486373901 z:23.097999572753906
- atom: C5 x: 19.947999954223633 y:-3.859999895095825 z:22.822999954223633
- atom: C7 x: 21.301000595092773 y:-3.927000045776367 z:23.461000442504883
- atom: C6 x: 19.29599952697754 y:-4.940000057220459 z:22.368000030517578
- residue DC has 19 atoms
- atom: P x: 17.084999084472656 y:-9.819999694824219 z:19.219999313354492
- atom: OP1 x: 16.177000045776367 y:-10.982000350952148 z:18.999000549316406
- atom: OP2 x: 18.55699920654297 y:-10.012999534606934 z:19.167999267578125
- atom: O5' x: 16.697999954223633 y:-8.699999809265137 z:18.16200065612793
- atom: C5' x: 15.357000350952148 y:-8.246999740600586 z:18.04599952697754
- atom: C4' x: 15.291000366210938 y:-7.078000068664551 z:17.093000411987305
- atom: O4' x: 15.998000144958496 y:-5.955999851226807 z:17.679000854492188
- atom: C3' x: 15.972000122070312 y:-7.322999954223633 z:15.744999885559082
- atom: O3' x: 15.348999977111816 y:-6.510000228881836 z:14.746000289916992
- atom: C2' x: 17.37299919128418 y:-6.801000118255615 z:15.98900032043457
- atom: C1' x: 17.03700065612793 y:-5.560999870300293 z:16.798999786376953
- atom: N1 x: 18.117000579833984 y:-4.954999923706055 z:17.600000381469727
- atom: C2 x: 18.066999435424805 y:-3.5810000896453857 z:17.847000122070312
- atom: O2 x: 17.121999740600586 y:-2.9189999103546143 z:17.381999969482422
- atom: N3 x: 19.047000885009766 y:-3.00600004196167 z:18.57200050354004
- atom: C4 x: 20.05699920654297 y:-3.744999885559082 z:19.03499984741211
- atom: N4 x: 21.01300048828125 y:-3.13100004196167 z:19.738000869750977
- atom: C5 x: 20.13599967956543 y:-5.1479997634887695 z:18.79599952697754
- atom: C6 x: 19.152999877929688 y:-5.706999778747559 z:18.086000442504883
- residue DG has 22 atoms
- atom: P x: 15.234000205993652 y:-7.048999786376953 z:13.239999771118164
- atom: OP1 x: 14.206999778747559 y:-8.126999855041504 z:13.246000289916992
- atom: OP2 x: 16.608999252319336 y:-7.3379998207092285 z:12.744999885559082
- atom: O5' x: 14.673999786376953 y:-5.798999786376953 z:12.423999786376953
- atom: C5' x: 13.835000038146973 y:-4.823999881744385 z:13.045000076293945
- atom: C4' x: 14.350000381469727 y:-3.431999921798706 z:12.758999824523926
- atom: O4' x: 15.515000343322754 y:-3.1540000438690186 z:13.57800006866455
- atom: C3' x: 14.777999877929688 y:-3.1989998817443848 z:11.3100004196167
- atom: O3' x: 14.291000366210938 y:-1.9329999685287476 z:10.85200023651123
- atom: C2' x: 16.29599952697754 y:-3.2109999656677246 z:11.37399959564209
- atom: C1' x: 16.589000701904297 y:-2.687999963760376 z:12.770999908447266
- atom: N9 x: 17.82900047302246 y:-3.2009999752044678 z:13.35200023651123
- atom: C8 x: 18.270000457763672 y:-4.50600004196167 z:13.321000099182129
- atom: N7 x: 19.4060001373291 y:-4.679999828338623 z:13.937999725341797
- atom: C5 x: 19.740999221801758 y:-3.4179999828338623 z:14.406999588012695
- atom: C6 x: 20.8700008392334 y:-2.99399995803833 z:15.142999649047852
- atom: O6 x: 21.81599998474121 y:-3.6710000038146973 z:15.54800033569336
- atom: N1 x: 20.833999633789062 y:-1.628999948501587 z:15.395999908447266
- atom: C2 x: 19.836000442504883 y:-0.7789999842643738 z:14.994000434875488
- atom: N2 x: 19.996999740600586 y:0.5090000033378601 z:15.331999778747559
- atom: N3 x: 18.766000747680664 y:-1.1640000343322754 z:14.309000015258789
- atom: C4 x: 18.785999298095703 y:-2.489000082015991 z:14.050000190734863
- residue DG has 22 atoms
- atom: P x: 14.321999549865723 y:-1.5820000171661377 z:9.281999588012695
- atom: OP1 x: 13.01200008392334 y:-0.9649999737739563 z:8.95199966430664
- atom: OP2 x: 14.77400016784668 y:-2.7820000648498535 z:8.529999732971191
- atom: O5' x: 15.46500015258789 y:-0.47600001096725464 z:9.168999671936035
- atom: C5' x: 15.302000045776367 y:0.796999990940094 z:9.78600025177002
- atom: C4' x: 16.645999908447266 y:1.4179999828338623 z:10.090999603271484
- atom: O4' x: 17.479999542236328 y:0.46399998664855957 z:10.789999961853027
- atom: C3' x: 17.46299934387207 y:1.8680000305175781 z:8.876999855041504
- atom: O3' x: 18.23699951171875 y:3.005000114440918 z:9.279000282287598
- atom: C2' x: 18.448999404907227 y:0.7289999723434448 z:8.701000213623047
- atom: C1' x: 18.743999481201172 y:0.4269999861717224 z:10.154000282287598
- atom: N9 x: 19.35700035095215 y:-0.8669999837875366 z:10.437000274658203
- atom: C8 x: 18.961999893188477 y:-2.0980000495910645 z:9.970000267028809
- atom: N7 x: 19.707000732421875 y:-3.0769999027252197 z:10.41100025177002
- atom: C5 x: 20.650999069213867 y:-2.4560000896453857 z:11.215999603271484
- atom: C6 x: 21.711999893188477 y:-3.006999969482422 z:11.972000122070312
- atom: O6 x: 22.041000366210938 y:-4.203999996185303 z:12.086999893188477
- atom: N1 x: 22.422000885009766 y:-2.015000104904175 z:12.651000022888184
- atom: C2 x: 22.142000198364258 y:-0.6679999828338623 z:12.607999801635742
- atom: N2 x: 22.93899917602539 y:0.13600000739097595 z:13.335000038146973
- atom: N3 x: 21.152999877929688 y:-0.1459999978542328 z:11.904999732971191
- atom: C4 x: 20.45199966430664 y:-1.090000033378601 z:11.239999771118164
- residue HOH has 1 atoms
- atom: O x: 18.135000228881836 y:3.9839999675750732 z:12.008999824523926
- residue HOH has 1 atoms
- atom: O x: 13.862000465393066 y:-5.619999885559082 z:23.08300018310547
- residue HOH has 1 atoms
- atom: O x: 21.132999420166016 y:-7.02400016784668 z:13.020999908447266
- residue HOH has 1 atoms
- atom: O x: 24.173999786376953 y:-5.079999923706055 z:33.534000396728516
- chain <Chain id=A> has 427 residues
- residue THR has 7 atoms
- atom: N x: 3.50600004196167 y:-24.027999877929688 z:29.959999084472656
- atom: CA x: 4.690999984741211 y:-23.68400001525879 z:30.798999786376953
- atom: C x: 5.771999835968018 y:-24.729000091552734 z:30.599000930786133
- atom: O x: 6.264999866485596 y:-25.347000122070312 z:31.542999267578125
- atom: CB x: 4.321000099182129 y:-23.61400032043457 z:32.292999267578125
- atom: OG1 x: 4.0879998207092285 y:-24.940000534057617 z:32.81100082397461
- atom: CG2 x: 3.069000005722046 y:-22.75 z:32.46699905395508
- residue LEU has 8 atoms
- atom: N x: 6.114999771118164 y:-24.933000564575195 z:29.336999893188477
- atom: CA x: 7.14900016784668 y:-25.878000259399414 z:28.98900032043457
- atom: C x: 8.472999572753906 y:-25.23200035095215 z:29.381999969482422
- atom: O x: 9.387999534606934 y:-25.909000396728516 z:29.861000061035156
- atom: CB x: 7.109000205993652 y:-26.163999557495117 z:27.488000869750977
- atom: CG x: 5.886000156402588 y:-26.91900062561035 z:26.95199966430664
- atom: CD1 x: 6.002999782562256 y:-27.079999923706055 z:25.44099998474121
- atom: CD2 x: 5.789999961853027 y:-28.275999069213867 z:27.613000869750977
- residue ASN has 8 atoms
- atom: N x: 8.552000045776367 y:-23.913999557495117 z:29.201000213623047
- atom: CA x: 9.74899959564209 y:-23.145999908447266 z:29.527999877929688
- atom: C x: 9.545999526977539 y:-22.253000259399414 z:30.756999969482422
- atom: O x: 10.102999687194824 y:-21.159000396728516 z:30.836000442504883
- atom: CB x: 10.137999534606934 y:-22.27899932861328 z:28.33799934387207
- atom: CG x: 10.458000183105469 y:-23.090999603271484 z:27.111000061035156
- atom: OD1 x: 11.486000061035156 y:-23.759000778198242 z:27.051000595092773
- atom: ND2 x: 9.572999954223633 y:-23.04400062561035 z:26.121000289916992
- residue GLY has 4 atoms
- atom: N x: 8.763999938964844 y:-22.740999221801758 z:31.716999053955078
- atom: CA x: 8.47599983215332 y:-21.97800064086914 z:32.922000885009766
- atom: C x: 9.657999992370605 y:-21.47800064086914 z:33.73500061035156
- atom: O x: 9.645999908447266 y:-20.341999053955078 z:34.20500183105469
- residue GLY has 4 atoms
- atom: N x: 10.67199993133545 y:-22.316999435424805 z:33.91999816894531
- atom: CA x: 11.829999923706055 y:-21.899999618530273 z:34.689998626708984
- atom: C x: 12.550999641418457 y:-20.709999084472656 z:34.073001861572266
- atom: O x: 13.067000389099121 y:-19.834999084472656 z:34.7869987487793
- residue ILE has 8 atoms
- atom: N x: 12.583999633789062 y:-20.67799949645996 z:32.74399948120117
- atom: CA x: 13.246000289916992 y:-19.611000061035156 z:32.01900100708008
- atom: C x: 12.480999946594238 y:-18.308000564575195 z:32.0890007019043
- atom: O x: 13.067999839782715 y:-17.257999420166016 z:32.32899856567383
- atom: CB x: 13.434000015258789 y:-19.965999603271484 z:30.530000686645508
- atom: CG1 x: 14.45300006866455 y:-21.104000091552734 z:30.38800048828125
- atom: CG2 x: 13.859999656677246 y:-18.719999313354492 z:29.7450008392334
- atom: CD1 x: 14.708000183105469 y:-21.54400062561035 z:28.957000732421875
- residue THR has 7 atoms
- atom: N x: 11.17199993133545 y:-18.36400032043457 z:31.886999130249023
- atom: CA x: 10.392000198364258 y:-17.139999389648438 z:31.91200065612793
- atom: C x: 10.234000205993652 y:-16.545000076293945 z:33.3129997253418
- atom: O x: 9.973999977111816 y:-15.357000350952148 z:33.44300079345703
- atom: CB x: 9.015999794006348 y:-17.327999114990234 z:31.190000534057617
- atom: OG1 x: 8.112000465393066 y:-18.10099983215332 z:31.989999771118164
- atom: CG2 x: 9.234999656677246 y:-18.034000396728516 z:29.868000030517578
- residue ASP has 8 atoms
- atom: N x: 10.395000457763672 y:-17.35700035095215 z:34.356998443603516
- atom: CA x: 10.33899974822998 y:-16.850000381469727 z:35.73699951171875
- atom: C x: 11.638999938964844 y:-16.07200050354004 z:35.959999084472656
- atom: O x: 11.659000396728516 y:-14.982999801635742 z:36.53799819946289
- atom: CB x: 10.298999786376953 y:-17.98699951171875 z:36.75400161743164
- atom: CG x: 8.946999549865723 y:-18.631000518798828 z:36.85300064086914
- atom: OD1 x: 7.943999767303467 y:-17.89299964904785 z:36.93299865722656
- atom: OD2 x: 8.88599967956543 y:-19.878000259399414 z:36.87099838256836
- residue MET has 8 atoms
- atom: N x: 12.729999542236328 y:-16.667999267578125 z:35.49599838256836
- atom: CA x: 14.029999732971191 y:-16.049999237060547 z:35.595001220703125
- atom: C x: 13.96500015258789 y:-14.680999755859375 z:34.904998779296875
- atom: O x: 14.3149995803833 y:-13.659000396728516 z:35.48699951171875
- atom: CB x: 15.060999870300293 y:-16.926000595092773 z:34.89899826049805
- atom: CG x: 16.468000411987305 y:-16.416000366210938 z:35.000999450683594
- atom: SD x: 17.45599937438965 y:-17.030000686645508 z:33.643001556396484
- atom: CE x: 18.0049991607666 y:-15.479999542236328 z:32.88600158691406
- residue LEU has 8 atoms
- atom: N x: 13.51099967956543 y:-14.67199993133545 z:33.659000396728516
- atom: CA x: 13.411999702453613 y:-13.447999954223633 z:32.88999938964844
- atom: C x: 12.569999694824219 y:-12.394000053405762 z:33.59400177001953
- atom: O x: 12.833000183105469 y:-11.189000129699707 z:33.472999572753906
- atom: CB x: 12.795000076293945 y:-13.741000175476074 z:31.5310001373291
- atom: CG x: 13.562000274658203 y:-14.668999671936035 z:30.604000091552734
- atom: CD1 x: 12.758000373840332 y:-14.875 z:29.336999893188477
- atom: CD2 x: 14.91100025177002 y:-14.074000358581543 z:30.27899932861328
- residue THR has 7 atoms
- atom: N x: 11.553000450134277 y:-12.848999977111816 z:34.323001861572266
- atom: CA x: 10.657999992370605 y:-11.9399995803833 z:35.02000045776367
- atom: C x: 11.28600025177002 y:-11.27299976348877 z:36.21799850463867
- atom: O x: 11.097000122070312 y:-10.074999809265137 z:36.4109992980957
- atom: CB x: 9.369000434875488 y:-12.640999794006348 z:35.45600128173828
- atom: OG1 x: 8.581999778747559 y:-12.916000366210938 z:34.29399871826172
- atom: CG2 x: 8.564000129699707 y:-11.765999794006348 z:36.387001037597656
- residue GLU has 9 atoms
- atom: N x: 12.020999908447266 y:-12.038000106811523 z:37.02199935913086
- atom: CA x: 12.682999610900879 y:-11.47599983215332 z:38.189998626708984
- atom: C x: 13.690999984741211 y:-10.45199966430664 z:37.67300033569336
- atom: O x: 13.807000160217285 y:-9.345000267028809 z:38.196998596191406
- atom: CB x: 13.37399959564209 y:-12.588000297546387 z:38.98899841308594
- atom: CG x: 14.23799991607666 y:-12.11400032043457 z:40.15599822998047
- atom: CD x: 14.40999984741211 y:-13.187000274658203 z:41.233001708984375
- atom: OE1 x: 14.732999801635742 y:-14.33899974822998 z:40.88600158691406
- atom: OE2 x: 14.22599983215332 y:-12.878000259399414 z:42.43600082397461
- residue LEU has 8 atoms
- atom: N x: 14.407999992370605 y:-10.817999839782715 z:36.62200164794922
- atom: CA x: 15.376999855041504 y:-9.906000137329102 z:36.029998779296875
- atom: C x: 14.710000038146973 y:-8.588000297546387 z:35.63999938964844
- atom: O x: 15.276000022888184 y:-7.519999980926514 z:35.840999603271484
- atom: CB x: 16.006000518798828 y:-10.550999641418457 z:34.801998138427734
- atom: CG x: 17.10099983215332 y:-11.543000221252441 z:35.15599822998047
- atom: CD1 x: 17.541000366210938 y:-12.317999839782715 z:33.928001403808594
- atom: CD2 x: 18.26300048828125 y:-10.758000373840332 z:35.744998931884766
- residue ALA has 5 atoms
- atom: N x: 13.50100040435791 y:-8.6850004196167 z:35.09000015258789
- atom: CA x: 12.727999687194824 y:-7.525000095367432 z:34.66899871826172
- atom: C x: 12.454999923706055 y:-6.618000030517578 z:35.85900115966797
- atom: O x: 12.86400032043457 y:-5.453999996185303 z:35.887001037597656
- atom: CB x: 11.416000366210938 y:-7.9730000495910645 z:34.04499816894531
- residue ASN has 8 atoms
- atom: N x: 11.75100040435791 y:-7.1519999504089355 z:36.84299850463867
- atom: CA x: 11.447999954223633 y:-6.377999782562256 z:38.02799987792969
- atom: C x: 12.694999694824219 y:-5.685999870300293 z:38.54800033569336
- atom: O x: 12.654999732971191 y:-4.507999897003174 z:38.917999267578125
- atom: CB x: 10.857000350952148 y:-7.275000095367432 z:39.09700012207031
- atom: CG x: 9.361000061035156 y:-7.355999946594238 z:38.999000549316406
- atom: OD1 x: 8.668000221252441 y:-6.34499979019165 z:39.154998779296875
- atom: ND2 x: 8.843999862670898 y:-8.548999786376953 z:38.73500061035156
- residue PHE has 11 atoms
- atom: N x: 13.807000160217285 y:-6.414000034332275 z:38.56399917602539
- atom: CA x: 15.053000450134277 y:-5.831999778747559 z:39.0260009765625
- atom: C x: 15.369000434875488 y:-4.565999984741211 z:38.233001708984375
- atom: O x: 15.411999702453613 y:-3.4700000286102295 z:38.79100036621094
- atom: CB x: 16.20800018310547 y:-6.817999839782715 z:38.86600112915039
- atom: CG x: 17.55500030517578 y:-6.203999996185303 z:39.13100051879883
- atom: CD1 x: 18.569000244140625 y:-6.275000095367432 z:38.180999755859375
- atom: CD2 x: 17.791000366210938 y:-5.498000144958496 z:40.30799865722656
- atom: CE1 x: 19.79800033569336 y:-5.644000053405762 z:38.39899826049805
- atom: CE2 x: 19.00200080871582 y:-4.873000144958496 z:40.52799987792969
- atom: CZ x: 20.007999420166016 y:-4.941999912261963 z:39.57600021362305
- residue GLU has 9 atoms
- atom: N x: 15.581000328063965 y:-4.728000164031982 z:36.926998138427734
- atom: CA x: 15.913999557495117 y:-3.611999988555908 z:36.04999923706055
- atom: C x: 14.92199993133545 y:-2.4560000896453857 z:36.1609992980957
- atom: O x: 15.28499984741211 y:-1.3009999990463257 z:35.96900177001953
- atom: CB x: 16.007999420166016 y:-4.086999893188477 z:34.59299850463867
- atom: CG x: 17.152000427246094 y:-5.060999870300293 z:34.27799987792969
- atom: CD x: 18.538000106811523 y:-4.489999771118164 z:34.58700180053711
- atom: OE1 x: 18.69700050354004 y:-3.260999917984009 z:34.5260009765625
- atom: OE2 x: 19.479000091552734 y:-5.265999794006348 z:34.875
- residue LYS has 9 atoms
- atom: N x: 13.677000045776367 y:-2.7669999599456787 z:36.48400115966797
- atom: CA x: 12.642999649047852 y:-1.753000020980835 z:36.61600112915039
- atom: C x: 12.543999671936035 y:-1.121999979019165 z:37.99599838256836
- atom: O x: 12.244000434875488 y:0.06400000303983688 z:38.12799835205078
- atom: CB x: 11.277999877929688 y:-2.3440001010894775 z:36.2859992980957
- atom: CG x: 10.192999839782715 y:-1.8370000123977661 z:37.207000732421875
- atom: CD x: 8.888999938964844 y:-1.6490000486373901 z:36.49800109863281
- atom: CE x: 8.100000381469727 y:-0.546999990940094 z:37.20000076293945
- atom: NZ x: 8.9350004196167 y:0.6930000185966492 z:37.34199905395508
- residue ASN has 8 atoms
- atom: N x: 12.75100040435791 y:-1.9199999570846558 z:39.03200149536133
- atom: CA x: 12.637999534606934 y:-1.3869999647140503 z:40.36899948120117
- atom: C x: 13.968000411987305 y:-0.8429999947547913 z:40.900001525878906
- atom: O x: 14.02299976348877 y:0.24799999594688416 z:41.45899963378906
- atom: CB x: 12.067999839782715 y:-2.4579999446868896 z:41.319000244140625
- atom: CG x: 10.592000007629395 y:-2.7790000438690186 z:41.04800033569336
- atom: OD1 x: 9.795999526977539 y:-1.8949999809265137 z:40.73699951171875
- atom: ND2 x: 10.22700023651123 y:-4.045000076293945 z:41.18899917602539
- residue VAL has 7 atoms
- atom: N x: 15.041999816894531 y:-1.590999960899353 z:40.698001861572266
- atom: CA x: 16.341999053955078 y:-1.1859999895095825 z:41.19900131225586
- atom: C x: 17.093000411987305 y:-0.3190000057220459 z:40.21500015258789
- atom: O x: 17.384000778198242 y:0.828000009059906 z:40.51300048828125
- atom: CB x: 17.204999923706055 y:-2.4189999103546143 z:41.53900146484375
- atom: CG1 x: 18.464000701904297 y:-1.99399995803833 z:42.32699966430664
- atom: CG2 x: 16.385000228881836 y:-3.4179999828338623 z:42.33000183105469
- residue SER has 6 atoms
- atom: N x: 17.406999588012695 y:-0.871999979019165 z:39.04600143432617
- atom: CA x: 18.14699935913086 y:-0.14800000190734863 z:37.999000549316406
- atom: C x: 17.43199920654297 y:1.0440000295639038 z:37.369998931884766
- atom: O x: 18.065000534057617 y:1.8589999675750732 z:36.69300079345703
- atom: CB x: 18.55500030517578 y:-1.0989999771118164 z:36.875
- atom: OG x: 19.535999298095703 y:-2.0239999294281006 z:37.31100082397461
- residue GLN has 9 atoms
- atom: N x: 16.125 y:1.1460000276565552 z:37.58000183105469
- atom: CA x: 15.355999946594238 y:2.244999885559082 z:37.012001037597656
- atom: C x: 15.548999786376953 y:2.385999917984009 z:35.499000549316406
- atom: O x: 15.527999877929688 y:3.4839999675750732 z:34.96200180053711
- atom: CB x: 15.715999603271484 y:3.553999900817871 z:37.7140007019043
- atom: CG x: 15.02299976348877 y:3.7219998836517334 z:39.07899856567383
- atom: CD x: 15.668000221252441 y:4.795000076293945 z:39.96500015258789
- atom: OE1 x: 16.8799991607666 y:4.752999782562256 z:40.2400016784668
- atom: NE2 x: 14.861000061035156 y:5.743000030517578 z:40.42499923706055
- residue ALA has 5 atoms
- atom: N x: 15.746000289916992 y:1.2569999694824219 z:34.82899856567383
- atom: CA x: 15.914999961853027 y:1.1920000314712524 z:33.37699890136719
- atom: C x: 14.652999877929688 y:0.49300000071525574 z:32.85499954223633
- atom: O x: 14.583000183105469 y:-0.7369999885559082 z:32.79999923706055
- atom: CB x: 17.15399932861328 y:0.3790000081062317 z:33.03300094604492
- residue ILE has 8 atoms
- atom: N x: 13.656999588012695 y:1.2949999570846558 z:32.49599838256836
- atom: CA x: 12.378000259399414 y:0.7940000295639038 z:32.0260009765625
- atom: C x: 12.460000038146973 y:0.032999999821186066 z:30.702999114990234
- atom: O x: 11.57699966430664 y:-0.7519999742507935 z:30.37299919128418
- atom: CB x: 11.407999992370605 y:1.9550000429153442 z:31.85700035095215
- atom: CG1 x: 10.034000396728516 y:1.4700000286102295 z:31.36199951171875
- atom: CG2 x: 12.008999824523926 y:2.937000036239624 z:30.867000579833984
- atom: CD1 x: 9.13700008392334 y:0.8830000162124634 z:32.4379997253418
- residue HIS has 10 atoms
- atom: N x: 13.517000198364258 y:0.2529999911785126 z:29.94099998474121
- atom: CA x: 13.626999855041504 y:-0.42500001192092896 z:28.665000915527344
- atom: C x: 14.244000434875488 y:-1.7960000038146973 z:28.760000228881836
- atom: O x: 14.008999824523926 y:-2.6500000953674316 z:27.905000686645508
- atom: CB x: 14.366999626159668 y:0.4620000123977661 z:27.674999237060547
- atom: CG x: 13.645999908447266 y:1.7430000305175781 z:27.393999099731445
- atom: ND1 x: 12.3100004196167 y:1.7760000228881836 z:27.051000595092773
- atom: CD2 x: 14.04800033569336 y:3.0329999923706055 z:27.476999282836914
- atom: CE1 x: 11.918999671936035 y:3.0320000648498535 z:26.941999435424805
- atom: NE2 x: 12.954000473022461 y:3.813999891281128 z:27.19499969482422
- residue LYS has 9 atoms
- atom: N x: 15.031999588012695 y:-2.0220000743865967 z:29.798999786376953
- atom: CA x: 15.621000289916992 y:-3.3359999656677246 z:29.981000900268555
- atom: C x: 14.463000297546387 y:-4.136000156402588 z:30.52199935913086
- atom: O x: 14.262999534606934 y:-5.2829999923706055 z:30.141000747680664
- atom: CB x: 16.773000717163086 y:-3.299999952316284 z:30.996000289916992
- atom: CG x: 17.975000381469727 y:-2.4779999256134033 z:30.540000915527344
- atom: CD x: 19.246000289916992 y:-2.9200000762939453 z:31.253000259399414
- atom: CE x: 20.474000930786133 y:-2.2990000247955322 z:30.60099983215332
- atom: NZ x: 21.74799919128418 y:-2.9100000858306885 z:31.034000396728516
- residue TYR has 12 atoms
- atom: N x: 13.689000129699707 y:-3.5139999389648438 z:31.408000946044922
- atom: CA x: 12.527999877929688 y:-4.175000190734863 z:31.989999771118164
- atom: C x: 11.668999671936035 y:-4.672999858856201 z:30.836999893188477
- atom: O x: 11.380999565124512 y:-5.86899995803833 z:30.731000900268555
- atom: CB x: 11.722999572753906 y:-3.194999933242798 z:32.847999572753906
- atom: CG x: 10.309000015258789 y:-3.6470000743865967 z:33.15999984741211
- atom: CD1 x: 10.064000129699707 y:-4.732999801635742 z:33.992000579833984
- atom: CD2 x: 9.215999603271484 y:-2.9639999866485596 z:32.64899826049805
- atom: CE1 x: 8.758999824523926 y:-5.125 z:34.310001373291016
- atom: CE2 x: 7.9070000648498535 y:-3.3469998836517334 z:32.96200180053711
- atom: CZ x: 7.689000129699707 y:-4.423999786376953 z:33.79100036621094
- atom: OH x: 6.39900016784668 y:-4.795000076293945 z:34.09600067138672
- residue ASN has 8 atoms
- atom: N x: 11.267000198364258 y:-3.75 z:29.965999603271484
- atom: CA x: 10.454999923706055 y:-4.125 z:28.819000244140625
- atom: C x: 11.135000228881836 y:-5.242000102996826 z:28.03499984741211
- atom: O x: 10.5 y:-6.247000217437744 z:27.711999893188477
- atom: CB x: 10.20300006866455 y:-2.9200000762939453 z:27.91200065612793
- atom: CG x: 9.14900016784668 y:-2.003999948501587 z:28.468000411987305
- atom: OD1 x: 8.194000244140625 y:-2.4619998931884766 z:29.083999633789062
- atom: ND2 x: 9.305000305175781 y:-0.7049999833106995 z:28.249000549316406
- residue ALA has 5 atoms
- atom: N x: 12.42199993133545 y:-5.059999942779541 z:27.74799919128418
- atom: CA x: 13.201000213623047 y:-6.046000003814697 z:27.020999908447266
- atom: C x: 13.07800006866455 y:-7.461999893188477 z:27.60099983215332
- atom: O x: 12.82699966430664 y:-8.409000396728516 z:26.867000579833984
- atom: CB x: 14.645999908447266 y:-5.619999885559082 z:26.993999481201172
- residue TYR has 12 atoms
- atom: N x: 13.26200008392334 y:-7.61299991607666 z:28.910999298095703
- atom: CA x: 13.152000427246094 y:-8.927000045776367 z:29.538000106811523
- atom: C x: 11.708000183105469 y:-9.369000434875488 z:29.48699951171875
- atom: O x: 11.395999908447266 y:-10.520000457763672 z:29.2189998626709
- atom: CB x: 13.609999656677246 y:-8.871000289916992 z:31.00200080871582
- atom: CG x: 15.104999542236328 y:-8.961999893188477 z:31.177000045776367
- atom: CD1 x: 15.8100004196167 y:-10.065999984741211 z:30.708999633789062
- atom: CD2 x: 15.821000099182129 y:-7.946000099182129 z:31.804000854492188
- atom: CE1 x: 17.191999435424805 y:-10.159000396728516 z:30.85700035095215
- atom: CE2 x: 17.207000732421875 y:-8.029999732971191 z:31.95599937438965
- atom: CZ x: 17.881999969482422 y:-9.13700008392334 z:31.481000900268555
- atom: OH x: 19.249000549316406 y:-9.23799991607666 z:31.62700080871582
- residue ARG has 11 atoms
- atom: N x: 10.82800006866455 y:-8.425999641418457 z:29.774999618530273
- atom: CA x: 9.402000427246094 y:-8.663000106811523 z:29.78499984741211
- atom: C x: 8.987000465393066 y:-9.234000205993652 z:28.422000885009766
- atom: O x: 8.211000442504883 y:-10.1850004196167 z:28.336999893188477
- atom: CB x: 8.715999603271484 y:-7.334000110626221 z:30.06999969482422
- atom: CG x: 7.258999824523926 y:-7.432000160217285 z:30.378000259399414
- atom: CD x: 7.006999969482422 y:-7.331999778747559 z:31.860000610351562
- atom: NE x: 5.626999855041504 y:-6.922999858856201 z:32.09299850463867
- atom: CZ x: 5.074999809265137 y:-5.839000225067139 z:31.549999237060547
- atom: NH1 x: 5.791999816894531 y:-5.061999797821045 z:30.73699951171875
- atom: NH2 x: 3.812000036239624 y:-5.519999980926514 z:31.82900047302246
- residue LYS has 9 atoms
- atom: N x: 9.53499984741211 y:-8.657999992370605 z:27.354999542236328
- atom: CA x: 9.25 y:-9.10099983215332 z:25.996000289916992
- atom: C x: 9.82699966430664 y:-10.49899959564209 z:25.763999938964844
- atom: O x: 9.098999977111816 y:-11.430000305175781 z:25.424999237060547
- atom: CB x: 9.835000038146973 y:-8.100000381469727 z:24.999000549316406
- atom: CG x: 9.510000228881836 y:-8.36299991607666 z:23.541000366210938
- atom: CD x: 9.970000267028809 y:-7.190000057220459 z:22.68400001525879
- atom: CE x: 10.038000106811523 y:-7.559000015258789 z:21.20800018310547
- atom: NZ x: 10.956999778747559 y:-8.722000122070312 z:20.97100067138672
- residue ALA has 5 atoms
- atom: N x: 11.128999710083008 y:-10.652999877929688 z:25.959999084472656
- atom: CA x: 11.76200008392334 y:-11.949000358581543 z:25.777999877929688
- atom: C x: 10.984999656677246 y:-13.067000389099121 z:26.46299934387207
- atom: O x: 10.824000358581543 y:-14.14799976348877 z:25.902999877929688
- atom: CB x: 13.173999786376953 y:-11.914999961853027 z:26.304000854492188
- residue ALA has 5 atoms
- atom: N x: 10.5 y:-12.812000274658203 z:27.672000885009766
- atom: CA x: 9.753999710083008 y:-13.829999923706055 z:28.402000427246094
- atom: C x: 8.461000442504883 y:-14.230999946594238 z:27.68199920654297
- atom: O x: 8.182000160217285 y:-15.414999961853027 z:27.506999969482422
- atom: CB x: 9.442999839782715 y:-13.34000015258789 z:29.815000534057617
- residue SER has 6 atoms
- atom: N x: 7.676000118255615 y:-13.246000289916992 z:27.266000747680664
- atom: CA x: 6.428999900817871 y:-13.508999824523926 z:26.575000762939453
- atom: C x: 6.638999938964844 y:-14.333000183105469 z:25.29599952697754
- atom: O x: 5.808000087738037 y:-15.168999671936035 z:24.929000854492188
- atom: CB x: 5.763000011444092 y:-12.182000160217285 z:26.229999542236328
- atom: OG x: 4.60099983215332 y:-12.369999885559082 z:25.44099998474121
- residue VAL has 7 atoms
- atom: N x: 7.751999855041504 y:-14.08899974822998 z:24.615999221801758
- atom: CA x: 8.069000244140625 y:-14.795999526977539 z:23.388999938964844
- atom: C x: 8.357000350952148 y:-16.267000198364258 z:23.677000045776367
- atom: O x: 7.839000225067139 y:-17.152999877929688 z:22.985000610351562
- atom: CB x: 9.284000396728516 y:-14.144000053405762 z:22.694000244140625
- atom: CG1 x: 10.064000129699707 y:-15.180999755859375 z:21.92300033569336
- atom: CG2 x: 8.812999725341797 y:-13.031000137329102 z:21.76099967956543
- residue ILE has 8 atoms
- atom: N x: 9.189000129699707 y:-16.523000717163086 z:24.68899917602539
- atom: CA x: 9.541000366210938 y:-17.88800048828125 z:25.08799934387207
- atom: C x: 8.321999549865723 y:-18.58099937438965 z:25.70199966430664
- atom: O x: 8.041000366210938 y:-19.75 z:25.413000106811523
- atom: CB x: 10.6850004196167 y:-17.89900016784668 z:26.131999969482422
- atom: CG1 x: 12.006999969482422 y:-17.5049991607666 z:25.482999801635742
- atom: CG2 x: 10.8100004196167 y:-19.267000198364258 z:26.743000030517578
- atom: CD1 x: 13.130999565124512 y:-17.316999435424805 z:26.476999282836914
- residue ALA has 5 atoms
- atom: N x: 7.605999946594238 y:-17.854999542236328 z:26.55299949645996
- atom: CA x: 6.414000034332275 y:-18.388999938964844 z:27.195999145507812
- atom: C x: 5.311999797821045 y:-18.68000030517578 z:26.170000076293945
- atom: O x: 4.185999870300293 y:-19.033000946044922 z:26.5310001373291
- atom: CB x: 5.906000137329102 y:-17.415000915527344 z:28.23200035095215
- residue LYS has 9 atoms
- atom: N x: 5.626999855041504 y:-18.524999618530273 z:24.888999938964844
- atom: CA x: 4.650000095367432 y:-18.802000045776367 z:23.851999282836914
- atom: C x: 5.250999927520752 y:-19.749000549316406 z:22.81100082397461
- atom: O x: 4.5879998207092285 y:-20.131999969482422 z:21.847999572753906
- atom: CB x: 4.186999797821045 y:-17.496999740600586 z:23.204999923706055
- atom: CG x: 2.924999952316284 y:-17.617000579833984 z:22.378999710083008
- atom: CD x: 2.450000047683716 y:-16.24799919128418 z:21.92099952697754
- atom: CE x: 3.4739999771118164 y:-15.571999549865723 z:21.01799964904785
- atom: NZ x: 3.049999952316284 y:-14.184000015258789 z:20.684999465942383
- residue TYR has 12 atoms
- atom: N x: 6.513000011444092 y:-20.1200008392334 z:23.009000778198242
- atom: CA x: 7.193999767303467 y:-21.051000595092773 z:22.108999252319336
- atom: C x: 6.574999809265137 y:-22.388999938964844 z:22.45599937438965
- atom: O x: 6.429999828338623 y:-22.719999313354492 z:23.631000518798828
- atom: CB x: 8.675000190734863 y:-21.06599998474121 z:22.42099952697754
- atom: CG x: 9.553000450134277 y:-21.915000915527344 z:21.53700065612793
- atom: CD1 x: 9.6850004196167 y:-21.6560001373291 z:20.166000366210938
- atom: CD2 x: 10.39799976348877 y:-22.868000030517578 z:22.111000061035156
- atom: CE1 x: 10.666999816894531 y:-22.320999145507812 z:19.39699935913086
- atom: CE2 x: 11.368000030517578 y:-23.527999877929688 z:21.361000061035156
- atom: CZ x: 11.506999969482422 y:-23.253999710083008 z:20.016000747680664
- atom: OH x: 12.527999877929688 y:-23.892000198364258 z:19.347999572753906
- residue PRO has 7 atoms
- atom: N x: 6.186999797821045 y:-23.167999267578125 z:21.437999725341797
- atom: CA x: 5.563000202178955 y:-24.483999252319336 z:21.61400032043457
- atom: C x: 6.4720001220703125 y:-25.672000885009766 z:21.94700050354004
- atom: O x: 5.98199987411499 y:-26.764999389648438 z:22.20800018310547
- atom: CB x: 4.800000190734863 y:-24.670000076293945 z:20.30299949645996
- atom: CG x: 5.709000110626221 y:-24.02400016784668 z:19.30900001525879
- atom: CD x: 6.133999824523926 y:-22.7450008392334 z:20.025999069213867
- residue HIS has 10 atoms
- atom: N x: 7.7820000648498535 y:-25.472000122070312 z:21.944000244140625
- atom: CA x: 8.687000274658203 y:-26.566999435424805 z:22.27199935913086
- atom: C x: 9.373000144958496 y:-26.291000366210938 z:23.597000122070312
- atom: O x: 9.204000473022461 y:-25.219999313354492 z:24.173999786376953
- atom: CB x: 9.75100040435791 y:-26.72800064086914 z:21.19099998474121
- atom: CG x: 9.192999839782715 y:-26.843000411987305 z:19.81100082397461
- atom: ND1 x: 8.234000205993652 y:-27.770999908447266 z:19.472000122070312
- atom: CD2 x: 9.461999893188477 y:-26.148000717163086 z:18.680999755859375
- atom: CE1 x: 7.934999942779541 y:-27.64299964904785 z:18.191999435424805
- atom: NE2 x: 8.666000366210938 y:-26.665000915527344 z:17.687999725341797
- residue LYS has 9 atoms
- atom: N x: 10.135000228881836 y:-27.26099967956543 z:24.09000015258789
- atom: CA x: 10.866999626159668 y:-27.077999114990234 z:25.336000442504883
- atom: C x: 12.291999816894531 y:-26.701000213623047 z:24.979000091552734
- atom: O x: 13.027999877929688 y:-27.5 z:24.395999908447266
- atom: CB x: 10.859999656677246 y:-28.347000122070312 z:26.18000030517578
- atom: CG x: 12.022000312805176 y:-28.41900062561035 z:27.149999618530273
- atom: CD x: 11.635000228881836 y:-29.1200008392334 z:28.43199920654297
- atom: CE x: 10.968999862670898 y:-28.14699935913086 z:29.37700080871582
- atom: NZ x: 11.902000427246094 y:-27.017000198364258 z:29.71500015258789
- residue ILE has 8 atoms
- atom: N x: 12.661999702453613 y:-25.47100067138672 z:25.326000213623047
- atom: CA x: 13.979999542236328 y:-24.924999237060547 z:25.03700065612793
- atom: C x: 15.112000465393066 y:-25.763999938964844 z:25.604999542236328
- atom: O x: 15.272000312805176 y:-25.878999710083008 z:26.81800079345703
- atom: CB x: 14.07800006866455 y:-23.479999542236328 z:25.554000854492188
- atom: CG1 x: 13.07699966430664 y:-22.618000030517578 z:24.783000946044922
- atom: CG2 x: 15.498000144958496 y:-22.948999404907227 z:25.399999618530273
- atom: CD1 x: 13.050000190734863 y:-21.170000076293945 z:25.19499969482422
- residue LYS has 9 atoms
- atom: N x: 15.897000312805176 y:-26.341999053955078 z:24.70400047302246
- atom: CA x: 17.009000778198242 y:-27.194000244140625 z:25.08300018310547
- atom: C x: 18.363000869750977 y:-26.479000091552734 z:25.097000122070312
- atom: O x: 19.3799991607666 y:-27.075000762939453 z:25.45400047302246
- atom: CB x: 17.05900001525879 y:-28.413999557495117 z:24.1560001373291
- atom: CG x: 15.869000434875488 y:-29.34600067138672 z:24.302000045776367
- atom: CD x: 16.128000259399414 y:-30.667999267578125 z:23.60300064086914
- atom: CE x: 15.015000343322754 y:-31.684999465942383 z:23.892000198364258
- atom: NZ x: 15.324999809265137 y:-33.077999114990234 z:23.42300033569336
- residue SER has 6 atoms
- atom: N x: 18.378000259399414 y:-25.202999114990234 z:24.72100067138672
- atom: CA x: 19.618999481201172 y:-24.429000854492188 z:24.722000122070312
- atom: C x: 19.31399917602539 y:-22.95199966430664 z:24.527000427246094
- atom: O x: 18.201000213623047 y:-22.58300018310547 z:24.15399932861328
- atom: CB x: 20.55699920654297 y:-24.892000198364258 z:23.604000091552734
- atom: OG x: 20.27899932861328 y:-24.198999404907227 z:22.398000717163086
- residue GLY has 4 atoms
- atom: N x: 20.309999465942383 y:-22.110000610351562 z:24.777999877929688
- atom: CA x: 20.1200008392334 y:-20.68199920654297 z:24.617000579833984
- atom: C x: 20.091999053955078 y:-20.316999435424805 z:23.14699935913086
- atom: O x: 19.503999710083008 y:-19.30699920654297 z:22.756000518798828
- residue ALA has 5 atoms
- atom: N x: 20.73200035095215 y:-21.145999908447266 z:22.327999114990234
- atom: CA x: 20.773000717163086 y:-20.899999618530273 z:20.902000427246094
- atom: C x: 19.391000747680664 y:-21.14299964904785 z:20.302000045776367
- atom: O x: 18.961999893188477 y:-20.430999755859375 z:19.392000198364258
- atom: CB x: 21.799999237060547 y:-21.798999786376953 z:20.253000259399414
- residue GLU has 9 atoms
- atom: N x: 18.69300079345703 y:-22.150999069213867 z:20.809999465942383
- atom: CA x: 17.35700035095215 y:-22.451000213623047 z:20.31999969482422
- atom: C x: 16.514999389648438 y:-21.20599937438965 z:20.593000411987305
- atom: O x: 15.798999786376953 y:-20.719999313354492 z:19.715999603271484
- atom: CB x: 16.768999099731445 y:-23.655000686645508 z:21.06100082397461
- atom: CG x: 15.47700023651123 y:-24.17300033569336 z:20.458999633789062
- atom: CD x: 14.970999717712402 y:-25.433000564575195 z:21.138999938964844
- atom: OE1 x: 15.795999526977539 y:-26.31999969482422 z:21.44700050354004
- atom: OE2 x: 13.744999885559082 y:-25.54800033569336 z:21.347999572753906
- residue ALA has 5 atoms
- atom: N x: 16.632999420166016 y:-20.677000045776367 z:21.808000564575195
- atom: CA x: 15.897000312805176 y:-19.48900032043457 z:22.211000442504883
- atom: C x: 16.354000091552734 y:-18.23699951171875 z:21.452999114990234
- atom: O x: 15.574999809265137 y:-17.315000534057617 z:21.225000381469727
- atom: CB x: 16.05699920654297 y:-19.281999588012695 z:23.701000213623047
- residue LYS has 9 atoms
- atom: N x: 17.624000549316406 y:-18.20800018310547 z:21.069000244140625
- atom: CA x: 18.18400001525879 y:-17.07699966430664 z:20.341999053955078
- atom: C x: 17.55699920654297 y:-16.8799991607666 z:18.937999725341797
- atom: O x: 17.700000762939453 y:-15.824000358581543 z:18.320999145507812
- atom: CB x: 19.695999145507812 y:-17.263999938964844 z:20.235000610351562
- atom: CG x: 20.41699981689453 y:-16.229000091552734 z:19.392000198364258
- atom: CD x: 20.399999618530273 y:-14.847999572753906 z:20.023000717163086
- atom: CE x: 21.18199920654297 y:-13.862000465393066 z:19.165000915527344
- atom: NZ x: 22.56599998474121 y:-14.347000122070312 z:18.958999633789062
- residue LYS has 9 atoms
- atom: N x: 16.861000061035156 y:-17.892000198364258 z:18.434999465942383
- atom: CA x: 16.226999282836914 y:-17.773000717163086 z:17.131000518798828
- atom: C x: 15.065999984741211 y:-16.77199935913086 z:17.200000762939453
- atom: O x: 14.831000328063965 y:-16.006999969482422 z:16.256999969482422
- atom: CB x: 15.673999786376953 y:-19.125 z:16.680999755859375
- atom: CG x: 16.683000564575195 y:-20.246999740600586 z:16.594999313354492
- atom: CD x: 15.987000465393066 y:-21.54400062561035 z:16.172000885009766
- atom: CE x: 16.908000946044922 y:-22.753999710083008 z:16.27899932861328
- atom: NZ x: 16.2549991607666 y:-24.025999069213867 z:15.857000350952148
- residue LEU has 8 atoms
- atom: N x: 14.343999862670898 y:-16.790000915527344 z:18.32200050354004
- atom: CA x: 13.184000015258789 y:-15.925999641418457 z:18.53700065612793
- atom: C x: 13.527999877929688 y:-14.432999610900879 z:18.64699935913086
- atom: O x: 14.597000122070312 y:-14.064000129699707 z:19.136999130249023
- atom: CB x: 12.437000274658203 y:-16.3799991607666 z:19.795000076293945
- atom: CG x: 12.102999687194824 y:-17.868000030517578 z:19.90399932861328
- atom: CD1 x: 11.484999656677246 y:-18.17799949645996 z:21.260000228881836
- atom: CD2 x: 11.161999702453613 y:-18.250999450683594 z:18.78499984741211
- residue PRO has 7 atoms
- atom: N x: 12.616000175476074 y:-13.555999755859375 z:18.187000274658203
- atom: CA x: 12.782999992370605 y:-12.100000381469727 z:18.21500015258789
- atom: C x: 12.5 y:-11.564000129699707 z:19.618000030517578
- atom: O x: 11.369999885559082 y:-11.609999656677246 z:20.106000900268555
- atom: CB x: 11.753000259399414 y:-11.631999969482422 z:17.20800018310547
- atom: CG x: 10.605999946594238 y:-12.545000076293945 z:17.520000457763672
- atom: CD x: 11.295999526977539 y:-13.909000396728516 z:17.631999969482422
- residue GLY has 4 atoms
- atom: N x: 13.532999992370605 y:-11.04699993133545 z:20.26300048828125
- atom: CA x: 13.359999656677246 y:-10.550000190734863 z:21.61199951171875
- atom: C x: 14.352999687194824 y:-11.239999771118164 z:22.52199935913086
- atom: O x: 14.593999862670898 y:-10.791000366210938 z:23.634000778198242
- residue VAL has 7 atoms
- atom: N x: 14.920000076293945 y:-12.342000007629395 z:22.047000885009766
- atom: CA x: 15.909000396728516 y:-13.072999954223633 z:22.801000595092773
- atom: C x: 17.238000869750977 y:-12.873000144958496 z:22.11199951171875
- atom: O x: 17.503000259399414 y:-13.482999801635742 z:21.072999954223633
- atom: CB x: 15.623000144958496 y:-14.553999900817871 z:22.81399917602539
- atom: CG1 x: 16.7549991607666 y:-15.277000427246094 z:23.52199935913086
- atom: CG2 x: 14.295000076293945 y:-14.815999984741211 z:23.481000900268555
- residue GLY has 4 atoms
- atom: N x: 18.07200050354004 y:-12.015999794006348 z:22.69700050354004
- atom: CA x: 19.378999710083008 y:-11.729999542236328 z:22.134000778198242
- atom: C x: 20.488000869750977 y:-12.513999938964844 z:22.802000045776367
- atom: O x: 20.222000122070312 y:-13.487000465393066 z:23.506000518798828
- residue THR has 7 atoms
- atom: N x: 21.72800064086914 y:-12.062999725341797 z:22.60300064086914
- atom: CA x: 22.920000076293945 y:-12.718999862670898 z:23.145999908447266
- atom: C x: 22.94099998474121 y:-12.92199993133545 z:24.6560001373291
- atom: O x: 23.170000076293945 y:-14.029999732971191 z:25.128000259399414
- atom: CB x: 24.21299934387207 y:-11.954999923706055 z:22.770000457763672
- atom: OG1 x: 24.249000549316406 y:-11.710000038146973 z:21.356000900268555
- atom: CG2 x: 25.434999465942383 y:-12.774999618530273 z:23.156999588012695
- residue LYS has 9 atoms
- atom: N x: 22.709999084472656 y:-11.857999801635742 z:25.413000106811523
- atom: CA x: 22.726999282836914 y:-11.961000442504883 z:26.865999221801758
- atom: C x: 21.701000213623047 y:-12.954000473022461 z:27.388999938964844
- atom: O x: 22.0 y:-13.739999771118164 z:28.275999069213867
- atom: CB x: 22.475000381469727 y:-10.595999717712402 z:27.5
- atom: CG x: 23.288000106811523 y:-9.480999946594238 z:26.8700008392334
- atom: CD x: 24.777000427246094 y:-9.682999610900879 z:27.093000411987305
- atom: CE x: 25.266000747680664 y:-8.854999542236328 z:28.26300048828125
- atom: NZ x: 25.291000366210938 y:-7.4070000648498535 z:27.913999557495117
- residue ILE has 8 atoms
- atom: N x: 20.489999771118164 y:-12.942000389099121 z:26.85099983215332
- atom: CA x: 19.493000030517578 y:-13.871000289916992 z:27.351999282836914
- atom: C x: 19.766000747680664 y:-15.331000328063965 z:26.969999313354492
- atom: O x: 19.400999069213867 y:-16.253000259399414 z:27.704999923706055
- atom: CB x: 18.073999404907227 y:-13.446999549865723 z:26.920000076293945
- atom: CG1 x: 17.691999435424805 y:-12.152999877929688 z:27.6560001373291
- atom: CG2 x: 17.062999725341797 y:-14.581000328063965 z:27.211999893188477
- atom: CD1 x: 16.2549991607666 y:-11.734999656677246 z:27.492000579833984
- residue ALA has 5 atoms
- atom: N x: 20.427000045776367 y:-15.54800033569336 z:25.836999893188477
- atom: CA x: 20.742000579833984 y:-16.9060001373291 z:25.4060001373291
- atom: C x: 21.82200050354004 y:-17.413000106811523 z:26.351999282836914
- atom: O x: 21.839000701904297 y:-18.582000732421875 z:26.763999938964844
- atom: CB x: 21.256999969482422 y:-16.88800048828125 z:23.981000900268555
- residue GLU has 9 atoms
- atom: N x: 22.719999313354492 y:-16.493000030517578 z:26.68899917602539
- atom: CA x: 23.83099937438965 y:-16.760000228881836 z:27.58300018310547
- atom: C x: 23.28700065612793 y:-17.075000762939453 z:28.95800018310547
- atom: O x: 23.738000869750977 y:-18.0049991607666 z:29.625999450683594
- atom: CB x: 24.726999282836914 y:-15.53600025177002 z:27.64900016784668
- atom: CG x: 25.850000381469727 y:-15.63599967956543 z:28.64299964904785
- atom: CD x: 26.965999603271484 y:-14.670000076293945 z:28.30900001525879
- atom: OE1 x: 27.51799964904785 y:-14.795999526977539 z:27.19700050354004
- atom: OE2 x: 27.283000946044922 y:-13.788999557495117 z:29.141000747680664
- residue LYS has 9 atoms
- atom: N x: 22.308000564575195 y:-16.295000076293945 z:29.381999969482422
- atom: CA x: 21.725000381469727 y:-16.541000366210938 z:30.672000885009766
- atom: C x: 20.95199966430664 y:-17.840999603271484 z:30.590999603271484
- atom: O x: 20.99799919128418 y:-18.648000717163086 z:31.51300048828125
- atom: CB x: 20.82699966430664 y:-15.378999710083008 z:31.089000701904297
- atom: CG x: 21.610000610351562 y:-14.130999565124512 z:31.437000274658203
- atom: CD x: 20.827999114990234 y:-13.210000038146973 z:32.361000061035156
- atom: CE x: 21.672000885009766 y:-12.029999732971191 z:32.82699966430664
- atom: NZ x: 22.187999725341797 y:-11.217000007629395 z:31.687999725341797
- residue ILE has 8 atoms
- atom: N x: 20.256000518798828 y:-18.055999755859375 z:29.479000091552734
- atom: CA x: 19.496000289916992 y:-19.285999298095703 z:29.30500030517578
- atom: C x: 20.44300079345703 y:-20.496999740600586 z:29.367000579833984
- atom: O x: 20.117000579833984 y:-21.52899932861328 z:29.961999893188477
- atom: CB x: 18.714000701904297 y:-19.270000457763672 z:27.961999893188477
- atom: CG1 x: 17.535999298095703 y:-18.297000885009766 z:28.06399917602539
- atom: CG2 x: 18.194000244140625 y:-20.665000915527344 z:27.6299991607666
- atom: CD1 x: 16.844999313354492 y:-18.011999130249023 z:26.757999420166016
- residue ASP has 8 atoms
- atom: N x: 21.618000030517578 y:-20.37299919128418 z:28.761999130249023
- atom: CA x: 22.56999969482422 y:-21.466999053955078 z:28.795000076293945
- atom: C x: 22.993999481201172 y:-21.802000045776367 z:30.23200035095215
- atom: O x: 23.159000396728516 y:-22.97800064086914 z:30.573999404907227
- atom: CB x: 23.785999298095703 y:-21.145999908447266 z:27.93199920654297
- atom: CG x: 23.558000564575195 y:-21.47599983215332 z:26.459999084472656
- atom: OD1 x: 22.81999969482422 y:-22.45199966430664 z:26.187999725341797
- atom: OD2 x: 24.12299919128418 y:-20.783000946044922 z:25.57900047302246
- residue GLU has 9 atoms
- atom: N x: 23.165000915527344 y:-20.785999298095703 z:31.07900047302246
- atom: CA x: 23.533000946044922 y:-21.05699920654297 z:32.4640007019043
- atom: C x: 22.351999282836914 y:-21.722000122070312 z:33.15700149536133
- atom: O x: 22.476999282836914 y:-22.834999084472656 z:33.65800094604492
- atom: CB x: 23.89900016784668 y:-19.783000946044922 z:33.233001708984375
- atom: CG x: 24.15999984741211 y:-20.05900001525879 z:34.72200012207031
- atom: CD x: 24.485000610351562 y:-18.812999725341797 z:35.542999267578125
- atom: OE1 x: 25.302000045776367 y:-17.989999771118164 z:35.09000015258789
- atom: OE2 x: 23.93899917602539 y:-18.665000915527344 z:36.654998779296875
- residue PHE has 11 atoms
- atom: N x: 21.201000213623047 y:-21.04800033569336 z:33.17599868774414
- atom: CA x: 20.01799964904785 y:-21.60300064086914 z:33.83700180053711
- atom: C x: 19.79599952697754 y:-23.05900001525879 z:33.45500183105469
- atom: O x: 19.496999740600586 y:-23.89900016784668 z:34.303001403808594
- atom: CB x: 18.76099967956543 y:-20.81599998474121 z:33.494998931884766
- atom: CG x: 17.554000854492188 y:-21.259000778198242 z:34.27399826049805
- atom: CD1 x: 17.402999877929688 y:-20.89900016784668 z:35.61000061035156
- atom: CD2 x: 16.577999114990234 y:-22.05699920654297 z:33.68299865722656
- atom: CE1 x: 16.29599952697754 y:-21.326000213623047 z:36.34700012207031
- atom: CE2 x: 15.472000122070312 y:-22.486000061035156 z:34.4119987487793
- atom: CZ x: 15.331999778747559 y:-22.1200008392334 z:35.74599838256836
- residue LEU has 8 atoms
- atom: N x: 19.929000854492188 y:-23.354999542236328 z:32.16999816894531
- atom: CA x: 19.76099967956543 y:-24.719999313354492 z:31.724000930786133
- atom: C x: 20.87299919128418 y:-25.54400062561035 z:32.38100051879883
- atom: O x: 20.597000122070312 y:-26.49799919128418 z:33.11199951171875
- atom: CB x: 19.84000015258789 y:-24.78700065612793 z:30.19499969482422
- atom: CG x: 18.53700065612793 y:-25.14900016784668 z:29.46299934387207
- atom: CD1 x: 17.368999481201172 y:-24.40399932861328 z:30.06100082397461
- atom: CD2 x: 18.67099952697754 y:-24.833999633789062 z:27.979999542236328
- residue ALA has 5 atoms
- atom: N x: 22.125 y:-25.1560001373291 z:32.15299987792969
- atom: CA x: 23.2549991607666 y:-25.881000518798828 z:32.73099899291992
- atom: C x: 23.19700050354004 y:-25.913000106811523 z:34.263999938964844
- atom: O x: 22.674999237060547 y:-26.856000900268555 z:34.8650016784668
- atom: CB x: 24.572999954223633 y:-25.256999969482422 z:32.26499938964844
- residue THR has 7 atoms
- atom: N x: 23.732999801635742 y:-24.874000549316406 z:34.891998291015625
- atom: CA x: 23.746999740600586 y:-24.791000366210938 z:36.345001220703125
- atom: C x: 22.393999099731445 y:-25.16200065612793 z:36.95800018310547
- atom: O x: 22.26799964904785 y:-26.194000244140625 z:37.60900115966797
- atom: CB x: 24.17799949645996 y:-23.371000289916992 z:36.810001373291016
- atom: OG1 x: 23.086000442504883 y:-22.448999404907227 z:36.68899917602539
- atom: CG2 x: 25.349000930786133 y:-22.87700080871582 z:35.946998596191406
- residue GLY has 4 atoms
- atom: N x: 21.3799991607666 y:-24.339000701904297 z:36.72800064086914
- atom: CA x: 20.069000244140625 y:-24.611000061035156 z:37.29199981689453
- atom: C x: 19.61400032043457 y:-23.41699981689453 z:38.10900115966797
- atom: O x: 18.61400032043457 y:-23.454999923706055 z:38.83599853515625
- residue LYS has 9 atoms
- atom: N x: 20.375999450683594 y:-22.34000015258789 z:37.97700119018555
- atom: CA x: 20.104999542236328 y:-21.104000091552734 z:38.680999755859375
- atom: C x: 20.933000564575195 y:-20.047000885009766 z:37.987998962402344
- atom: O x: 21.757999420166016 y:-20.365999221801758 z:37.137001037597656
- atom: CB x: 20.530000686645508 y:-21.229999542236328 z:40.150001525878906
- atom: CG x: 22.016000747680664 y:-21.55299949645996 z:40.37799835205078
- atom: CD x: 22.30500030517578 y:-21.792999267578125 z:41.87099838256836
- atom: CE x: 23.71500015258789 y:-22.350000381469727 z:42.15399932861328
- atom: NZ x: 24.823999404907227 y:-21.365999221801758 z:41.97200012207031
- residue LEU has 8 atoms
- atom: N x: 20.711000442504883 y:-18.78700065612793 z:38.33000183105469
- atom: CA x: 21.5 y:-17.73200035095215 z:37.724998474121094
- atom: C x: 22.31999969482422 y:-17.052000045776367 z:38.80699920654297
- atom: O x: 21.7810001373291 y:-16.632999420166016 z:39.83000183105469
- atom: CB x: 20.608999252319336 y:-16.709999084472656 z:37.027000427246094
- atom: CG x: 21.32699966430664 y:-15.911999702453613 z:35.935001373291016
- atom: CD1 x: 21.85099983215332 y:-16.854000091552734 z:34.85599899291992
- atom: CD2 x: 20.36400032043457 y:-14.904999732971191 z:35.32699966430664
- residue ARG has 11 atoms
- atom: N x: 23.6299991607666 y:-16.968000411987305 z:38.57899856567383
- atom: CA x: 24.55500030517578 y:-16.33300018310547 z:39.516998291015625
- atom: C x: 24.148000717163086 y:-14.880000114440918 z:39.749000549316406
- atom: O x: 24.016000747680664 y:-14.442000389099121 z:40.891998291015625
- atom: CB x: 25.979000091552734 y:-16.405000686645508 z:38.9640007019043
- atom: CG x: 26.475000381469727 y:-17.833999633789062 z:38.73099899291992
- atom: CD x: 27.805999755859375 y:-17.840999603271484 z:37.98899841308594
- atom: NE x: 27.750999450683594 y:-16.979000091552734 z:36.808998107910156
- atom: CZ x: 28.722999572753906 y:-16.86400032043457 z:35.904998779296875
- atom: NH1 x: 29.840999603271484 y:-17.56399917602539 z:36.03200149536133
- atom: NH2 x: 28.58300018310547 y:-16.033000946044922 z:34.875999450683594
- residue LYS has 9 atoms
- atom: N x: 23.94099998474121 y:-14.14799976348877 z:38.65700149536133
- atom: CA x: 23.523000717163086 y:-12.746999740600586 z:38.71799850463867
- atom: C x: 22.263999938964844 y:-12.520000457763672 z:39.571998596191406
- atom: O x: 22.094999313354492 y:-11.446999549865723 z:40.1609992980957
- atom: CB x: 23.275999069213867 y:-12.211000442504883 z:37.30699920654297
- atom: CG x: 22.777999877929688 y:-10.774999618530273 z:37.26499938964844
- atom: CD x: 22.426000595092773 y:-10.364999771118164 z:35.8489990234375
- atom: CE x: 21.812000274658203 y:-8.97700023651123 z:35.79999923706055
- atom: NZ x: 22.783000946044922 y:-7.9079999923706055 z:36.16999816894531
- residue LEU has 8 atoms
- atom: N x: 21.37700080871582 y:-13.51099967956543 z:39.630001068115234
- atom: CA x: 20.15399932861328 y:-13.38599967956543 z:40.43600082397461
- atom: C x: 20.409000396728516 y:-13.715999603271484 z:41.909000396728516
- atom: O x: 19.76099967956543 y:-13.151000022888184 z:42.79199981689453
- atom: CB x: 19.0310001373291 y:-14.29800033569336 z:39.91299819946289
- atom: CG x: 18.204999923706055 y:-13.871000289916992 z:38.69599914550781
- atom: CD1 x: 17.20599937438965 y:-14.956000328063965 z:38.374000549316406
- atom: CD2 x: 17.489999771118164 y:-12.565999984741211 z:38.97100067138672
- residue GLU has 9 atoms
- atom: N x: 21.33099937438965 y:-14.642000198364258 z:42.17399978637695
- atom: CA x: 21.6560001373291 y:-14.987000465393066 z:43.553001403808594
- atom: C x: 22.179000854492188 y:-13.70199966430664 z:44.17900085449219
- atom: O x: 21.764999389648438 y:-13.3149995803833 z:45.27199935913086
- atom: CB x: 22.73900032043457 y:-16.07699966430664 z:43.624000549316406
- atom: CG x: 22.267000198364258 y:-17.479999542236328 z:43.24599838256836
- atom: CD x: 21.235000610351562 y:-18.04599952697754 z:44.209999084472656
- atom: OE1 x: 20.523000717163086 y:-18.98900032043457 z:43.81399917602539
- atom: OE2 x: 21.13599967956543 y:-17.562999725341797 z:45.36000061035156
- residue LYS has 9 atoms
- atom: N x: 23.073999404907227 y:-13.038000106811523 z:43.45399856567383
- atom: CA x: 23.663999557495117 y:-11.78600025177002 z:43.90700149536133
- atom: C x: 22.57200050354004 y:-10.781999588012695 z:44.24700164794922
- atom: O x: 22.555999755859375 y:-10.211999893188477 z:45.334999084472656
- atom: CB x: 24.594999313354492 y:-11.241999626159668 z:42.821998596191406
- atom: CG x: 25.749000549316406 y:-12.201000213623047 z:42.54100036621094
- atom: CD x: 26.69700050354004 y:-11.706000328063965 z:41.46500015258789
- atom: CE x: 27.738000869750977 y:-12.774999618530273 z:41.16299819946289
- atom: NZ x: 28.597999572753906 y:-12.456000328063965 z:39.9900016784668
- residue ILE has 8 atoms
- atom: N x: 21.650999069213867 y:-10.579999923706055 z:43.3129997253418
- atom: CA x: 20.538999557495117 y:-9.666999816894531 z:43.53300094604492
- atom: C x: 19.79400062561035 y:-10.114999771118164 z:44.78499984741211
- atom: O x: 19.698999404907227 y:-9.368000030517578 z:45.75299835205078
- atom: CB x: 19.576000213623047 y:-9.663000106811523 z:42.31800079345703
- atom: CG1 x: 20.308000564575195 y:-9.105999946594238 z:41.09299850463867
- atom: CG2 x: 18.336999893188477 y:-8.845999717712402 z:42.625
- atom: CD1 x: 19.481000900268555 y:-9.064000129699707 z:39.84400177001953
- residue ARG has 11 atoms
- atom: N x: 19.283000946044922 y:-11.342000007629395 z:44.7599983215332
- atom: CA x: 18.551000595092773 y:-11.920999526977539 z:45.88999938964844
- atom: C x: 19.215999603271484 y:-11.687000274658203 z:47.249000549316406
- atom: O x: 18.5310001373291 y:-11.527000427246094 z:48.262001037597656
- atom: CB x: 18.378999710083008 y:-13.430000305175781 z:45.68199920654297
- atom: CG x: 17.430999755859375 y:-13.803000450134277 z:44.56800079345703
- atom: CD x: 17.413000106811523 y:-15.305000305175781 z:44.323001861572266
- atom: NE x: 16.273000717163086 y:-15.689000129699707 z:43.492000579833984
- atom: CZ x: 15.977999687194824 y:-16.937000274658203 z:43.132999420166016
- atom: NH1 x: 16.740999221801758 y:-17.950000762939453 z:43.525001525878906
- atom: NH2 x: 14.906000137329102 y:-17.176000595092773 z:42.38800048828125
- residue GLN has 9 atoms
- atom: N x: 20.548999786376953 y:-11.678999900817871 z:47.263999938964844
- atom: CA x: 21.320999145507812 y:-11.486000061035156 z:48.492000579833984
- atom: C x: 21.540000915527344 y:-10.038999557495117 z:48.88999938964844
- atom: O x: 21.20199966430664 y:-9.645999908447266 z:50.005001068115234
- atom: CB x: 22.667999267578125 y:-12.187999725341797 z:48.374000549316406
- atom: CG x: 22.65399932861328 y:-13.574000358581543 z:48.97700119018555
- atom: CD x: 23.506999969482422 y:-14.543000221252441 z:48.20399856567383
- atom: OE1 x: 24.591999053955078 y:-14.189000129699707 z:47.731998443603516
- atom: NE2 x: 23.027000427246094 y:-15.782999992370605 z:48.07099914550781
- residue ASP has 8 atoms
- atom: N x: 22.11400032043457 y:-9.253000259399414 z:47.983001708984375
- atom: CA x: 22.3700008392334 y:-7.834000110626221 z:48.22999954223633
- atom: C x: 21.216999053955078 y:-7.169000148773193 z:48.99300003051758
- atom: O x: 20.115999221801758 y:-7.050000190734863 z:48.47700119018555
- atom: CB x: 22.594999313354492 y:-7.125999927520752 z:46.89099884033203
- atom: CG x: 22.950000762939453 y:-5.663000106811523 z:47.05400085449219
- atom: OD1 x: 23.440000534057617 y:-5.063000202178955 z:46.07400131225586
- atom: OD2 x: 22.735000610351562 y:-5.116000175476074 z:48.15800094604492
- residue ASP has 8 atoms
- atom: N x: 21.47599983215332 y:-6.7230000495910645 z:50.21699905395508
- atom: CA x: 20.43600082397461 y:-6.09499979019165 z:51.03499984741211
- atom: C x: 19.680999755859375 y:-4.929999828338623 z:50.38100051879883
- atom: O x: 18.44499969482422 y:-4.921999931335449 z:50.34199905395508
- atom: CB x: 21.023000717163086 y:-5.610000133514404 z:52.36600112915039
- atom: CG x: 20.0 y:-4.864999771118164 z:53.21699905395508
- atom: OD1 x: 19.062999725341797 y:-5.508999824523926 z:53.75
- atom: OD2 x: 20.125 y:-3.630000114440918 z:53.34400177001953
- residue THR has 7 atoms
- atom: N x: 20.41900062561035 y:-3.941999912261963 z:49.88199996948242
- atom: CA x: 19.788000106811523 y:-2.7799999713897705 z:49.266998291015625
- atom: C x: 18.878999710083008 y:-3.131999969482422 z:48.10300064086914
- atom: O x: 17.701000213623047 y:-2.7730000019073486 z:48.104000091552734
- atom: CB x: 20.826000213623047 y:-1.7740000486373901 z:48.766998291015625
- atom: OG1 x: 21.684999465942383 y:-1.3969999551773071 z:49.84700012207031
- atom: CG2 x: 20.131000518798828 y:-0.531000018119812 z:48.229000091552734
- residue SER has 6 atoms
- atom: N x: 19.43400001525879 y:-3.8239998817443848 z:47.11199951171875
- atom: CA x: 18.676000595092773 y:-4.2210001945495605 z:45.930999755859375
- atom: C x: 17.445999145507812 y:-4.991000175476074 z:46.375999450683594
- atom: O x: 16.354000091552734 y:-4.8429999351501465 z:45.827999114990234
- atom: CB x: 19.527999877929688 y:-5.125999927520752 z:45.04399871826172
- atom: OG x: 20.857999801635742 y:-4.6479997634887695 z:44.95500183105469
- residue SER has 6 atoms
- atom: N x: 17.650999069213867 y:-5.809000015258789 z:47.39699935913086
- atom: CA x: 16.614999771118164 y:-6.6579999923706055 z:47.946998596191406
- atom: C x: 15.543000221252441 y:-5.864999771118164 z:48.672000885009766
- atom: O x: 14.366999626159668 y:-6.239999771118164 z:48.676998138427734
- atom: CB x: 17.256999969482422 y:-7.659999847412109 z:48.895999908447266
- atom: OG x: 16.29199981689453 y:-8.527000427246094 z:49.439998626708984
- residue SER has 6 atoms
- atom: N x: 15.956999778747559 y:-4.765999794006348 z:49.28799819946289
- atom: CA x: 15.032999992370605 y:-3.927000045776367 z:50.02299880981445
- atom: C x: 14.21399974822998 y:-3.0350000858306885 z:49.106998443603516
- atom: O x: 13.001999855041504 y:-2.947000026702881 z:49.257999420166016
- atom: CB x: 15.791999816894531 y:-3.0929999351501465 z:51.06100082397461
- atom: OG x: 16.2549991607666 y:-3.9210000038146973 z:52.12300109863281
- residue ILE has 8 atoms
- atom: N x: 14.859999656677246 y:-2.371999979019165 z:48.159000396728516
- atom: CA x: 14.121000289916992 y:-1.5190000534057617 z:47.24399948120117
- atom: C x: 13.07699966430664 y:-2.390000104904175 z:46.57600021362305
- atom: O x: 11.907999992370605 y:-2.01200008392334 z:46.41999816894531
- atom: CB x: 15.031999588012695 y:-0.9359999895095825 z:46.16899871826172
- atom: CG1 x: 16.11400032043457 y:-0.07800000160932541 z:46.83300018310547
- atom: CG2 x: 14.199000358581543 y:-0.11400000005960464 z:45.18199920654297
- atom: CD1 x: 17.23699951171875 y:0.3479999899864197 z:45.91999816894531
- residue ASN has 8 atoms
- atom: N x: 13.520000457763672 y:-3.5810000896453857 z:46.20199966430664
- atom: CA x: 12.65999984741211 y:-4.548999786376953 z:45.5620002746582
- atom: C x: 11.432000160217285 y:-4.789000034332275 z:46.38999938964844
- atom: O x: 10.333999633789062 y:-4.831999778747559 z:45.874000549316406
- atom: CB x: 13.383999824523926 y:-5.864999771118164 z:45.374000549316406
- atom: CG x: 13.378999710083008 y:-6.310999870300293 z:43.948001861572266
- atom: OD1 x: 12.390000343322754 y:-6.114999771118164 z:43.23500061035156
- atom: ND2 x: 14.47599983215332 y:-6.923999786376953 z:43.51100158691406
- residue PHE has 11 atoms
- atom: N x: 11.60099983215332 y:-4.936999797821045 z:47.6879997253418
- atom: CA x: 10.439000129699707 y:-5.195000171661377 z:48.50699996948242
- atom: C x: 9.46399974822998 y:-4.026000022888184 z:48.55799865722656
- atom: O x: 8.288000106811523 y:-4.184000015258789 z:48.26900100708008
- atom: CB x: 10.843999862670898 y:-5.577000141143799 z:49.92599868774414
- atom: CG x: 9.680000305175781 y:-5.688000202178955 z:50.8489990234375
- atom: CD1 x: 8.789999961853027 y:-6.736999988555908 z:50.729000091552734
- atom: CD2 x: 9.430999755859375 y:-4.703000068664551 z:51.792999267578125
- atom: CE1 x: 7.666999816894531 y:-6.803999900817871 z:51.534000396728516
- atom: CE2 x: 8.303000450134277 y:-4.763999938964844 z:52.60100173950195
- atom: CZ x: 7.425000190734863 y:-5.815000057220459 z:52.47100067138672
- residue LEU has 8 atoms
- atom: N x: 9.954999923706055 y:-2.8559999465942383 z:48.935001373291016
- atom: CA x: 9.11299991607666 y:-1.6629999876022339 z:49.029998779296875
- atom: C x: 8.187000274658203 y:-1.444000005722046 z:47.8489990234375
- atom: O x: 6.998000144958496 y:-1.2089999914169312 z:48.0359992980957
- atom: CB x: 9.97599983215332 y:-0.42399999499320984 z:49.19599914550781
- atom: CG x: 10.741999626159668 y:-0.367000013589859 z:50.50699996948242
- atom: CD1 x: 11.949000358581543 y:0.5139999985694885 z:50.32600021362305
- atom: CD2 x: 9.82699966430664 y:0.1289999932050705 z:51.612998962402344
- residue THR has 7 atoms
- atom: N x: 8.727999687194824 y:-1.5180000066757202 z:46.63600158691406
- atom: CA x: 7.913000106811523 y:-1.3020000457763672 z:45.45000076293945
- atom: C x: 6.660999774932861 y:-2.1670000553131104 z:45.41999816894531
- atom: O x: 5.74399995803833 y:-1.86899995803833 z:44.67499923706055
- atom: CB x: 8.699999809265137 y:-1.5509999990463257 z:44.16999816894531
- atom: OG1 x: 8.991000175476074 y:-2.943000078201294 z:44.060001373291016
- atom: CG2 x: 9.998000144958496 y:-0.7699999809265137 z:44.17599868774414
- residue ARG has 11 atoms
- atom: N x: 6.604000091552734 y:-3.2290000915527344 z:46.2239990234375
- atom: CA x: 5.4070000648498535 y:-4.083000183105469 z:46.25
- atom: C x: 4.270999908447266 y:-3.384000062942505 z:46.97600173950195
- atom: O x: 3.1610000133514404 y:-3.9130001068115234 z:47.06999969482422
- atom: CB x: 5.684999942779541 y:-5.426000118255615 z:46.926998138427734
- atom: CG x: 6.485000133514404 y:-6.410999774932861 z:46.06700134277344
- atom: CD x: 7.070000171661377 y:-7.552000045776367 z:46.89799880981445
- atom: NE x: 6.085000038146973 y:-8.112000465393066 z:47.81800079345703
- atom: CZ x: 6.336999893188477 y:-9.085000038146973 z:48.68600082397461
- atom: NH1 x: 7.546000003814697 y:-9.621999740600586 z:48.762001037597656
- atom: NH2 x: 5.382999897003174 y:-9.510000228881836 z:49.492000579833984
- residue VAL has 7 atoms
- atom: N x: 4.554999828338623 y:-2.2019999027252197 z:47.51300048828125
- atom: CA x: 3.5380001068115234 y:-1.4140000343322754 z:48.19200134277344
- atom: C x: 3.002000093460083 y:-0.4729999899864197 z:47.124000549316406
- atom: O x: 3.7679998874664307 y:0.1459999978542328 z:46.38100051879883
- atom: CB x: 4.129000186920166 y:-0.6010000109672546 z:49.367000579833984
- atom: CG1 x: 3.115000009536743 y:0.40299999713897705 z:49.87699890136719
- atom: CG2 x: 4.514999866485596 y:-1.5449999570846558 z:50.49800109863281
- residue SER has 6 atoms
- atom: N x: 1.6820000410079956 y:-0.3880000114440918 z:47.029998779296875
- atom: CA x: 1.0529999732971191 y:0.453000009059906 z:46.0260009765625
- atom: C x: 1.2309999465942383 y:1.902999997138977 z:46.388999938964844
- atom: O x: 0.7540000081062317 y:2.3459999561309814 z:47.4370002746582
- atom: CB x: -0.4350000023841858 y:0.12800000607967377 z:45.922000885009766
- atom: OG x: -0.9639999866485596 y:0.6510000228881836 z:44.733001708984375
- residue GLY has 4 atoms
- atom: N x: 1.9040000438690186 y:2.6449999809265137 z:45.51599884033203
- atom: CA x: 2.1429998874664307 y:4.053999900817871 z:45.7760009765625
- atom: C x: 3.634999990463257 y:4.316999912261963 z:45.90299987792969
- atom: O x: 4.10099983215332 y:5.461999893188477 z:45.915000915527344
- residue ILE has 8 atoms
- atom: N x: 4.392000198364258 y:3.2300000190734863 z:45.9900016784668
- atom: CA x: 5.824999809265137 y:3.325000047683716 z:46.11600112915039
- atom: C x: 6.491000175476074 y:2.7769999504089355 z:44.880001068115234
- atom: O x: 6.464000225067139 y:1.5800000429153442 z:44.64099884033203
- atom: CB x: 6.308000087738037 y:2.569000005722046 z:47.356998443603516
- atom: CG1 x: 5.689000129699707 y:3.2200000286102295 z:48.59600067138672
- atom: CG2 x: 7.823999881744385 y:2.5880000591278076 z:47.42300033569336
- atom: CD1 x: 5.960000038146973 y:2.489000082015991 z:49.89400100708008
- residue GLY has 4 atoms
- atom: N x: 7.071000099182129 y:3.6670000553131104 z:44.08700180053711
- atom: CA x: 7.74399995803833 y:3.2360000610351562 z:42.8849983215332
- atom: C x: 9.239999771118164 y:3.2160000801086426 z:43.108001708984375
- atom: O x: 9.706999778747559 y:3.369999885559082 z:44.23500061035156
- residue PRO has 7 atoms
- atom: N x: 10.027999877929688 y:3.0280001163482666 z:42.04600143432617
- atom: CA x: 11.480999946594238 y:3.003999948501587 z:42.20600128173828
- atom: C x: 11.973999977111816 y:4.1529998779296875 z:43.07600021362305
- atom: O x: 12.366000175476074 y:3.944999933242798 z:44.2140007019043
- atom: CB x: 11.97599983215332 y:3.0999999046325684 z:40.766998291015625
- atom: CG x: 10.942999839782715 y:2.306999921798706 z:40.03300094604492
- atom: CD x: 9.645000457763672 y:2.819000005722046 z:40.638999938964844
- residue SER has 6 atoms
- atom: N x: 11.925999641418457 y:5.367000102996826 z:42.54199981689453
- atom: CA x: 12.390000343322754 y:6.557000160217285 z:43.24700164794922
- atom: C x: 12.029000282287598 y:6.611000061035156 z:44.720001220703125
- atom: O x: 12.913999557495117 y:6.75 z:45.55099868774414
- atom: CB x: 11.88700008392334 y:7.824999809265137 z:42.54899978637695
- atom: OG x: 12.267000198364258 y:9.003000259399414 z:43.255001068115234
- residue ALA has 5 atoms
- atom: N x: 10.75 y:6.5229997634887695 z:45.060001373291016
- atom: CA x: 10.368000030517578 y:6.559999942779541 z:46.47700119018555
- atom: C x: 11.04699993133545 y:5.427999973297119 z:47.2599983215332
- atom: O x: 11.673999786376953 y:5.670000076293945 z:48.2869987487793
- atom: CB x: 8.85200023651123 y:6.466000080108643 z:46.63600158691406
- residue ALA has 5 atoms
- atom: N x: 10.935999870300293 y:4.192999839782715 z:46.78499984741211
- atom: CA x: 11.574999809265137 y:3.0989999771118164 z:47.499000549316406
- atom: C x: 13.069999694824219 y:3.3540000915527344 z:47.66600036621094
- atom: O x: 13.619000434875488 y:3.138000011444092 z:48.733001708984375
- atom: CB x: 11.357000350952148 y:1.7940000295639038 z:46.77399826049805
- residue ARG has 11 atoms
- atom: N x: 13.737000465393066 y:3.808000087738037 z:46.617000579833984
- atom: CA x: 15.163999557495117 y:4.068999767303467 z:46.73899841308594
- atom: C x: 15.439000129699707 y:5.125999927520752 z:47.801998138427734
- atom: O x: 16.441999435424805 y:5.046999931335449 z:48.50899887084961
- atom: CB x: 15.765000343322754 y:4.5269999504089355 z:45.41400146484375
- atom: CG x: 17.187000274658203 y:5.013999938964844 z:45.55500030517578
- atom: CD x: 17.774999618530273 y:5.38100004196167 z:44.2130012512207
- atom: NE x: 17.91900062561035 y:4.206999778747559 z:43.36199951171875
- atom: CZ x: 18.624000549316406 y:3.128000020980835 z:43.6879997253418
- atom: NH1 x: 19.253999710083008 y:3.075000047683716 z:44.85200119018555
- atom: NH2 x: 18.694000244140625 y:2.1010000705718994 z:42.85100173950195
- residue LYS has 9 atoms
- atom: N x: 14.557000160217285 y:6.117000102996826 z:47.91299819946289
- atom: CA x: 14.75 y:7.156000137329102 z:48.909000396728516
- atom: C x: 14.637999534606934 y:6.564000129699707 z:50.31399917602539
- atom: O x: 15.583000183105469 y:6.656000137329102 z:51.0880012512207
- atom: CB x: 13.739999771118164 y:8.288999557495117 z:48.73099899291992
- atom: CG x: 13.96399974822998 y:9.401000022888184 z:49.72600173950195
- atom: CD x: 13.178999900817871 y:10.670000076293945 z:49.441001892089844
- atom: CE x: 13.61400032043457 y:11.75100040435791 z:50.43299865722656
- atom: NZ x: 12.967000007629395 y:13.07800006866455 z:50.22100067138672
- residue PHE has 11 atoms
- atom: N x: 13.501999855041504 y:5.952000141143799 z:50.64099884033203
- atom: CA x: 13.32699966430664 y:5.343999862670898 z:51.95600128173828
- atom: C x: 14.543999671936035 y:4.506999969482422 z:52.38100051879883
- atom: O x: 15.128999710083008 y:4.742000102996826 z:53.430999755859375
- atom: CB x: 12.090999603271484 y:4.448999881744385 z:51.974998474121094
- atom: CG x: 10.807000160217285 y:5.189000129699707 z:51.819000244140625
- atom: CD1 x: 10.470999717712402 y:6.210000038146973 z:52.6879997253418
- atom: CD2 x: 9.913000106811523 y:4.8480000495910645 z:50.8129997253418
- atom: CE1 x: 9.260000228881836 y:6.885000228881836 z:52.5629997253418
- atom: CE2 x: 8.70199966430664 y:5.513000011444092 z:50.67900085449219
- atom: CZ x: 8.378000259399414 y:6.534999847412109 z:51.560001373291016
- residue VAL has 7 atoms
- atom: N x: 14.911999702453613 y:3.5230000019073486 z:51.564998626708984
- atom: CA x: 16.048999786376953 y:2.6570000648498535 z:51.86399841308594
- atom: C x: 17.27199935913086 y:3.493000030517578 z:52.22100067138672
- atom: O x: 17.93000030517578 y:3.2239999771118164 z:53.21799850463867
- atom: CB x: 16.365999221801758 y:1.7050000429153442 z:50.66899871826172
- atom: CG1 x: 17.589000701904297 y:0.8560000061988831 z:50.96099853515625
- atom: CG2 x: 15.1850004196167 y:0.796999990940094 z:50.41600036621094
- residue ASP has 8 atoms
- atom: N x: 17.565000534057617 y:4.51800012588501 z:51.428001403808594
- atom: CA x: 18.70800018310547 y:5.386000156402588 z:51.70800018310547
- atom: C x: 18.582000732421875 y:6.093999862670898 z:53.05699920654297
- atom: O x: 19.562000274658203 y:6.625999927520752 z:53.564998626708984
- atom: CB x: 18.885000228881836 y:6.446000099182129 z:50.612998962402344
- atom: CG x: 19.240999221801758 y:5.841000080108643 z:49.27000045776367
- atom: OD1 x: 19.964000701904297 y:4.815999984741211 z:49.257999420166016
- atom: OD2 x: 18.80900001525879 y:6.396999835968018 z:48.229000091552734
- residue GLU has 9 atoms
- atom: N x: 17.381000518798828 y:6.117000102996826 z:53.62699890136719
- atom: CA x: 17.163999557495117 y:6.752999782562256 z:54.92300033569336
- atom: C x: 16.847999572753906 y:5.6570000648498535 z:55.96799850463867
- atom: O x: 16.23900032043457 y:5.9070000648498535 z:57.007999420166016
- atom: CB x: 16.024999618530273 y:7.790999889373779 z:54.821998596191406
- atom: CG x: 16.170000076293945 y:8.746000289916992 z:53.61800003051758
- atom: CD x: 15.095000267028809 y:9.843000411987305 z:53.54600143432617
- atom: OE1 x: 13.904000282287598 y:9.550999641418457 z:53.82699966430664
- atom: OE2 x: 15.446000099182129 y:10.996000289916992 z:53.183998107910156
- residue GLY has 4 atoms
- atom: N x: 17.257999420166016 y:4.429999828338623 z:55.65800094604492
- atom: CA x: 17.05900001525879 y:3.325000047683716 z:56.571998596191406
- atom: C x: 15.710000038146973 y:2.6449999809265137 z:56.645999908447266
- atom: O x: 15.593000411987305 y:1.6239999532699585 z:57.33100128173828
- residue ILE has 8 atoms
- atom: N x: 14.696999549865723 y:3.197999954223633 z:55.98099899291992
- atom: CA x: 13.359000205993652 y:2.5959999561309814 z:55.972999572753906
- atom: C x: 13.357000350952148 y:1.5210000276565552 z:54.89799880981445
- atom: O x: 13.423999786376953 y:1.8480000495910645 z:53.7130012512207
- atom: CB x: 12.27299976348877 y:3.614000082015991 z:55.59700012207031
- atom: CG1 x: 12.300999641418457 y:4.796999931335449 z:56.5620002746582
- atom: CG2 x: 10.91100025177002 y:2.947999954223633 z:55.63399887084961
- atom: CD1 x: 11.234000205993652 y:5.835999965667725 z:56.28099822998047
- residue LYS has 9 atoms
- atom: N x: 13.265000343322754 y:0.25099998712539673 z:55.29199981689453
- atom: CA x: 13.29800033569336 y:-0.828000009059906 z:54.305999755859375
- atom: C x: 12.36299991607666 y:-2.01200008392334 z:54.54800033569336
- atom: O x: 12.54699993133545 y:-3.068000078201294 z:53.96500015258789
- atom: CB x: 14.72599983215332 y:-1.3580000400543213 z:54.194000244140625
- atom: CG x: 15.210000038146973 y:-2.0199999809265137 z:55.479000091552734
- atom: CD x: 16.617000579833984 y:-2.6059999465942383 z:55.35300064086914
- atom: CE x: 17.683000564575195 y:-1.5269999504089355 z:55.19200134277344
- atom: NZ x: 19.045000076293945 y:-2.1089999675750732 z:55.125999450683594
- residue THR has 7 atoms
- atom: N x: 11.362000465393066 y:-1.8580000400543213 z:55.39500045776367
- atom: CA x: 10.472999572753906 y:-2.9719998836517334 z:55.65399932861328
- atom: C x: 9.10200023651123 y:-2.507999897003174 z:56.108001708984375
- atom: O x: 8.946999549865723 y:-1.378999948501587 z:56.555999755859375
- atom: CB x: 11.092000007629395 y:-3.8940000534057617 z:56.70600128173828
- atom: OG1 x: 11.718000411987305 y:-3.0959999561309814 z:57.71200180053711
- atom: CG2 x: 12.14799976348877 y:-4.789000034332275 z:56.07899856567383
- residue LEU has 8 atoms
- atom: N x: 8.11299991607666 y:-3.38700008392334 z:55.98899841308594
- atom: CA x: 6.741000175476074 y:-3.065000057220459 z:56.361000061035156
- atom: C x: 6.663000106811523 y:-2.3540000915527344 z:57.698001861572266
- atom: O x: 5.9079999923706055 y:-1.3930000066757202 z:57.867000579833984
- atom: CB x: 5.900000095367432 y:-4.335999965667725 z:56.41899871826172
- atom: CG x: 4.75600004196167 y:-4.4770002365112305 z:55.40999984741211
- atom: CD1 x: 5.265999794006348 y:-4.355999946594238 z:53.98500061035156
- atom: CD2 x: 4.0980000495910645 y:-5.828000068664551 z:55.604000091552734
- residue GLU has 9 atoms
- atom: N x: 7.443999767303467 y:-2.8399999141693115 z:58.652000427246094
- atom: CA x: 7.4720001220703125 y:-2.259000062942505 z:59.97999954223633
- atom: C x: 7.995999813079834 y:-0.824999988079071 z:59.93000030517578
- atom: O x: 7.494999885559082 y:0.04899999871850014 z:60.625
- atom: CB x: 8.338000297546387 y:-3.124000072479248 z:60.90299987792969
- atom: CG x: 7.71999979019165 y:-4.488999843597412 z:61.23899841308594
- atom: CD x: 7.673999786376953 y:-5.454999923706055 z:60.05400085449219
- atom: OE1 x: 8.753000259399414 y:-5.8520002365112305 z:59.5629997253418
- atom: OE2 x: 6.560999870300293 y:-5.826000213623047 z:59.61600112915039
- residue ASP has 8 atoms
- atom: N x: 9.005000114440918 y:-0.5849999785423279 z:59.104000091552734
- atom: CA x: 9.571999549865723 y:0.7480000257492065 z:58.9739990234375
- atom: C x: 8.531999588012695 y:1.718000054359436 z:58.41600036621094
- atom: O x: 8.362000465393066 y:2.8380000591278076 z:58.92399978637695
- atom: CB x: 10.795999526977539 y:0.6819999814033508 z:58.07600021362305
- atom: CG x: 11.92300033569336 y:-0.08399999886751175 z:58.7140007019043
- atom: OD1 x: 11.635000228881836 y:-1.0809999704360962 z:59.4010009765625
- atom: OD2 x: 13.090999603271484 y:0.3059999942779541 z:58.529998779296875
- residue LEU has 8 atoms
- atom: N x: 7.834000110626221 y:1.2890000343322754 z:57.37099838256836
- atom: CA x: 6.793000221252441 y:2.117000102996826 z:56.79399871826172
- atom: C x: 5.763000011444092 y:2.321000099182129 z:57.895999908447266
- atom: O x: 5.111000061035156 y:3.3589999675750732 z:57.95600128173828
- atom: CB x: 6.164000034332275 y:1.4190000295639038 z:55.58599853515625
- atom: CG x: 7.113999843597412 y:1.1069999933242798 z:54.428001403808594
- atom: CD1 x: 6.370999813079834 y:0.3479999899864197 z:53.361000061035156
- atom: CD2 x: 7.696000099182129 y:2.390000104904175 z:53.86399841308594
- residue ARG has 11 atoms
- atom: N x: 5.632999897003174 y:1.3179999589920044 z:58.76499938964844
- atom: CA x: 4.715000152587891 y:1.3680000305175781 z:59.90700149536133
- atom: C x: 5.168000221252441 y:2.438999891281128 z:60.90299987792969
- atom: O x: 4.3460001945495605 y:3.1530001163482666 z:61.48099899291992
- atom: CB x: 4.678999900817871 y:0.017999999225139618 z:60.619998931884766
- atom: CG x: 3.812999963760376 y:-1.0190000534057617 z:59.95800018310547
- atom: CD x: 2.361999988555908 y:-0.7979999780654907 z:60.33000183105469
- atom: NE x: 1.4429999589920044 y:-1.5540000200271606 z:59.483001708984375
- atom: CZ x: 1.4910000562667847 y:-2.869999885559082 z:59.29999923706055
- atom: NH1 x: 2.4179999828338623 y:-3.5999999046325684 z:59.909000396728516
- atom: NH2 x: 0.6159999966621399 y:-3.4560000896453857 z:58.4900016784668
- residue LYS has 9 atoms
- atom: N x: 6.4770002365112305 y:2.5450000762939453 z:61.104000091552734
- atom: CA x: 7.011000156402588 y:3.5309998989105225 z:62.02199935913086
- atom: C x: 6.9720001220703125 y:4.920000076293945 z:61.40399932861328
- atom: O x: 6.544000148773193 y:5.894000053405762 z:62.04800033569336
- atom: CB x: 8.460000038146973 y:3.2070000171661377 z:62.402000427246094
- atom: CG x: 9.081999778747559 y:4.255000114440918 z:63.327999114990234
- atom: CD x: 10.49899959564209 y:3.9030001163482666 z:63.790000915527344
- atom: CE x: 11.552000045776367 y:4.183000087738037 z:62.72600173950195
- atom: NZ x: 12.932000160217285 y:4.047999858856201 z:63.28200149536133
- residue ASN has 8 atoms
- atom: N x: 7.419000148773193 y:5.011000156402588 z:60.154998779296875
- atom: CA x: 7.459000110626221 y:6.291999816894531 z:59.483001708984375
- atom: C x: 6.232999801635742 y:6.5929999351501465 z:58.65599822998047
- atom: O x: 6.293000221252441 y:7.327000141143799 z:57.68299865722656
- atom: CB x: 8.72700023651123 y:6.385000228881836 z:58.63999938964844
- atom: CG x: 9.965999603271484 y:6.585999965667725 z:59.49399948120117
- atom: OD1 x: 11.059000015258789 y:6.823999881744385 z:58.986000061035156
- atom: ND2 x: 9.795000076293945 y:6.491000175476074 z:60.81100082397461
- residue GLU has 9 atoms
- atom: N x: 5.109000205993652 y:6.044000148773193 z:59.08000183105469
- atom: CA x: 3.8510000705718994 y:6.230999946594238 z:58.387001037597656
- atom: C x: 3.5390000343322754 y:7.684000015258789 z:58.02299880981445
- atom: O x: 3.0429999828338623 y:7.9670000076293945 z:56.933998107910156
- atom: CB x: 2.7279999256134033 y:5.677000045776367 z:59.244998931884766
- atom: CG x: 1.3849999904632568 y:5.681000232696533 z:58.58300018310547
- atom: CD x: 0.2879999876022339 y:5.394999980926514 z:59.57400131225586
- atom: OE1 x: 0.3709999918937683 y:4.359000205993652 z:60.27399826049805
- atom: OE2 x: -0.6549999713897705 y:6.210999965667725 z:59.65399932861328
- residue ASP has 8 atoms
- atom: N x: 3.8320000171661377 y:8.607999801635742 z:58.926998138427734
- atom: CA x: 3.5360000133514404 y:10.008000373840332 z:58.665000915527344
- atom: C x: 4.449999809265137 y:10.621000289916992 z:57.61399841308594
- atom: O x: 4.502999782562256 y:11.836999893188477 z:57.472999572753906
- atom: CB x: 3.615000009536743 y:10.812000274658203 z:59.96900177001953
- atom: CG x: 5.039000034332275 y:11.223999977111816 z:60.327999114990234
- atom: OD1 x: 5.9720001220703125 y:10.38599967956543 z:60.19599914550781
- atom: OD2 x: 5.216000080108643 y:12.392000198364258 z:60.75600051879883
- residue LYS has 9 atoms
- atom: N x: 5.159999847412109 y:9.774999618530273 z:56.874000549316406
- atom: CA x: 6.084000110626221 y:10.223999977111816 z:55.83000183105469
- atom: C x: 5.663000106811523 y:9.597999572753906 z:54.479000091552734
- atom: O x: 6.453000068664551 y:9.491999626159668 z:53.529998779296875
- atom: CB x: 7.515999794006348 y:9.8149995803833 z:56.21200180053711
- atom: CG x: 8.607000350952148 y:10.362000465393066 z:55.303001403808594
- atom: CD x: 9.99899959564209 y:9.871000289916992 z:55.709999084472656
- atom: CE x: 10.60200023651123 y:10.678999900817871 z:56.86199951171875
- atom: NZ x: 9.82699966430664 y:10.61400032043457 z:58.130001068115234
- residue LEU has 8 atoms
- atom: N x: 4.395999908447266 y:9.199000358581543 z:54.41299819946289
- atom: CA x: 3.8239998817443848 y:8.581000328063965 z:53.22800064086914
- atom: C x: 2.6070001125335693 y:9.369999885559082 z:52.75899887084961
- atom: O x: 1.850000023841858 y:9.902000427246094 z:53.573001861572266
- atom: CB x: 3.36299991607666 y:7.158999919891357 z:53.55099868774414
- atom: CG x: 4.328999996185303 y:6.171999931335449 z:54.19900131225586
- atom: CD1 x: 3.621999979019165 y:4.828999996185303 z:54.38100051879883
- atom: CD2 x: 5.563000202178955 y:6.019000053405762 z:53.32899856567383
- residue ASN has 8 atoms
- atom: N x: 2.4019999504089355 y:9.430999755859375 z:51.45000076293945
- atom: CA x: 1.2419999837875366 y:10.133999824523926 z:50.926998138427734
- atom: C x: 0.014000000432133675 y:9.26099967956543 z:51.11600112915039
- atom: O x: 0.12300000339746475 y:8.086999893188477 z:51.41600036621094
- atom: CB x: 1.4190000295639038 y:10.456000328063965 z:49.446998596191406
- atom: CG x: 1.8220000267028809 y:9.25100040435791 z:48.641998291015625
- atom: OD1 x: 1.2480000257492065 y:8.178000450134277 z:48.77899932861328
- atom: ND2 x: 2.812999963760376 y:9.425999641418457 z:47.790000915527344
- residue HIS has 10 atoms
- atom: N x: -1.1540000438690186 y:9.850000381469727 z:50.94499969482422
- atom: CA x: -2.4070000648498535 y:9.142999649047852 z:51.106998443603516
- atom: C x: -2.4030001163482666 y:7.800000190734863 z:50.391998291015625
- atom: O x: -2.8350000381469727 y:6.7829999923706055 z:50.939998626708984
- atom: CB x: -3.5369999408721924 y:10.003999710083008 z:50.566001892089844
- atom: CG x: -4.88100004196167 y:9.364999771118164 z:50.6619987487793
- atom: ND1 x: -5.572999954223633 y:9.265000343322754 z:51.8489990234375
- atom: CD2 x: -5.666999816894531 y:8.79800033569336 z:49.720001220703125
- atom: CE1 x: -6.730000019073486 y:8.668000221252441 z:51.6349983215332
- atom: NE2 x: -6.811999797821045 y:8.37399959564209 z:50.35100173950195
- residue HIS has 10 atoms
- atom: N x: -1.8949999809265137 y:7.797999858856201 z:49.17100143432617
- atom: CA x: -1.8609999418258667 y:6.583000183105469 z:48.375
- atom: C x: -0.9599999785423279 y:5.51200008392334 z:48.986000061035156
- atom: O x: -1.3209999799728394 y:4.3420000076293945 z:49.013999938964844
- atom: CB x: -1.4359999895095825 y:6.927999973297119 z:46.933998107910156
- atom: CG x: -1.406000018119812 y:5.757999897003174 z:45.99700164794922
- atom: ND1 x: -1.434999942779541 y:5.908999919891357 z:44.62900161743164
- atom: CD2 x: -1.2580000162124634 y:4.429999828338623 z:46.2239990234375
- atom: CE1 x: -1.3009999990463257 y:4.728000164031982 z:44.05400085449219
- atom: NE2 x: -1.190999984741211 y:3.815000057220459 z:45.000999450683594
- residue GLN has 9 atoms
- atom: N x: 0.20800000429153442 y:5.910999774932861 z:49.47100067138672
- atom: CA x: 1.1390000581741333 y:4.968999862670898 z:50.07500076293945
- atom: C x: 0.5680000185966492 y:4.394000053405762 z:51.38800048828125
- atom: O x: 0.800000011920929 y:3.2219998836517334 z:51.69599914550781
- atom: CB x: 2.499000072479248 y:5.65500020980835 z:50.30099868774414
- atom: CG x: 3.200000047683716 y:6.076000213623047 z:49.00299835205078
- atom: CD x: 4.383999824523926 y:7.015999794006348 z:49.22100067138672
- atom: OE1 x: 4.260000228881836 y:8.043000221252441 z:49.88100051879883
- atom: NE2 x: 5.531000137329102 y:6.669000148773193 z:48.65399932861328
- residue ARG has 11 atoms
- atom: N x: -0.18000000715255737 y:5.201000213623047 z:52.150001525878906
- atom: CA x: -0.777999997138977 y:4.710000038146973 z:53.39099884033203
- atom: C x: -1.7100000381469727 y:3.572999954223633 z:53.02399826049805
- atom: O x: -1.562999963760376 y:2.4649999141693115 z:53.52199935913086
- atom: CB x: -1.6130000352859497 y:5.7779998779296875 z:54.10200119018555
- atom: CG x: -0.9010000228881836 y:6.5980000495910645 z:55.172000885009766
- atom: CD x: -0.2150000035762787 y:7.790999889373779 z:54.56999969482422
- atom: NE x: 0.1120000034570694 y:8.810999870300293 z:55.56100082397461
- atom: CZ x: -0.7559999823570251 y:9.329000473022461 z:56.428001403808594
- atom: NH1 x: -2.0209999084472656 y:8.916000366210938 z:56.444000244140625
- atom: NH2 x: -0.3630000054836273 y:10.286999702453613 z:57.26100158691406
- residue ILE has 8 atoms
- atom: N x: -2.6760001182556152 y:3.8610000610351562 z:52.15399932861328
- atom: CA x: -3.6410000324249268 y:2.8570001125335693 z:51.694000244140625
- atom: C x: -2.88700008392334 y:1.61899995803833 z:51.20600128173828
- atom: O x: -3.2730000019073486 y:0.48100000619888306 z:51.500999450683594
- atom: CB x: -4.520999908447266 y:3.4000000953674316 z:50.507999420166016
- atom: CG1 x: -5.324999809265137 y:4.625999927520752 z:50.95399856567383
- atom: CG2 x: -5.440999984741211 y:2.302999973297119 z:49.98400115966797
- atom: CD1 x: -6.333000183105469 y:4.361000061035156 z:52.060001373291016
- residue GLY has 4 atoms
- atom: N x: -1.8070000410079956 y:1.8609999418258667 z:50.465999603271484
- atom: CA x: -0.996999979019165 y:0.7850000262260437 z:49.92599868774414
- atom: C x: -0.5400000214576721 y:-0.16500000655651093 z:51.00400161743164
- atom: O x: -0.7350000143051147 y:-1.371000051498413 z:50.88600158691406
- residue LEU has 8 atoms
- atom: N x: 0.05900000035762787 y:0.4000000059604645 z:52.053001403808594
- atom: CA x: 0.5699999928474426 y:-0.34200000762939453 z:53.20199966430664
- atom: C x: -0.5519999861717224 y:-1.0260000228881836 z:53.93899917602539
- atom: O x: -0.4169999957084656 y:-2.1730000972747803 z:54.332000732421875
- atom: CB x: 1.2879999876022339 y:0.6060000061988831 z:54.16699981689453
- atom: CG x: 1.7599999904632568 y:0.08100000023841858 z:55.53300094604492
- atom: CD1 x: 2.7009999752044678 y:-1.0989999771118164 z:55.36000061035156
- atom: CD2 x: 2.4820001125335693 y:1.2120000123977661 z:56.27399826049805
- residue LYS has 9 atoms
- atom: N x: -1.6549999713897705 y:-0.3050000071525574 z:54.11899948120117
- atom: CA x: -2.8510000705718994 y:-0.7960000038146973 z:54.805999755859375
- atom: C x: -3.437999963760376 y:-2.068000078201294 z:54.21099853515625
- atom: O x: -3.943000078201294 y:-2.9210000038146973 z:54.93199920654297
- atom: CB x: -3.940000057220459 y:0.2750000059604645 z:54.79199981689453
- atom: CG x: -5.296000003814697 y:-0.2150000035762787 z:55.270999908447266
- atom: CD x: -6.254000186920166 y:0.9430000185966492 z:55.45000076293945
- atom: CE x: -7.507999897003174 y:0.5070000290870667 z:56.176998138427734
- atom: NZ x: -8.45300006866455 y:1.6299999952316284 z:56.4119987487793
- residue TYR has 12 atoms
- atom: N x: -3.3940000534057617 y:-2.177999973297119 z:52.891998291015625
- atom: CA x: -3.928999900817871 y:-3.3459999561309814 z:52.2140007019043
- atom: C x: -2.806999921798706 y:-4.0879998207092285 z:51.51499938964844
- atom: O x: -3.015000104904175 y:-4.678999900817871 z:50.43899917602539
- atom: CB x: -4.980999946594238 y:-2.921999931335449 z:51.1870002746582
- atom: CG x: -6.118000030517578 y:-2.1530001163482666 z:51.79399871826172
- atom: CD1 x: -6.923999786376953 y:-2.7249999046325684 z:52.77000045776367
- atom: CD2 x: -6.373000144958496 y:-0.8399999737739563 z:51.41600036621094
- atom: CE1 x: -7.953999996185303 y:-2.003000020980835 z:53.3650016784668
- atom: CE2 x: -7.40500020980835 y:-0.10899999737739563 z:51.999000549316406
- atom: CZ x: -8.187999725341797 y:-0.6949999928474426 z:52.97100067138672
- atom: OH x: -9.218999862670898 y:0.01899999938905239 z:53.53499984741211
- residue PHE has 11 atoms
- atom: N x: -1.6200000047683716 y:-4.072000026702881 z:52.117000579833984
- atom: CA x: -0.4959999918937683 y:-4.738999843597412 z:51.47700119018555
- atom: C x: -0.7870000004768372 y:-6.201000213623047 z:51.15299987792969
- atom: O x: -0.6729999780654907 y:-6.626999855041504 z:50.005001068115234
- atom: CB x: 0.7450000047683716 y:-4.664000034332275 z:52.33300018310547
- atom: CG x: 1.934000015258789 y:-5.28000020980835 z:51.691001892089844
- atom: CD1 x: 2.6610000133514404 y:-4.579999923706055 z:50.74100112915039
- atom: CD2 x: 2.321000099182129 y:-6.566999912261963 z:52.01900100708008
- atom: CE1 x: 3.7679998874664307 y:-5.1479997634887695 z:50.12099838256836
- atom: CE2 x: 3.427000045776367 y:-7.1579999923706055 z:51.409000396728516
- atom: CZ x: 4.156000137329102 y:-6.446000099182129 z:50.45500183105469
- residue GLY has 4 atoms
- atom: N x: -1.159999966621399 y:-6.968999862670898 z:52.16699981689453
- atom: CA x: -1.4630000591278076 y:-8.36299991607666 z:51.941001892089844
- atom: C x: -2.6440000534057617 y:-8.527000427246094 z:51.00699996948242
- atom: O x: -2.572000026702881 y:-9.300000190734863 z:50.05500030517578
- residue ASP has 8 atoms
- atom: N x: -3.7300000190734863 y:-7.806000232696533 z:51.2760009765625
- atom: CA x: -4.914000034332275 y:-7.888999938964844 z:50.43600082397461
- atom: C x: -4.5960001945495605 y:-7.710999965667725 z:48.95600128173828
- atom: O x: -4.974999904632568 y:-8.550000190734863 z:48.137001037597656
- atom: CB x: -5.949999809265137 y:-6.8480000495910645 z:50.856998443603516
- atom: CG x: -6.870999813079834 y:-7.361999988555908 z:51.93000030517578
- atom: OD1 x: -6.843999862670898 y:-8.590999603271484 z:52.15800094604492
- atom: OD2 x: -7.624000072479248 y:-6.559999942779541 z:52.5369987487793
- residue PHE has 11 atoms
- atom: N x: -3.8889999389648438 y:-6.633999824523926 z:48.61899948120117
- atom: CA x: -3.5399999618530273 y:-6.348999977111816 z:47.233001708984375
- atom: C x: -2.683000087738037 y:-7.379000186920166 z:46.516998291015625
- atom: O x: -2.6549999713897705 y:-7.396999835968018 z:45.290000915527344
- atom: CB x: -2.8589999675750732 y:-4.974999904632568 z:47.108001708984375
- atom: CG x: -3.7939999103546143 y:-3.812000036239624 z:47.305999755859375
- atom: CD1 x: -5.133999824523926 y:-4.020999908447266 z:47.62699890136719
- atom: CD2 x: -3.3239998817443848 y:-2.5139999389648438 z:47.233001708984375
- atom: CE1 x: -5.98199987411499 y:-2.9639999866485596 z:47.88100051879883
- atom: CE2 x: -4.168000221252441 y:-1.437999963760376 z:47.48699951171875
- atom: CZ x: -5.502999782562256 y:-1.6649999618530273 z:47.814998626708984
- residue GLU has 9 atoms
- atom: N x: -1.9630000591278076 y:-8.22700023651123 z:47.244998931884766
- atom: CA x: -1.1390000581741333 y:-9.21399974822998 z:46.55099868774414
- atom: C x: -1.9110000133514404 y:-10.48900032043457 z:46.32899856567383
- atom: O x: -1.409000039100647 y:-11.414999961853027 z:45.70899963378906
- atom: CB x: 0.16899999976158142 y:-9.505000114440918 z:47.30400085449219
- atom: CG x: 1.1510000228881836 y:-8.329999923706055 z:47.29899978637695
- atom: CD x: 2.6040000915527344 y:-8.77299976348877 z:47.356998443603516
- atom: OE1 x: 2.9189999103546143 y:-9.692000389099121 z:48.141998291015625
- atom: OE2 x: 3.434000015258789 y:-8.196000099182129 z:46.624000549316406
- residue LYS has 9 atoms
- atom: N x: -3.138000011444092 y:-10.534000396728516 z:46.82699966430664
- atom: CA x: -3.9719998836517334 y:-11.711000442504883 z:46.63999938964844
- atom: C x: -4.692999839782715 y:-11.647000312805176 z:45.2859992980957
- atom: O x: -5.2129998207092285 y:-10.595000267028809 z:44.89500045776367
- atom: CB x: -5.033999919891357 y:-11.817000389099121 z:47.742000579833984
- atom: CG x: -4.519999980926514 y:-12.019000053405762 z:49.15399932861328
- atom: CD x: -5.681000232696533 y:-12.40999984741211 z:50.0629997253418
- atom: CE x: -5.315000057220459 y:-12.395000457763672 z:51.53200149536133
- atom: NZ x: -4.199999809265137 y:-13.324000358581543 z:51.86800003051758
- residue ARG has 11 atoms
- atom: N x: -4.708000183105469 y:-12.767999649047852 z:44.57099914550781
- atom: CA x: -5.4120001792907715 y:-12.85200023651123 z:43.29800033569336
- atom: C x: -6.906000137329102 y:-12.857999801635742 z:43.64899826049805
- atom: O x: -7.281000137329102 y:-13.098999977111816 z:44.79600143432617
- atom: CB x: -5.052000045776367 y:-14.151000022888184 z:42.57400131225586
- atom: CG x: -3.5899999141693115 y:-14.277000427246094 z:42.189998626708984
- atom: CD x: -3.253000020980835 y:-13.343000411987305 z:41.04800033569336
- atom: NE x: -4.007999897003174 y:-13.678000450134277 z:39.84000015258789
- atom: CZ x: -4.105000019073486 y:-12.894000053405762 z:38.768001556396484
- atom: NH1 x: -3.496999979019165 y:-11.711999893188477 z:38.73899841308594
- atom: NH2 x: -4.809000015258789 y:-13.298999786376953 z:37.71799850463867
- residue ILE has 8 atoms
- atom: N x: -7.75600004196167 y:-12.595000267028809 z:42.66600036621094
- atom: CA x: -9.199000358581543 y:-12.581000328063965 z:42.89099884033203
- atom: C x: -9.857999801635742 y:-13.762999534606934 z:42.17300033569336
- atom: O x: -9.720000267028809 y:-13.904000282287598 z:40.957000732421875
- atom: CB x: -9.817000389099121 y:-11.27400016784668 z:42.358001708984375
- atom: CG1 x: -9.052000045776367 y:-10.076000213623047 z:42.92499923706055
- atom: CG2 x: -11.300999641418457 y:-11.206000328063965 z:42.729000091552734
- atom: CD1 x: -9.505000114440918 y:-8.73900032043457 z:42.39799880981445
- residue PRO has 7 atoms
- atom: N x: -10.585000038146973 y:-14.626999855041504 z:42.9119987487793
- atom: CA x: -11.241999626159668 y:-15.781999588012695 z:42.277000427246094
- atom: C x: -12.177000045776367 y:-15.265999794006348 z:41.198001861572266
- atom: O x: -12.9399995803833 y:-14.333000183105469 z:41.44900131225586
- atom: CB x: -12.015000343322754 y:-16.426000595092773 z:43.42599868774414
- atom: CG x: -11.246999740600586 y:-15.991999626159668 z:44.65399932861328
- atom: CD x: -10.90999984741211 y:-14.5600004196167 z:44.3489990234375
- residue ARG has 11 atoms
- atom: N x: -12.13700008392334 y:-15.86400032043457 z:40.007999420166016
- atom: CA x: -12.998000144958496 y:-15.402000427246094 z:38.92300033569336
- atom: C x: -14.454999923706055 y:-15.329000473022461 z:39.33000183105469
- atom: O x: -15.230999946594238 y:-14.598999977111816 z:38.73400115966797
- atom: CB x: -12.876999855041504 y:-16.285999298095703 z:37.683998107910156
- atom: CG x: -13.494000434875488 y:-15.621000289916992 z:36.470001220703125
- atom: CD x: -13.788999557495117 y:-16.57900047302246 z:35.345001220703125
- atom: NE x: -14.845000267028809 y:-16.03700065612793 z:34.49399948120117
- atom: CZ x: -14.718000411987305 y:-14.97599983215332 z:33.696998596191406
- atom: NH1 x: -13.567000389099121 y:-14.322999954223633 z:33.61399841308594
- atom: NH2 x: -15.767000198364258 y:-14.541999816894531 z:33.007999420166016
- residue GLU has 9 atoms
- atom: N x: -14.829000473022461 y:-16.084999084472656 z:40.34700012207031
- atom: CA x: -16.200000762939453 y:-16.082000732421875 z:40.83100128173828
- atom: C x: -16.530000686645508 y:-14.770999908447266 z:41.529998779296875
- atom: O x: -17.562000274658203 y:-14.151000022888184 z:41.26499938964844
- atom: CB x: -16.413999557495117 y:-17.25200080871582 z:41.79399871826172
- atom: CG x: -17.667999267578125 y:-17.152000427246094 z:42.63999938964844
- atom: CD x: -18.077999114990234 y:-18.496999740600586 z:43.21699905395508
- atom: OE1 x: -18.999000549316406 y:-18.52400016784668 z:44.064998626708984
- atom: OE2 x: -17.48699951171875 y:-19.530000686645508 z:42.816001892089844
- residue GLU has 9 atoms
- atom: N x: -15.652999877929688 y:-14.359000205993652 z:42.4370002746582
- atom: CA x: -15.861000061035156 y:-13.123000144958496 z:43.167999267578125
- atom: C x: -15.913000106811523 y:-11.949999809265137 z:42.1879997253418
- atom: O x: -16.642000198364258 y:-10.979999542236328 z:42.409000396728516
- atom: CB x: -14.75100040435791 y:-12.937999725341797 z:44.20800018310547
- atom: CG x: -14.975000381469727 y:-13.76099967956543 z:45.46699905395508
- atom: CD x: -13.857000350952148 y:-13.616000175476074 z:46.49100112915039
- atom: OE1 x: -13.395000457763672 y:-12.477999687194824 z:46.71699905395508
- atom: OE2 x: -13.449999809265137 y:-14.640999794006348 z:47.08100128173828
- residue MET has 8 atoms
- atom: N x: -15.138999938964844 y:-12.048999786376953 z:41.106998443603516
- atom: CA x: -15.130000114440918 y:-11.010000228881836 z:40.0890007019043
- atom: C x: -16.57699966430664 y:-10.881999969482422 z:39.64799880981445
- atom: O x: -17.172000885009766 y:-9.8100004196167 z:39.71099853515625
- atom: CB x: -14.267999649047852 y:-11.425999641418457 z:38.893001556396484
- atom: CG x: -12.784000396728516 y:-11.329000473022461 z:39.141998291015625
- atom: SD x: -12.277000427246094 y:-9.61400032043457 z:39.38199996948242
- atom: CE x: -11.970999717712402 y:-9.13599967956543 z:37.689998626708984
- residue LEU has 8 atoms
- atom: N x: -17.142000198364258 y:-12.005999565124512 z:39.222999572753906
- atom: CA x: -18.52199935913086 y:-12.043999671936035 z:38.777000427246094
- atom: C x: -19.43400001525879 y:-11.295000076293945 z:39.74399948120117
- atom: O x: -20.256000518798828 y:-10.489999771118164 z:39.3129997253418
- atom: CB x: -18.979000091552734 y:-13.49899959564209 z:38.625999450683594
- atom: CG x: -18.22599983215332 y:-14.336000442504883 z:37.57699966430664
- atom: CD1 x: -18.56999969482422 y:-15.805999755859375 z:37.749000549316406
- atom: CD2 x: -18.573999404907227 y:-13.864999771118164 z:36.16899871826172
- residue GLN has 9 atoms
- atom: N x: -19.2810001373291 y:-11.53499984741211 z:41.04499816894531
- atom: CA x: -20.1299991607666 y:-10.86299991607666 z:42.040000915527344
- atom: C x: -19.868999481201172 y:-9.359000205993652 z:42.04899978637695
- atom: O x: -20.73900032043457 y:-8.557000160217285 z:42.40599822998047
- atom: CB x: -19.88800048828125 y:-11.430999755859375 z:43.44499969482422
- atom: CG x: -19.590999603271484 y:-12.925000190734863 z:43.465999603271484
- atom: CD x: -19.812999725341797 y:-13.557999610900879 z:44.827999114990234
- atom: OE1 x: -19.44499969482422 y:-14.71399974822998 z:45.05099868774414
- atom: NE2 x: -20.426000595092773 y:-12.809000015258789 z:45.742000579833984
- residue MET has 8 atoms
- atom: N x: -18.6560001373291 y:-8.982999801635742 z:41.66299819946289
- atom: CA x: -18.284000396728516 y:-7.578999996185303 z:41.612998962402344
- atom: C x: -18.82900047302246 y:-7.03000020980835 z:40.29999923706055
- atom: O x: -19.385000228881836 y:-5.929999828338623 z:40.25899887084961
- atom: CB x: -16.759000778198242 y:-7.435999870300293 z:41.68299865722656
- atom: CG x: -16.158000946044922 y:-7.941999912261963 z:42.99399948120117
- atom: SD x: -14.380999565124512 y:-8.246999740600586 z:42.926998138427734
- atom: CE x: -13.717000007629395 y:-6.666999816894531 z:43.327999114990234
- residue GLN has 9 atoms
- atom: N x: -18.690000534057617 y:-7.821000099182129 z:39.236000061035156
- atom: CA x: -19.16900062561035 y:-7.436999797821045 z:37.9119987487793
- atom: C x: -20.66699981689453 y:-7.296000003814697 z:37.957000732421875
- atom: O x: -21.280000686645508 y:-6.793000221252441 z:37.0260009765625
- atom: CB x: -18.819000244140625 y:-8.5 z:36.875999450683594
- atom: CG x: -19.424999237060547 y:-8.256999969482422 z:35.5
- atom: CD x: -19.215999603271484 y:-9.430999755859375 z:34.56100082397461
- atom: OE1 x: -19.83799934387207 y:-10.493000030517578 z:34.7140007019043
- atom: NE2 x: -18.32699966430664 y:-9.251999855041504 z:33.58399963378906
- residue ASP has 8 atoms
- atom: N x: -21.257999420166016 y:-7.749000072479248 z:39.04999923706055
- atom: CA x: -22.69499969482422 y:-7.681000232696533 z:39.194000244140625
- atom: C x: -23.049999237060547 y:-6.394999980926514 z:39.89699935913086
- atom: O x: -23.94499969482422 y:-5.671999931335449 z:39.46900177001953
- atom: CB x: -23.18600082397461 y:-8.876999855041504 z:40.00299835205078
- atom: CG x: -24.58799934387207 y:-9.300999641418457 z:39.630001068115234
- atom: OD1 x: -25.54599952697754 y:-8.54699993133545 z:39.91600036621094
- atom: OD2 x: -24.722000122070312 y:-10.397000312805176 z:39.04600143432617
- residue ILE has 8 atoms
- atom: N x: -22.33099937438965 y:-6.107999801635742 z:40.97600173950195
- atom: CA x: -22.56999969482422 y:-4.901000022888184 z:41.7599983215332
- atom: C x: -22.198999404907227 y:-3.635999917984009 z:40.992000579833984
- atom: O x: -22.82900047302246 y:-2.5940001010894775 z:41.16600036621094
- atom: CB x: -21.783000946044922 y:-4.942999839782715 z:43.0989990234375
- atom: CG1 x: -22.229999542236328 y:-6.1579999923706055 z:43.92100143432617
- atom: CG2 x: -22.006999969482422 y:-3.6570000648498535 z:43.88999938964844
- atom: CD1 x: -21.645999908447266 y:-6.208000183105469 z:45.327999114990234
- residue VAL has 7 atoms
- atom: N x: -21.18000030517578 y:-3.7290000915527344 z:40.14099884033203
- atom: CA x: -20.750999450683594 y:-2.5759999752044678 z:39.361000061035156
- atom: C x: -21.81100082397461 y:-2.3359999656677246 z:38.30500030517578
- atom: O x: -22.53499984741211 y:-1.3489999771118164 z:38.35900115966797
- atom: CB x: -19.393999099731445 y:-2.825000047683716 z:38.67300033569336
- atom: CG1 x: -18.95199966430664 y:-1.5759999752044678 z:37.946998596191406
- atom: CG2 x: -18.347000122070312 y:-3.2209999561309814 z:39.69900131225586
- residue LEU has 8 atoms
- atom: N x: -21.909000396728516 y:-3.263000011444092 z:37.358001708984375
- atom: CA x: -22.89699935913086 y:-3.177999973297119 z:36.290000915527344
- atom: C x: -24.26300048828125 y:-2.7330000400543213 z:36.8120002746582
- atom: O x: -24.941999435424805 y:-1.906000018119812 z:36.19200134277344
- atom: CB x: -23.040000915527344 y:-4.533999919891357 z:35.59600067138672
- atom: CG x: -22.295000076293945 y:-4.75 z:34.27399826049805
- atom: CD1 x: -20.80900001525879 y:-4.521999835968018 z:34.46500015258789
- atom: CD2 x: -22.566999435424805 y:-6.160999774932861 z:33.75899887084961
- residue ASN has 8 atoms
- atom: N x: -24.6560001373291 y:-3.2720000743865967 z:37.96200180053711
- atom: CA x: -25.947999954223633 y:-2.943000078201294 z:38.551998138427734
- atom: C x: -26.011999130249023 y:-1.4980000257492065 z:39.018001556396484
- atom: O x: -26.774999618530273 y:-0.6959999799728394 z:38.49100112915039
- atom: CB x: -26.240999221801758 y:-3.865999937057495 z:39.736000061035156
- atom: CG x: -27.707000732421875 y:-3.8570001125335693 z:40.130001068115234
- atom: OD1 x: -28.28499984741211 y:-2.805999994277954 z:40.42100143432617
- atom: ND2 x: -28.31800079345703 y:-5.035999774932861 z:40.14099884033203
- residue GLU has 9 atoms
- atom: N x: -25.208999633789062 y:-1.1749999523162842 z:40.02000045776367
- atom: CA x: -25.179000854492188 y:0.16699999570846558 z:40.577999114990234
- atom: C x: -25.06399917602539 y:1.25 z:39.516998291015625
- atom: O x: -25.56100082397461 y:2.3570001125335693 z:39.70199966430664
- atom: CB x: -24.020999908447266 y:0.2759999930858612 z:41.569000244140625
- atom: CG x: -24.288000106811523 y:-0.4399999976158142 z:42.861000061035156
- atom: CD x: -25.4689998626709 y:0.15700000524520874 z:43.57600021362305
- atom: OE1 x: -25.375999450683594 y:1.3259999752044678 z:43.999000549316406
- atom: OE2 x: -26.4950008392334 y:-0.5339999794960022 z:43.70399856567383
- residue VAL has 7 atoms
- atom: N x: -24.398000717163086 y:0.9309999942779541 z:38.41400146484375
- atom: CA x: -24.229999542236328 y:1.8899999856948853 z:37.33399963378906
- atom: C x: -25.618999481201172 y:2.247999906539917 z:36.79499816894531
- atom: O x: -25.95599937438965 y:3.4240000247955322 z:36.630001068115234
- atom: CB x: -23.381000518798828 y:1.2999999523162842 z:36.17900085449219
- atom: CG1 x: -23.075000762939453 y:2.36899995803833 z:35.16899871826172
- atom: CG2 x: -22.10099983215332 y:0.7269999980926514 z:36.702999114990234
- residue LYS has 9 atoms
- atom: N x: -26.413999557495117 y:1.215000033378601 z:36.52299880981445
- atom: CA x: -27.770000457763672 y:1.378000020980835 z:36.016998291015625
- atom: C x: -28.56100082397461 y:2.3529999256134033 z:36.87699890136719
- atom: O x: -29.222999572753906 y:3.249000072479248 z:36.358001708984375
- atom: CB x: -28.500999450683594 y:0.03500000014901161 z:36.00199890136719
- atom: CG x: -29.937999725341797 y:0.13699999451637268 z:35.51100158691406
- atom: CD x: -30.6560001373291 y:-1.2070000171661377 z:35.52299880981445
- atom: CE x: -31.038000106811523 y:-1.6349999904632568 z:36.933998107910156
- atom: NZ x: -31.767000198364258 y:-2.940999984741211 z:36.91899871826172
- residue LYS has 9 atoms
- atom: N x: -28.483999252319336 y:2.1700000762939453 z:38.189998626708984
- atom: CA x: -29.195999145507812 y:3.01200008392334 z:39.145999908447266
- atom: C x: -28.899999618530273 y:4.515999794006348 z:39.060001373291016
- atom: O x: -29.618000030517578 y:5.326000213623047 z:39.63399887084961
- atom: CB x: -28.916000366210938 y:2.5190000534057617 z:40.564998626708984
- atom: CG x: -29.30299949645996 y:1.0679999589920044 z:40.792999267578125
- atom: CD x: -29.030000686645508 y:0.6269999742507935 z:42.22800064086914
- atom: CE x: -29.3700008392334 y:-0.847000002861023 z:42.40999984741211
- atom: NZ x: -29.13800048828125 y:-1.3320000171661377 z:43.79899978637695
- residue VAL has 7 atoms
- atom: N x: -27.844999313354492 y:4.8979997634887695 z:38.35499954223633
- atom: CA x: -27.518999099731445 y:6.308000087738037 z:38.22700119018555
- atom: C x: -28.152000427246094 y:6.7729997634887695 z:36.92399978637695
- atom: O x: -28.701000213623047 y:7.872000217437744 z:36.827999114990234
- atom: CB x: -25.989999771118164 y:6.511000156402588 z:38.16600036621094
- atom: CG1 x: -25.635000228881836 y:7.994999885559082 z:38.32899856567383
- atom: CG2 x: -25.32699966430664 y:5.671000003814697 z:39.244998931884766
- residue ASP has 8 atoms
- atom: N x: -28.059999465942383 y:5.916999816894531 z:35.91699981689453
- atom: CA x: -28.628000259399414 y:6.202000141143799 z:34.62099838256836
- atom: C x: -28.538000106811523 y:4.939000129699707 z:33.79800033569336
- atom: O x: -27.46500015258789 y:4.364999771118164 z:33.65299987792969
- atom: CB x: -27.874000549316406 y:7.335000038146973 z:33.917999267578125
- atom: CG x: -28.533000946044922 y:7.744999885559082 z:32.60300064086914
- atom: OD1 x: -29.73699951171875 y:8.086999893188477 z:32.624000549316406
- atom: OD2 x: -27.854000091552734 y:7.7210001945495605 z:31.55299949645996
- residue SER has 6 atoms
- atom: N x: -29.67799949645996 y:4.511000156402588 z:33.266998291015625
- atom: CA x: -29.750999450683594 y:3.305000066757202 z:32.45500183105469
- atom: C x: -29.03700065612793 y:3.424999952316284 z:31.115999221801758
- atom: O x: -29.08099937438965 y:2.493000030517578 z:30.319000244140625
- atom: CB x: -31.204999923706055 y:2.9260001182556152 z:32.183998107910156
- atom: OG x: -31.709999084472656 y:3.6610000133514404 z:31.082000732421875
- residue GLU has 9 atoms
- atom: N x: -28.38800048828125 y:4.552000045776367 z:30.847999572753906
- atom: CA x: -27.687999725341797 y:4.685999870300293 z:29.575000762939453
- atom: C x: -26.202999114990234 y:4.35099983215332 z:29.645999908447266
- atom: O x: -25.54199981689453 y:4.173999786376953 z:28.621999740600586
- atom: CB x: -27.898000717163086 y:6.085999965667725 z:29.003999710083008
- atom: CG x: -29.305999755859375 y:6.269999980926514 z:28.450000762939453
- atom: CD x: -29.743999481201172 y:5.085999965667725 z:27.591999053955078
- atom: OE1 x: -29.18400001525879 y:4.901000022888184 z:26.48900032043457
- atom: OE2 x: -30.64299964904785 y:4.333000183105469 z:28.02899932861328
- residue TYR has 12 atoms
- atom: N x: -25.69300079345703 y:4.261000156402588 z:30.868000030517578
- atom: CA x: -24.302000045776367 y:3.9110000133514404 z:31.118000030517578
- atom: C x: -24.009000778198242 y:2.4860000610351562 z:30.6299991607666
- atom: O x: -24.80500030517578 y:1.5779999494552612 z:30.854000091552734
- atom: CB x: -24.033000946044922 y:3.9600000381469727 z:32.612998962402344
- atom: CG x: -23.69300079345703 y:5.311999797821045 z:33.18600082397461
- atom: CD1 x: -22.573999404907227 y:6.00600004196167 z:32.75400161743164
- atom: CD2 x: -24.45400047302246 y:5.866000175476074 z:34.209999084472656
- atom: CE1 x: -22.222999572753906 y:7.206999778747559 z:33.33100128173828
- atom: CE2 x: -24.111000061035156 y:7.065999984741211 z:34.78499984741211
- atom: CZ x: -22.993999481201172 y:7.724999904632568 z:34.340999603271484
- atom: OH x: -22.635000228881836 y:8.914999961853027 z:34.90700149536133
- residue ILE has 8 atoms
- atom: N x: -22.875 y:2.2880001068115234 z:29.96299934387207
- atom: CA x: -22.486000061035156 y:0.9539999961853027 z:29.506000518798828
- atom: C x: -21.17099952697754 y:0.5669999718666077 z:30.18600082397461
- atom: O x: -20.097000122070312 y:0.6959999799728394 z:29.594999313354492
- atom: CB x: -22.257999420166016 y:0.8889999985694885 z:27.974000930786133
- atom: CG1 x: -23.577999114990234 y:1.0160000324249268 z:27.23200035095215
- atom: CG2 x: -21.613000869750977 y:-0.45100000500679016 z:27.584999084472656
- atom: CD1 x: -23.41699981689453 y:0.8740000128746033 z:25.736000061035156
- residue ALA has 5 atoms
- atom: N x: -21.249000549316406 y:0.10000000149011612 z:31.42799949645996
- atom: CA x: -20.040000915527344 y:-0.296999990940094 z:32.15399932861328
- atom: C x: -19.613000869750977 y:-1.6979999542236328 z:31.74799919128418
- atom: O x: -20.31399917602539 y:-2.6679999828338623 z:32.02799987792969
- atom: CB x: -20.28700065612793 y:-0.24199999868869781 z:33.65700149536133
- residue THR has 7 atoms
- atom: N x: -18.457000732421875 y:-1.7899999618530273 z:31.097999572753906
- atom: CA x: -17.916000366210938 y:-3.066999912261963 z:30.64299964904785
- atom: C x: -16.632999420166016 y:-3.4679999351501465 z:31.371000289916992
- atom: O x: -15.590999603271484 y:-2.819999933242798 z:31.200000762939453
- atom: CB x: -17.61199951171875 y:-3.0190000534057617 z:29.134000778198242
- atom: OG1 x: -18.81399917602539 y:-2.7090001106262207 z:28.420000076293945
- atom: CG2 x: -17.062000274658203 y:-4.354000091552734 z:28.64299964904785
- residue VAL has 7 atoms
- atom: N x: -16.701000213623047 y:-4.531000137329102 z:32.178001403808594
- atom: CA x: -15.51200008392334 y:-5.008999824523926 z:32.893001556396484
- atom: C x: -14.501999855041504 y:-5.539999961853027 z:31.885000228881836
- atom: O x: -14.866999626159668 y:-6.291999816894531 z:31.0
- atom: CB x: -15.82800006866455 y:-6.168000221252441 z:33.861000061035156
- atom: CG1 x: -14.53499984741211 y:-6.660999774932861 z:34.49399948120117
- atom: CG2 x: -16.80299949645996 y:-5.7170000076293945 z:34.933998107910156
- residue CYS has 6 atoms
- atom: N x: -13.236000061035156 y:-5.158999919891357 z:32.01599884033203
- atom: CA x: -12.208000183105469 y:-5.639999866485596 z:31.089000701904297
- atom: C x: -10.972000122070312 y:-6.2220001220703125 z:31.773000717163086
- atom: O x: -11.039999961853027 y:-6.798999786376953 z:32.85300064086914
- atom: CB x: -11.751999855041504 y:-4.51800012588501 z:30.163000106811523
- atom: SG x: -13.08899974822998 y:-3.6470000743865967 z:29.341999053955078
- residue GLY has 4 atoms
- atom: N x: -9.829999923706055 y:-6.051000118255615 z:31.124000549316406
- atom: CA x: -8.604000091552734 y:-6.572999954223633 z:31.680999755859375
- atom: C x: -8.550999641418457 y:-8.071999549865723 z:31.476999282836914
- atom: O x: -9.340999603271484 y:-8.630000114440918 z:30.722000122070312
- residue SER has 6 atoms
- atom: N x: -7.61899995803833 y:-8.729999542236328 z:32.15399932861328
- atom: CA x: -7.484000205993652 y:-10.166000366210938 z:32.025001525878906
- atom: C x: -8.803000450134277 y:-10.85200023651123 z:32.362998962402344
- atom: O x: -8.97700023651123 y:-12.031000137329102 z:32.077999114990234
- atom: CB x: -6.353000164031982 y:-10.680999755859375 z:32.926998138427734
- atom: OG x: -6.578000068664551 y:-10.366000175476074 z:34.28799819946289
- residue PHE has 11 atoms
- atom: N x: -9.734999656677246 y:-10.123000144958496 z:32.96799850463867
- atom: CA x: -11.02400016784668 y:-10.720999717712402 z:33.28300094604492
- atom: C x: -11.821999549865723 y:-10.930999755859375 z:32.000999450683594
- atom: O x: -12.414999961853027 y:-11.984999656677246 z:31.797000885009766
- atom: CB x: -11.848999977111816 y:-9.84000015258789 z:34.20500183105469
- atom: CG x: -13.270000457763672 y:-10.277000427246094 z:34.305999755859375
- atom: CD1 x: -13.663000106811523 y:-11.180000305175781 z:35.28200149536133
- atom: CD2 x: -14.206999778747559 y:-9.845999717712402 z:33.369998931884766
- atom: CE1 x: -14.968000411987305 y:-11.656000137329102 z:35.32699966430664
- atom: CE2 x: -15.517999649047852 y:-10.312000274658203 z:33.39799880981445
- atom: CZ x: -15.902999877929688 y:-11.220999717712402 z:34.37900161743164
- residue ARG has 11 atoms
- atom: N x: -11.862000465393066 y:-9.913000106811523 z:31.148000717163086
- atom: CA x: -12.595000267028809 y:-10.017999649047852 z:29.895000457763672
- atom: C x: -11.9350004196167 y:-11.093999862670898 z:29.05299949645996
- atom: O x: -12.581999778747559 y:-11.767000198364258 z:28.249000549316406
- atom: CB x: -12.574000358581543 y:-8.678999900817871 z:29.16200065612793
- atom: CG x: -13.28499984741211 y:-8.682000160217285 z:27.829999923706055
- atom: CD x: -14.185999870300293 y:-7.460000038146973 z:27.68899917602539
- atom: NE x: -14.734000205993652 y:-7.388000011444092 z:26.347000122070312
- atom: CZ x: -13.996999740600586 y:-7.210000038146973 z:25.257999420166016
- atom: NH1 x: -12.6850004196167 y:-7.070000171661377 z:25.35300064086914
- atom: NH2 x: -14.567999839782715 y:-7.215000152587891 z:24.062999725341797
- residue ARG has 11 atoms
- atom: N x: -10.635000228881836 y:-11.258999824523926 z:29.259000778198242
- atom: CA x: -9.885000228881836 y:-12.258999824523926 z:28.534000396728516
- atom: C x: -10.24899959564209 y:-13.630999565124512 z:29.086000442504883
- atom: O x: -9.66100025177002 y:-14.633999824523926 z:28.714000701904297
- atom: CB x: -8.387999534606934 y:-12.006999969482422 z:28.687999725341797
- atom: CG x: -7.964000225067139 y:-10.605999946594238 z:28.301000595092773
- atom: CD x: -6.538000106811523 y:-10.583000183105469 z:27.792999267578125
- atom: NE x: -5.581999778747559 y:-11.0600004196167 z:28.784000396728516
- atom: CZ x: -5.169000148773193 y:-10.347000122070312 z:29.82200050354004
- atom: NH1 x: -5.623000144958496 y:-9.119000434875488 z:30.011999130249023
- atom: NH2 x: -4.296000003814697 y:-10.855999946594238 z:30.66900062561035
- residue GLY has 4 atoms
- atom: N x: -11.241999626159668 y:-13.666000366210938 z:29.965999603271484
- atom: CA x: -11.654000282287598 y:-14.925000190734863 z:30.55900001525879
- atom: C x: -10.503999710083008 y:-15.541999816894531 z:31.332000732421875
- atom: O x: -9.788000106811523 y:-16.39900016784668 z:30.81100082397461
- residue ALA has 5 atoms
- atom: N x: -10.319000244140625 y:-15.102999687194824 z:32.573001861572266
- atom: CA x: -9.23900032043457 y:-15.609000205993652 z:33.4109992980957
- atom: C x: -9.798999786376953 y:-16.110000610351562 z:34.7239990234375
- atom: O x: -10.76099967956543 y:-15.543999671936035 z:35.250999450683594
- atom: CB x: -8.211999893188477 y:-14.51099967956543 z:33.6619987487793
- residue GLU has 9 atoms
- atom: N x: -9.192999839782715 y:-17.165000915527344 z:35.25699996948242
- atom: CA x: -9.666000366210938 y:-17.74799919128418 z:36.512001037597656
- atom: C x: -9.555000305175781 y:-16.80900001525879 z:37.69599914550781
- atom: O x: -10.270000457763672 y:-16.94700050354004 z:38.68600082397461
- atom: CB x: -8.932000160217285 y:-19.05900001525879 z:36.80099868774414
- atom: CG x: -9.420000076293945 y:-20.18199920654297 z:35.91999816894531
- atom: CD x: -10.944999694824219 y:-20.224000930786133 z:35.84400177001953
- atom: OE1 x: -11.60200023651123 y:-20.437999725341797 z:36.89699935913086
- atom: OE2 x: -11.484999656677246 y:-20.034000396728516 z:34.72700119018555
- residue SER has 6 atoms
- atom: N x: -8.654999732971191 y:-15.845999717712402 z:37.58000183105469
- atom: CA x: -8.458000183105469 y:-14.861000061035156 z:38.625999450683594
- atom: C x: -7.815999984741211 y:-13.618000030517578 z:38.0099983215332
- atom: O x: -7.223999977111816 y:-13.684000015258789 z:36.92599868774414
- atom: CB x: -7.578000068664551 y:-15.440999984741211 z:39.744998931884766
- atom: OG x: -6.326000213623047 y:-15.878999710083008 z:39.25
- residue SER has 6 atoms
- atom: N x: -7.935999870300293 y:-12.489999771118164 z:38.70100021362305
- atom: CA x: -7.374000072479248 y:-11.253000259399414 z:38.196998596191406
- atom: C x: -6.690999984741211 y:-10.42300033569336 z:39.26900100708008
- atom: O x: -7.107999801635742 y:-10.406000137329102 z:40.42399978637695
- atom: CB x: -8.47599983215332 y:-10.42199993133545 z:37.54199981689453
- atom: OG x: -9.085000038146973 y:-11.130999565124512 z:36.481998443603516
- residue GLY has 4 atoms
- atom: N x: -5.633999824523926 y:-9.72700023651123 z:38.882999420166016
- atom: CA x: -4.954999923706055 y:-8.890999794006348 z:39.84299850463867
- atom: C x: -5.926000118255615 y:-7.854000091552734 z:40.37900161743164
- atom: O x: -5.889999866485596 y:-7.50600004196167 z:41.551998138427734
- residue ASP has 8 atoms
- atom: N x: -6.810999870300293 y:-7.369999885559082 z:39.51900100708008
- atom: CA x: -7.783999919891357 y:-6.349999904632568 z:39.9119987487793
- atom: C x: -9.005000114440918 y:-6.341000080108643 z:38.992000579833984
- atom: O x: -9.175000190734863 y:-7.230999946594238 z:38.16699981689453
- atom: CB x: -7.130000114440918 y:-4.9670000076293945 z:39.8650016784668
- atom: CG x: -6.76800012588501 y:-4.546000003814697 z:38.452999114990234
- atom: OD1 x: -6.9720001220703125 y:-5.339000225067139 z:37.50899887084961
- atom: OD2 x: -6.2779998779296875 y:-3.4170000553131104 z:38.27899932861328
- residue MET has 8 atoms
- atom: N x: -9.845999717712402 y:-5.321000099182129 z:39.1510009765625
- atom: CA x: -11.045000076293945 y:-5.1479997634887695 z:38.334999084472656
- atom: C x: -10.956000328063965 y:-3.8489999771118164 z:37.55500030517578
- atom: O x: -10.967000007629395 y:-2.7790000438690186 z:38.13800048828125
- atom: CB x: -12.298999786376953 y:-5.109000205993652 z:39.194000244140625
- atom: CG x: -13.512999534606934 y:-4.709000110626221 z:38.38399887084961
- atom: SD x: -15.081000328063965 y:-5.085999965667725 z:39.16600036621094
- atom: CE x: -15.109999656677246 y:-6.809000015258789 z:38.875
- residue ASP has 8 atoms
- atom: N x: -10.873000144958496 y:-3.950000047683716 z:36.23500061035156
- atom: CA x: -10.781000137329102 y:-2.7780001163482666 z:35.367000579833984
- atom: C x: -12.133000373840332 y:-2.5320000648498535 z:34.70500183105469
- atom: O x: -12.66100025177002 y:-3.4049999713897705 z:34.04100036621094
- atom: CB x: -9.710000038146973 y:-3.0380001068115234 z:34.321998596191406
- atom: CG x: -8.418999671936035 y:-3.5199999809265137 z:34.94300079345703
- atom: OD1 x: -7.6579999923706055 y:-2.6649999618530273 z:35.45100021362305
- atom: OD2 x: -8.175999641418457 y:-4.752999782562256 z:34.95899963378906
- residue VAL has 7 atoms
- atom: N x: -12.694000244140625 y:-1.3459999561309814 z:34.887001037597656
- atom: CA x: -13.998000144958496 y:-1.0369999408721924 z:34.314998626708984
- atom: C x: -13.968999862670898 y:0.0860000029206276 z:33.28300094604492
- atom: O x: -13.496000289916992 y:1.1820000410079956 z:33.5629997253418
- atom: CB x: -14.99899959564209 y:-0.6549999713897705 z:35.433998107910156
- atom: CG1 x: -16.375 y:-0.4050000011920929 z:34.85599899291992
- atom: CG2 x: -15.0649995803833 y:-1.7660000324249268 z:36.45800018310547
- residue LEU has 8 atoms
- atom: N x: -14.458000183105469 y:-0.19699999690055847 z:32.082000732421875
- atom: CA x: -14.527999877929688 y:0.8050000071525574 z:31.0310001373291
- atom: C x: -15.949999809265137 y:1.3270000219345093 z:31.106000900268555
- atom: O x: -16.90399932861328 y:0.5569999814033508 z:31.158000946044922
- atom: CB x: -14.281000137329102 y:0.19300000369548798 z:29.663999557495117
- atom: CG x: -14.069000244140625 y:1.2020000219345093 z:28.530000686645508
- atom: CD1 x: -12.979000091552734 y:2.184999942779541 z:28.922000885009766
- atom: CD2 x: -13.649999618530273 y:0.48399999737739563 z:27.270000457763672
- residue LEU has 8 atoms
- atom: N x: -16.086999893188477 y:2.640000104904175 z:31.107999801635742
- atom: CA x: -17.38800048828125 y:3.260999917984009 z:31.239999771118164
- atom: C x: -17.714000701904297 y:4.26200008392334 z:30.121999740600586
- atom: O x: -16.847000122070312 y:5.017000198364258 z:29.67799949645996
- atom: CB x: -17.423999786376953 y:3.9570000171661377 z:32.59700012207031
- atom: CG x: -18.70199966430664 y:4.685999870300293 z:32.948001861572266
- atom: CD1 x: -19.889999389648438 y:3.7049999237060547 z:32.92599868774414
- atom: CD2 x: -18.520000457763672 y:5.311999797821045 z:34.292999267578125
- residue THR has 7 atoms
- atom: N x: -18.966999053955078 y:4.270999908447266 z:29.67099952697754
- atom: CA x: -19.382999420166016 y:5.206999778747559 z:28.621999740600586
- atom: C x: -20.781999588012695 y:5.7170000076293945 z:28.87299919128418
- atom: O x: -21.530000686645508 y:5.166999816894531 z:29.683000564575195
- atom: CB x: -19.409000396728516 y:4.563000202178955 z:27.23900032043457
- atom: OG1 x: -20.46500015258789 y:3.6029999256134033 z:27.19499969482422
- atom: CG2 x: -18.097000122070312 y:3.871000051498413 z:26.937999725341797
- residue HIS has 10 atoms
- atom: N x: -21.13599967956543 y:6.7769999504089355 z:28.163999557495117
- atom: CA x: -22.46500015258789 y:7.359000205993652 z:28.28700065612793
- atom: C x: -22.768999099731445 y:8.1899995803833 z:27.04800033569336
- atom: O x: -21.88599967956543 y:8.836999893188477 z:26.488000869750977
- atom: CB x: -22.566999435424805 y:8.227999687194824 z:29.542999267578125
- atom: CG x: -23.91200065612793 y:8.859999656677246 z:29.735000610351562
- atom: ND1 x: -24.489999771118164 y:9.684000015258789 z:28.79199981689453
- atom: CD2 x: -24.777999877929688 y:8.817000389099121 z:30.777000427246094
- atom: CE1 x: -25.650999069213867 y:10.123000144958496 z:29.243999481201172
- atom: NE2 x: -25.850000381469727 y:9.612000465393066 z:30.44700050354004
- residue PRO has 7 atoms
- atom: N x: -24.027999877929688 y:8.15999984741211 z:26.590999603271484
- atom: CA x: -24.441999435424805 y:8.918999671936035 z:25.409000396728516
- atom: C x: -24.042999267578125 y:10.402999877929688 z:25.429000854492188
- atom: O x: -23.601999282836914 y:10.946000099182129 z:24.416000366210938
- atom: CB x: -25.95199966430664 y:8.711999893188477 z:25.395999908447266
- atom: CG x: -26.070999145507812 y:7.288000106811523 z:25.88599967956543
- atom: CD x: -25.117000579833984 y:7.2789998054504395 z:27.059999465942383
- residue SER has 6 atoms
- atom: N x: -24.176000595092773 y:11.045000076293945 z:26.583999633789062
- atom: CA x: -23.854000091552734 y:12.461999893188477 z:26.711000442504883
- atom: C x: -22.368000030517578 y:12.763999938964844 z:26.673999786376953
- atom: O x: -21.957000732421875 y:13.888999938964844 z:26.972999572753906
- atom: CB x: -24.410999298095703 y:13.015000343322754 z:28.018999099731445
- atom: OG x: -23.520000457763672 y:12.762999534606934 z:29.091999053955078
- residue PHE has 11 atoms
- atom: N x: -21.558000564575195 y:11.779999732971191 z:26.30699920654297
- atom: CA x: -20.12299919128418 y:11.99899959564209 z:26.285999298095703
- atom: C x: -19.398000717163086 y:11.35200023651123 z:25.132999420166016
- atom: O x: -19.242000579833984 y:10.137999534606934 z:25.084999084472656
- atom: CB x: -19.506000518798828 y:11.520999908447266 z:27.60099983215332
- atom: CG x: -18.007999420166016 y:11.626999855041504 z:27.636999130249023
- atom: CD1 x: -17.367000579833984 y:12.77299976348877 z:27.167999267578125
- atom: CD2 x: -17.236000061035156 y:10.593999862670898 z:28.156999588012695
- atom: CE1 x: -15.989999771118164 y:12.890000343322754 z:27.218000411987305
- atom: CE2 x: -15.854999542236328 y:10.704000473022461 z:28.211000442504883
- atom: CZ x: -15.229999542236328 y:11.857000350952148 z:27.739999771118164
- residue THR has 7 atoms
- atom: N x: -18.934999465942383 y:12.182999610900879 z:24.211000442504883
- atom: CA x: -18.201000213623047 y:11.710000038146973 z:23.042999267578125
- atom: C x: -17.07200050354004 y:12.701000213623047 z:22.77400016784668
- atom: O x: -16.788000106811523 y:13.565999984741211 z:23.59600067138672
- atom: CB x: -19.110000610351562 y:11.645999908447266 z:21.799999237060547
- atom: OG1 x: -19.204999923706055 y:12.947999954223633 z:21.209999084472656
- atom: CG2 x: -20.5049991607666 y:11.180000305175781 z:22.18400001525879
- residue SER has 6 atoms
- atom: N x: -16.42799949645996 y:12.579000473022461 z:21.625999450683594
- atom: CA x: -15.345999717712402 y:13.48900032043457 z:21.288000106811523
- atom: C x: -15.72700023651123 y:14.932999610900879 z:21.63599967956543
- atom: O x: -15.057999610900879 y:15.576000213623047 z:22.45199966430664
- atom: CB x: -15.020000457763672 y:13.368000030517578 z:19.798999786376953
- atom: OG x: -14.71500015258789 y:12.024999618530273 z:19.464000701904297
- residue GLU has 9 atoms
- atom: N x: -16.80699920654297 y:15.42199993133545 z:21.023000717163086
- atom: CA x: -17.32900047302246 y:16.783000946044922 z:21.238000869750977
- atom: C x: -17.645000457763672 y:17.051000595092773 z:22.7189998626709
- atom: O x: -16.93400001525879 y:17.798999786376953 z:23.395999908447266
- atom: CB x: -18.590999603271484 y:16.97100067138672 z:20.389999389648438
- atom: CG x: -19.5049991607666 y:15.744000434875488 z:20.41900062561035
- atom: CD x: -20.75200080871582 y:15.880999565124512 z:19.555999755859375
- atom: OE1 x: -20.6200008392334 y:16.08300018310547 z:18.32900047302246
- atom: OE2 x: -21.8700008392334 y:15.776000022888184 z:20.10700035095215
- residue SER has 6 atoms
- atom: N x: -18.738000869750977 y:16.454999923706055 z:23.19099998474121
- atom: CA x: -19.179000854492188 y:16.530000686645508 z:24.583999633789062
- atom: C x: -19.48200035095215 y:17.86400032043457 z:25.290000915527344
- atom: O x: -20.475000381469727 y:17.961999893188477 z:26.020999908447266
- atom: CB x: -18.18199920654297 y:15.746000289916992 z:25.451000213623047
- atom: OG x: -16.867000579833984 y:16.288999557495117 z:25.367000579833984
- residue THR has 7 atoms
- atom: N x: -18.636999130249023 y:18.87299919128418 z:25.0939998626709
- atom: CA x: -18.801000595092773 y:20.159000396728516 z:25.781999588012695
- atom: C x: -18.413999557495117 y:19.841999053955078 z:27.225000381469727
- atom: O x: -18.558000564575195 y:20.67099952697754 z:28.12700080871582
- atom: CB x: -20.27400016784668 y:20.67799949645996 z:25.78700065612793
- atom: OG1 x: -20.80299949645996 y:20.674999237060547 z:24.45400047302246
- atom: CG2 x: -20.33799934387207 y:22.104999542236328 z:26.34600067138672
- residue LYS has 9 atoms
- atom: N x: -17.930999755859375 y:18.615999221801758 z:27.42099952697754
- atom: CA x: -17.509000778198242 y:18.101999282836914 z:28.725000381469727
- atom: C x: -18.625 y:18.062000274658203 z:29.767000198364258
- atom: O x: -19.027000427246094 y:19.090999603271484 z:30.31800079345703
- atom: CB x: -16.312000274658203 y:18.898000717163086 z:29.25200080871582
- atom: CG x: -14.979999542236328 y:18.506999969482422 z:28.608999252319336
- atom: CD x: -14.986000061035156 y:18.663999557495117 z:27.079999923706055
- atom: CE x: -13.618000030517578 y:18.32900047302246 z:26.48699951171875
- atom: NZ x: -13.541999816894531 y:18.54800033569336 z:25.016000747680664
- residue GLN has 9 atoms
- atom: N x: -19.118999481201172 y:16.850000381469727 z:30.014999389648438
- atom: CA x: -20.18400001525879 y:16.606000900268555 z:30.979000091552734
- atom: C x: -19.53700065612793 y:16.427000045776367 z:32.35100173950195
- atom: O x: -18.87299919128418 y:15.42199993133545 z:32.61600112915039
- atom: CB x: -20.966999053955078 y:15.35099983215332 z:30.586000442504883
- atom: CG x: -22.29400062561035 y:15.206999778747559 z:31.299999237060547
- atom: CD x: -23.20400047302246 y:16.392000198364258 z:31.062000274658203
- atom: OE1 x: -23.5310001373291 y:16.709999084472656 z:29.92300033569336
- atom: NE2 x: -23.618000030517578 y:17.05500030517578 z:32.137001037597656
- residue PRO has 7 atoms
- atom: N x: -19.719999313354492 y:17.417999267578125 z:33.23699951171875
- atom: CA x: -19.187000274658203 y:17.464000701904297 z:34.60200119018555
- atom: C x: -19.802000045776367 y:16.465999603271484 z:35.58100128173828
- atom: O x: -20.979000091552734 y:16.569000244140625 z:35.93000030517578
- atom: CB x: -19.45400047302246 y:18.90399932861328 z:35.012001037597656
- atom: CG x: -20.766000747680664 y:19.173999786376953 z:34.35300064086914
- atom: CD x: -20.55299949645996 y:18.604999542236328 z:32.970001220703125
- residue LYS has 9 atoms
- atom: N x: -18.98699951171875 y:15.51099967956543 z:36.02000045776367
- atom: CA x: -19.39900016784668 y:14.482000350952148 z:36.97200012207031
- atom: C x: -20.075000762939453 y:13.255000114440918 z:36.362998962402344
- atom: O x: -20.964000701904297 y:12.654999732971191 z:36.9739990234375
- atom: CB x: -20.297000885009766 y:15.085000038146973 z:38.06100082397461
- atom: CG x: -19.63599967956543 y:16.225000381469727 z:38.82099914550781
- atom: CD x: -20.55299949645996 y:16.827999114990234 z:39.87300109863281
- atom: CE x: -19.891000747680664 y:18.023000717163086 z:40.55099868774414
- atom: NZ x: -20.739999771118164 y:18.586000442504883 z:41.63999938964844
- residue LEU has 8 atoms
- atom: N x: -19.663999557495117 y:12.876999855041504 z:35.15700149536133
- atom: CA x: -20.231000900268555 y:11.685999870300293 z:34.54800033569336
- atom: C x: -19.660999298095703 y:10.541000366210938 z:35.36899948120117
- atom: O x: -20.357999801635742 y:9.57800006866455 z:35.69499969482422
- atom: CB x: -19.77899932861328 y:11.529000282287598 z:33.09600067138672
- atom: CG x: -20.839000701904297 y:11.605999946594238 z:31.996999740600586
- atom: CD1 x: -20.340999603271484 y:10.803999900817871 z:30.812000274658203
- atom: CD2 x: -22.187000274658203 y:11.057000160217285 z:32.479000091552734
- residue LEU has 8 atoms
- atom: N x: -18.3799991607666 y:10.666000366210938 z:35.709999084472656
- atom: CA x: -17.700000762939453 y:9.656000137329102 z:36.494998931884766
- atom: C x: -17.95599937438965 y:9.869999885559082 z:37.96799850463867
- atom: O x: -18.058000564575195 y:8.918999671936035 z:38.729000091552734
- atom: CB x: -16.20400047302246 y:9.694000244140625 z:36.222999572753906
- atom: CG x: -15.364999771118164 y:8.619000434875488 z:36.91600036621094
- atom: CD1 x: -15.930000305175781 y:7.230999946594238 z:36.617000579833984
- atom: CD2 x: -13.913000106811523 y:8.743000030517578 z:36.44200134277344
- residue HIS has 10 atoms
- atom: N x: -18.06999969482422 y:11.121999740600586 z:38.37699890136719
- atom: CA x: -18.312000274658203 y:11.401000022888184 z:39.779998779296875
- atom: C x: -19.5310001373291 y:10.654999732971191 z:40.31700134277344
- atom: O x: -19.44099998474121 y:9.95300006866455 z:41.316001892089844
- atom: CB x: -18.496999740600586 y:12.901000022888184 z:40.000999450683594
- atom: CG x: -18.812000274658203 y:13.258999824523926 z:41.41999816894531
- atom: ND1 x: -17.89900016784668 y:13.11299991607666 z:42.44200134277344
- atom: CD2 x: -19.959999084472656 y:13.682999610900879 z:41.99700164794922
- atom: CE1 x: -18.474000930786133 y:13.425000190734863 z:43.59000015258789
- atom: NE2 x: -19.725000381469727 y:13.77400016784668 z:43.347999572753906
- residue GLN has 9 atoms
- atom: N x: -20.66900062561035 y:10.812999725341797 z:39.64699935913086
- atom: CA x: -21.92300033569336 y:10.175999641418457 z:40.055999755859375
- atom: C x: -21.83099937438965 y:8.678000450134277 z:40.29800033569336
- atom: O x: -22.37700080871582 y:8.17300033569336 z:41.268001556396484
- atom: CB x: -23.016000747680664 y:10.432000160217285 z:39.018001556396484
- atom: CG x: -23.368000030517578 y:11.890999794006348 z:38.82099914550781
- atom: CD x: -24.46299934387207 y:12.07699966430664 z:37.78099822998047
- atom: OE1 x: -25.597999572753906 y:11.62600040435791 z:37.9640007019043
- atom: NE2 x: -24.124000549316406 y:12.73799991607666 z:36.67900085449219
- residue VAL has 7 atoms
- atom: N x: -21.155000686645508 y:7.968999862670898 z:39.409000396728516
- atom: CA x: -21.006000518798828 y:6.53000020980835 z:39.54600143432617
- atom: C x: -20.003000259399414 y:6.197000026702881 z:40.6510009765625
- atom: O x: -20.218000411987305 y:5.28000020980835 z:41.4379997253418
- atom: CB x: -20.562999725341797 y:5.888000011444092 z:38.20899963378906
- atom: CG1 x: -20.05699920654297 y:4.473999977111816 z:38.441001892089844
- atom: CG2 x: -21.73699951171875 y:5.868000030517578 z:37.24599838256836
- residue VAL has 7 atoms
- atom: N x: -18.913999557495117 y:6.947000026702881 z:40.720001220703125
- atom: CA x: -17.933000564575195 y:6.690000057220459 z:41.75199890136719
- atom: C x: -18.690000534057617 y:6.857999801635742 z:43.042999267578125
- atom: O x: -18.660999298095703 y:6.008999824523926 z:43.92399978637695
- atom: CB x: -16.781999588012695 y:7.709000110626221 z:41.72200012207031
- atom: CG1 x: -15.850000381469727 y:7.456999778747559 z:42.880001068115234
- atom: CG2 x: -16.020000457763672 y:7.6020002365112305 z:40.41999816894531
- residue GLU has 9 atoms
- atom: N x: -19.398000717163086 y:7.968999862670898 z:43.132999420166016
- atom: CA x: -20.167999267578125 y:8.276000022888184 z:44.319000244140625
- atom: C x: -21.114999771118164 y:7.140999794006348 z:44.65999984741211
- atom: O x: -21.065000534057617 y:6.604000091552734 z:45.75699996948242
- atom: CB x: -20.961000442504883 y:9.5600004196167 z:44.09700012207031
- atom: CG x: -21.607999801635742 y:10.109999656677246 z:45.33399963378906
- atom: CD x: -22.40399932861328 y:11.36299991607666 z:45.042999267578125
- atom: OE1 x: -23.4689998626709 y:11.255999565124512 z:44.395999908447266
- atom: OE2 x: -21.961999893188477 y:12.458000183105469 z:45.452999114990234
- residue GLN has 9 atoms
- atom: N x: -21.9689998626709 y:6.763000011444092 z:43.715999603271484
- atom: CA x: -22.940000534057617 y:5.702000141143799 z:43.96500015258789
- atom: C x: -22.292999267578125 y:4.389999866485596 z:44.44900131225586
- atom: O x: -22.858999252319336 y:3.684000015258789 z:45.28799819946289
- atom: CB x: -23.791000366210938 y:5.4720001220703125 z:42.70100021362305
- atom: CG x: -24.867000579833984 y:4.372000217437744 z:42.79600143432617
- atom: CD x: -26.01300048828125 y:4.7129998207092285 z:43.7400016784668
- atom: OE1 x: -25.9689998626709 y:5.706999778747559 z:44.46099853515625
- atom: NE2 x: -27.04400062561035 y:3.874000072479248 z:43.742000579833984
- residue LEU has 8 atoms
- atom: N x: -21.11199951171875 y:4.065000057220459 z:43.93299865722656
- atom: CA x: -20.437000274658203 y:2.8420000076293945 z:44.3489990234375
- atom: C x: -19.951000213623047 y:2.9660000801086426 z:45.7859992980957
- atom: O x: -19.659000396728516 y:1.9639999866485596 z:46.42499923706055
- atom: CB x: -19.267000198364258 y:2.5199999809265137 z:43.4109992980957
- atom: CG x: -19.673999786376953 y:1.9570000171661377 z:42.04199981689453
- atom: CD1 x: -18.472999572753906 y:1.777999997138977 z:41.165000915527344
- atom: CD2 x: -20.384000778198242 y:0.628000020980835 z:42.23400115966797
- residue GLN has 9 atoms
- atom: N x: -19.868000030517578 y:4.198999881744385 z:46.28799819946289
- atom: CA x: -19.44499969482422 y:4.461999893188477 z:47.66899871826172
- atom: C x: -20.687999725341797 y:4.511000156402588 z:48.558998107910156
- atom: O x: -20.60099983215332 y:4.388999938964844 z:49.7869987487793
- atom: CB x: -18.71500015258789 y:5.809000015258789 z:47.7859992980957
- atom: CG x: -17.40399932861328 y:5.919000148773193 z:47.03499984741211
- atom: CD x: -16.65999984741211 y:7.2210001945495605 z:47.33300018310547
- atom: OE1 x: -17.259000778198242 y:8.29800033569336 z:47.375999450683594
- atom: NE2 x: -15.347000122070312 y:7.123000144958496 z:47.527000427246094
- residue LYS has 9 atoms
- atom: N x: -21.84000015258789 y:4.710000038146973 z:47.92300033569336
- atom: CA x: -23.118000030517578 y:4.790999889373779 z:48.62099838256836
- atom: C x: -23.485000610351562 y:3.427999973297119 z:49.20899963378906
- atom: O x: -23.861000061035156 y:3.321000099182129 z:50.37699890136719
- atom: CB x: -24.209999084472656 y:5.244999885559082 z:47.6510009765625
- atom: CG x: -25.493000030517578 y:5.758999824523926 z:48.308998107910156
- atom: CD x: -25.284000396728516 y:7.151000022888184 z:48.91600036621094
- atom: CE x: -26.61400032043457 y:7.869999885559082 z:49.20199966430664
- atom: NZ x: -27.492000579833984 y:7.140999794006348 z:50.17300033569336
- residue VAL has 7 atoms
- atom: N x: -23.381000518798828 y:2.38700008392334 z:48.391998291015625
- atom: CA x: -23.690000534057617 y:1.0379999876022339 z:48.84199905395508
- atom: C x: -22.56100082397461 y:0.5149999856948853 z:49.72800064086914
- atom: O x: -22.729000091552734 y:-0.4690000116825104 z:50.45100021362305
- atom: CB x: -23.85300064086914 y:0.07800000160932541 z:47.645999908447266
- atom: CG1 x: -25.08300018310547 y:0.44999998807907104 z:46.845001220703125
- atom: CG2 x: -22.618999481201172 y:0.13099999725818634 z:46.76300048828125
- residue HIS has 10 atoms
- atom: N x: -21.413999557495117 y:1.187999963760376 z:49.66400146484375
- atom: CA x: -20.229000091552734 y:0.8109999895095825 z:50.428001403808594
- atom: C x: -19.409000396728516 y:-0.27000001072883606 z:49.709999084472656
- atom: O x: -18.84000015258789 y:-1.152999997138977 z:50.35200119018555
- atom: CB x: -20.610000610351562 y:0.33399999141693115 z:51.8390007019043
- atom: CG x: -21.040000915527344 y:1.437000036239624 z:52.7599983215332
- atom: ND1 x: -22.143999099731445 y:1.3350000381469727 z:53.582000732421875
- atom: CD2 x: -20.5 y:2.6549999713897705 z:53.0099983215332
- atom: CE1 x: -22.266000747680664 y:2.440000057220459 z:54.297000885009766
- atom: NE2 x: -21.281999588012695 y:3.257999897003174 z:53.96900177001953
- residue PHE has 11 atoms
- atom: N x: -19.360000610351562 y:-0.20000000298023224 z:48.37799835205078
- atom: CA x: -18.570999145507812 y:-1.1480000019073486 z:47.59000015258789
- atom: C x: -17.174999237060547 y:-0.5789999961853027 z:47.39500045776367
- atom: O x: -16.20800018310547 y:-1.3270000219345093 z:47.3650016784668
- atom: CB x: -19.187999725341797 y:-1.3940000534057617 z:46.220001220703125
- atom: CG x: -18.344999313354492 y:-2.2720000743865967 z:45.32500076293945
- atom: CD1 x: -18.054000854492188 y:-3.5820000171661377 z:45.685001373291016
- atom: CD2 x: -17.84600067138672 y:-1.784999966621399 z:44.11899948120117
- atom: CE1 x: -17.288999557495117 y:-4.38700008392334 z:44.86800003051758
- atom: CE2 x: -17.076000213623047 y:-2.5869998931884766 z:43.29399871826172
- atom: CZ x: -16.79800033569336 y:-3.8910000324249268 z:43.67100143432617
- residue ILE has 8 atoms
- atom: N x: -17.072999954223633 y:0.7419999837875366 z:47.24300003051758
- atom: CA x: -15.77400016784668 y:1.3860000371932983 z:47.08300018310547
- atom: C x: -15.430999755859375 y:1.9910000562667847 z:48.42300033569336
- atom: O x: -16.05900001525879 y:2.953000068664551 z:48.85200119018555
- atom: CB x: -15.774999618530273 y:2.503000020980835 z:45.97999954223633
- atom: CG1 x: -15.883000373840332 y:1.871000051498413 z:44.58399963378906
- atom: CG2 x: -14.479000091552734 y:3.2899999618530273 z:46.02199935913086
- atom: CD1 x: -15.685999870300293 y:2.8510000705718994 z:43.44300079345703
- residue THR has 7 atoms
- atom: N x: -14.427000045776367 y:1.4140000343322754 z:49.073001861572266
- atom: CA x: -13.984999656677246 y:1.8559999465942383 z:50.388999938964844
- atom: C x: -12.88599967956543 y:2.9140000343322754 z:50.402000427246094
- atom: O x: -12.743000030517578 y:3.63100004196167 z:51.39099884033203
- atom: CB x: -13.479000091552734 y:0.6610000133514404 z:51.25299835205078
- atom: OG1 x: -12.404000282287598 y:-0.0020000000949949026 z:50.58300018310547
- atom: CG2 x: -14.581000328063965 y:-0.32600000500679016 z:51.51499938964844
- residue ASP has 8 atoms
- atom: N x: -12.095000267028809 y:3.01200008392334 z:49.3390007019043
- atom: CA x: -11.015000343322754 y:4.000999927520752 z:49.31800079345703
- atom: C x: -10.654000282287598 y:4.551000118255615 z:47.93299865722656
- atom: O x: -10.78600025177002 y:3.868000030517578 z:46.915000915527344
- atom: CB x: -9.744000434875488 y:3.4130001068115234 z:49.9630012512207
- atom: CG x: -10.015000343322754 y:2.7699999809265137 z:51.31800079345703
- atom: OD1 x: -10.675000190734863 y:1.7079999446868896 z:51.349998474121094
- atom: OD2 x: -9.574000358581543 y:3.3239998817443848 z:52.35100173950195
- residue THR has 7 atoms
- atom: N x: -10.157999992370605 y:5.7870001792907715 z:47.93199920654297
- atom: CA x: -9.746999740600586 y:6.508999824523926 z:46.73899841308594
- atom: C x: -8.234999656677246 y:6.723999977111816 z:46.68000030517578
- atom: O x: -7.664999961853027 y:7.307000160217285 z:47.59000015258789
- atom: CB x: -10.407999992370605 y:7.89300012588501 z:46.715999603271484
- atom: OG1 x: -11.79800033569336 y:7.748000144958496 z:46.40999984741211
- atom: CG2 x: -9.73799991607666 y:8.803000450134277 z:45.6879997253418
- residue LEU has 8 atoms
- atom: N x: -7.583000183105469 y:6.265999794006348 z:45.612998962402344
- atom: CA x: -6.146999835968018 y:6.489999771118164 z:45.47800064086914
- atom: C x: -5.991000175476074 y:7.702000141143799 z:44.57099914550781
- atom: O x: -5.010000228881836 y:8.442000389099121 z:44.667999267578125
- atom: CB x: -5.427999973297119 y:5.298999786376953 z:44.83100128173828
- atom: CG x: -5.5980000495910645 y:3.871999979019165 z:45.35599899291992
- atom: CD1 x: -4.579999923706055 y:2.9730000495910645 z:44.696998596191406
- atom: CD2 x: -5.414999961853027 y:3.8259999752044678 z:46.847999572753906
- residue SER has 6 atoms
- atom: N x: -6.9710001945495605 y:7.901000022888184 z:43.694000244140625
- atom: CA x: -6.947999954223633 y:9.012999534606934 z:42.74399948120117
- atom: C x: -8.258999824523926 y:9.112000465393066 z:41.98500061035156
- atom: O x: -8.848999977111816 y:8.095000267028809 z:41.61399841308594
- atom: CB x: -5.817999839782715 y:8.831999778747559 z:41.74100112915039
- atom: OG x: -6.002999782562256 y:7.638999938964844 z:41.01300048828125
- residue LYS has 9 atoms
- atom: N x: -8.70300006866455 y:10.340999603271484 z:41.74800109863281
- atom: CA x: -9.954000473022461 y:10.569999694824219 z:41.04100036621094
- atom: C x: -9.918000221252441 y:11.857999801635742 z:40.21900177001953
- atom: O x: -9.762999534606934 y:12.961999893188477 z:40.74599838256836
- atom: CB x: -11.107999801635742 y:10.605999946594238 z:42.04499816894531
- atom: CG x: -12.496000289916992 y:10.840999603271484 z:41.47100067138672
- atom: CD x: -13.52299976348877 y:10.961000442504883 z:42.61000061035156
- atom: CE x: -14.862000465393066 y:11.560999870300293 z:42.15599822998047
- atom: NZ x: -14.739999771118164 y:12.946999549865723 z:41.57699966430664
- residue GLY has 4 atoms
- atom: N x: -10.03600025177002 y:11.694000244140625 z:38.90800094604492
- atom: CA x: -10.041999816894531 y:12.824000358581543 z:38.00600051879883
- atom: C x: -11.36400032043457 y:12.800000190734863 z:37.26900100708008
- atom: O x: -12.270999908447266 y:12.064000129699707 z:37.66899871826172
- residue GLU has 9 atoms
- atom: N x: -11.475000381469727 y:13.581999778747559 z:36.19599914550781
- atom: CA x: -12.708999633789062 y:13.637999534606934 z:35.41299819946289
- atom: C x: -12.991000175476074 y:12.404999732971191 z:34.569000244140625
- atom: O x: -14.145000457763672 y:12.163000106811523 z:34.23899841308594
- atom: CB x: -12.729000091552734 y:14.871000289916992 z:34.49399948120117
- atom: CG x: -12.994000434875488 y:16.202999114990234 z:35.20000076293945
- atom: CD x: -14.388999938964844 y:16.284000396728516 z:35.803001403808594
- atom: OE1 x: -14.821999549865723 y:15.300000190734863 z:36.452999114990234
- atom: OE2 x: -15.04800033569336 y:17.33300018310547 z:35.64099884033203
- residue THR has 7 atoms
- atom: N x: -11.963000297546387 y:11.63700008392334 z:34.209999084472656
- atom: CA x: -12.175000190734863 y:10.432999610900879 z:33.39699935913086
- atom: C x: -11.51200008392334 y:9.157999992370605 z:33.95399856567383
- atom: O x: -11.673999786376953 y:8.072999954223633 z:33.38600158691406
- atom: CB x: -11.6850004196167 y:10.630000114440918 z:31.908000946044922
- atom: OG1 x: -10.255999565124512 y:10.644000053405762 z:31.856000900268555
- atom: CG2 x: -12.185999870300293 y:11.944999694824219 z:31.336999893188477
- residue LYS has 9 atoms
- atom: N x: -10.781000137329102 y:9.277000427246094 z:35.06399917602539
- atom: CA x: -10.095999717712402 y:8.119999885559082 z:35.63800048828125
- atom: C x: -10.126999855041504 y:8.034000396728516 z:37.154998779296875
- atom: O x: -9.835000038146973 y:9.008000373840332 z:37.849998474121094
- atom: CB x: -8.642999649047852 y:8.10099983215332 z:35.18199920654297
- atom: CG x: -7.811999797821045 y:7.0980000495910645 z:35.92300033569336
- atom: CD x: -6.353000164031982 y:7.2220001220703125 z:35.58100128173828
- atom: CE x: -5.540999889373779 y:6.206999778747559 z:36.380001068115234
- atom: NZ x: -4.105000019073486 y:6.232999801635742 z:36.0
- residue PHE has 11 atoms
- atom: N x: -10.454000473022461 y:6.8460001945495605 z:37.65800094604492
- atom: CA x: -10.522000312805176 y:6.5879998207092285 z:39.090999603271484
- atom: C x: -9.812000274658203 y:5.298999786376953 z:39.49700164794922
- atom: O x: -10.163999557495117 y:4.2129998207092285 z:39.051998138427734
- atom: CB x: -11.984000205993652 y:6.501999855041504 z:39.547000885009766
- atom: CG x: -12.156000137329102 y:6.059999942779541 z:40.986000061035156
- atom: CD1 x: -11.930999755859375 y:6.936999797821045 z:42.0359992980957
- atom: CD2 x: -12.531000137329102 y:4.756999969482422 z:41.2859992980957
- atom: CE1 x: -12.079000473022461 y:6.519000053405762 z:43.36600112915039
- atom: CE2 x: -12.678999900817871 y:4.329999923706055 z:42.61800003051758
- atom: CZ x: -12.45300006866455 y:5.210999965667725 z:43.652000427246094
- residue MET has 8 atoms
- atom: N x: -8.805999755859375 y:5.428999900817871 z:40.35100173950195
- atom: CA x: -8.081999778747559 y:4.275000095367432 z:40.875
- atom: C x: -8.491999626159668 y:4.190000057220459 z:42.34199905395508
- atom: O x: -8.345999717712402 y:5.159999847412109 z:43.09000015258789
- atom: CB x: -6.578999996185303 y:4.486000061035156 z:40.77000045776367
- atom: CG x: -6.034999847412109 y:4.218999862670898 z:39.39500045776367
- atom: SD x: -4.295000076293945 y:4.629000186920166 z:39.29399871826172
- atom: CE x: -3.693000078201294 y:3.8350000381469727 z:40.74300003051758
- residue GLY has 4 atoms
- atom: N x: -9.01200008392334 y:3.0390000343322754 z:42.7599983215332
- atom: CA x: -9.442999839782715 y:2.933000087738037 z:44.13600158691406
- atom: C x: -9.482999801635742 y:1.5640000104904175 z:44.742000579833984
- atom: O x: -8.850000381469727 y:0.6309999823570251 z:44.27000045776367
- residue VAL has 7 atoms
- atom: N x: -10.26200008392334 y:1.4559999704360962 z:45.80400085449219
- atom: CA x: -10.385000228881836 y:0.21899999678134918 z:46.54199981689453
- atom: C x: -11.847000122070312 y:-0.14499999582767487 z:46.7239990234375
- atom: O x: -12.666000366210938 y:0.7099999785423279 z:47.07899856567383
- atom: CB x: -9.720000267028809 y:0.36800000071525574 z:47.94599914550781
- atom: CG1 x: -9.960000038146973 y:-0.8809999823570251 z:48.790000915527344
- atom: CG2 x: -8.218000411987305 y:0.6430000066757202 z:47.7869987487793
- residue CYS has 6 atoms
- atom: N x: -12.168999671936035 y:-1.4140000343322754 z:46.46799850463867
- atom: CA x: -13.529000282287598 y:-1.909000039100647 z:46.63399887084961
- atom: C x: -13.513999938964844 y:-3.187000036239624 z:47.46699905395508
- atom: O x: -12.456000328063965 y:-3.759000062942505 z:47.72200012207031
- atom: CB x: -14.20300006866455 y:-2.1549999713897705 z:45.277000427246094
- atom: SG x: -13.541000366210938 y:-3.48799991607666 z:44.275001525878906
- residue GLN has 9 atoms
- atom: N x: -14.690999984741211 y:-3.625999927520752 z:47.900001525878906
- atom: CA x: -14.809000015258789 y:-4.818999767303467 z:48.72600173950195
- atom: C x: -16.209999084472656 y:-5.434999942779541 z:48.64799880981445
- atom: O x: -17.215999603271484 y:-4.756999969482422 z:48.869998931884766
- atom: CB x: -14.467000007629395 y:-4.459000110626221 z:50.178001403808594
- atom: CG x: -14.763999938964844 y:-5.531000137329102 z:51.202999114990234
- atom: CD x: -14.333999633789062 y:-5.130000114440918 z:52.604000091552734
- atom: OE1 x: -14.741000175476074 y:-4.0879998207092285 z:53.11800003051758
- atom: NE2 x: -13.508000373840332 y:-5.961999893188477 z:53.231998443603516
- residue LEU has 8 atoms
- atom: N x: -16.267000198364258 y:-6.71999979019165 z:48.31399917602539
- atom: CA x: -17.533000946044922 y:-7.429999828338623 z:48.22800064086914
- atom: C x: -18.14900016784668 y:-7.479000091552734 z:49.61899948120117
- atom: O x: -17.454999923706055 y:-7.729000091552734 z:50.595001220703125
- atom: CB x: -17.297000885009766 y:-8.852999687194824 z:47.722999572753906
- atom: CG x: -16.979000091552734 y:-9.00100040435791 z:46.236000061035156
- atom: CD1 x: -16.43600082397461 y:-10.39799976348877 z:45.946998596191406
- atom: CD2 x: -18.249000549316406 y:-8.720000267028809 z:45.43000030517578
- residue PRO has 7 atoms
- atom: N x: -19.459999084472656 y:-7.241000175476074 z:49.733001708984375
- atom: CA x: -20.0939998626709 y:-7.28000020980835 z:51.053001403808594
- atom: C x: -20.091999053955078 y:-8.692999839782715 z:51.62099838256836
- atom: O x: -20.04400062561035 y:-9.668000221252441 z:50.87300109863281
- atom: CB x: -21.49799919128418 y:-6.7829999923706055 z:50.763999938964844
- atom: CG x: -21.75200080871582 y:-7.359000205993652 z:49.42300033569336
- atom: CD x: -20.466999053955078 y:-7.035999774932861 z:48.683998107910156
- residue SER has 6 atoms
- atom: N x: -20.14299964904785 y:-8.800000190734863 z:52.944000244140625
- atom: CA x: -20.150999069213867 y:-10.104999542236328 z:53.59000015258789
- atom: C x: -21.516000747680664 y:-10.470999717712402 z:54.14400100708008
- atom: O x: -22.22800064086914 y:-9.626999855041504 z:54.69300079345703
- atom: CB x: -19.11400032043457 y:-10.157999992370605 z:54.71099853515625
- atom: OG x: -17.80299949645996 y:-10.243000030517578 z:54.176998138427734
- residue LYS has 9 atoms
- atom: N x: -21.854999542236328 y:-11.748000144958496 z:53.99100112915039
- atom: CA x: -23.124000549316406 y:-12.317000389099121 z:54.44300079345703
- atom: C x: -23.631999969482422 y:-11.708000183105469 z:55.74700164794922
- atom: O x: -24.525999069213867 y:-10.859999656677246 z:55.74100112915039
- atom: CB x: -22.985000610351562 y:-13.836000442504883 z:54.61800003051758
- atom: CG x: -22.371000289916992 y:-14.569000244140625 z:53.42399978637695
- atom: CD x: -20.875999450683594 y:-14.298999786376953 z:53.28200149536133
- atom: CE x: -20.301000595092773 y:-14.970999717712402 z:52.04600143432617
- atom: NZ x: -18.827999114990234 y:-14.781999588012695 z:51.97600173950195
- residue ASN has 8 atoms
- atom: N x: -23.066999435424805 y:-12.161999702453613 z:56.861000061035156
- atom: CA x: -23.440000534057617 y:-11.675999641418457 z:58.18600082397461
- atom: C x: -22.19700050354004 y:-11.550000190734863 z:59.04600143432617
- atom: O x: -21.503999710083008 y:-10.529999732971191 z:59.018001556396484
- atom: CB x: -24.42300033569336 y:-12.637999534606934 z:58.86199951171875
- atom: CG x: -25.77899932861328 y:-12.663999557495117 z:58.180999755859375
- atom: OD1 x: -25.885000228881836 y:-12.98799991607666 z:56.99300003051758
- atom: ND2 x: -26.826000213623047 y:-12.321999549865723 z:58.93000030517578
- residue ASP has 8 atoms
- atom: N x: -21.91200065612793 y:-12.593999862670898 z:59.8120002746582
- atom: CA x: -20.743000030517578 y:-12.5649995803833 z:60.667999267578125
- atom: C x: -19.663999557495117 y:-13.559000015258789 z:60.22200012207031
- atom: O x: -19.101999282836914 y:-14.295999526977539 z:61.034000396728516
- atom: CB x: -21.1560001373291 y:-12.817000389099121 z:62.12099838256836
- atom: CG x: -20.41699981689453 y:-11.913000106811523 z:63.0989990234375
- atom: OD1 x: -20.413000106811523 y:-10.680999755859375 z:62.880001068115234
- atom: OD2 x: -19.844999313354492 y:-12.430999755859375 z:64.08399963378906
- residue GLU has 9 atoms
- atom: N x: -19.38800048828125 y:-13.57699966430664 z:58.917999267578125
- atom: CA x: -18.354000091552734 y:-14.447999954223633 z:58.375
- atom: C x: -17.06800079345703 y:-13.638999938964844 z:58.441001892089844
- atom: O x: -16.729000091552734 y:-13.08899974822998 z:59.4900016784668
- atom: CB x: -18.63800048828125 y:-14.824999809265137 z:56.91699981689453
- atom: CG x: -19.93899917602539 y:-15.576000213623047 z:56.67300033569336
- atom: CD x: -21.152000427246094 y:-14.701000213623047 z:56.88600158691406
- atom: OE1 x: -21.05900001525879 y:-13.493000030517578 z:56.584999084472656
- atom: OE2 x: -22.195999145507812 y:-15.218000411987305 z:57.3380012512207
- residue LYS has 9 atoms
- atom: N x: -16.361000061035156 y:-13.54699993133545 z:57.319000244140625
- atom: CA x: -15.116000175476074 y:-12.793999671936035 z:57.284000396728516
- atom: C x: -15.039999961853027 y:-11.869000434875488 z:56.07699966430664
- atom: O x: -15.192000389099121 y:-12.310999870300293 z:54.941001892089844
- atom: CB x: -13.92300033569336 y:-13.751999855041504 z:57.27399826049805
- atom: CG x: -12.5600004196167 y:-13.060999870300293 z:57.27399826049805
- atom: CD x: -11.418999671936035 y:-14.069999694824219 z:57.36899948120117
- atom: CE x: -11.454000473022461 y:-15.064000129699707 z:56.21500015258789
- atom: NZ x: -10.368000030517578 y:-16.07900047302246 z:56.319000244140625
- residue GLU has 9 atoms
- atom: N x: -14.805000305175781 y:-10.585000038146973 z:56.340999603271484
- atom: CA x: -14.687000274658203 y:-9.57800006866455 z:55.292999267578125
- atom: C x: -13.902999877929688 y:-10.180000305175781 z:54.125999450683594
- atom: O x: -12.942000389099121 y:-10.918999671936035 z:54.34199905395508
- atom: CB x: -13.907999992370605 y:-8.350000381469727 z:55.79999923706055
- atom: CG x: -14.197999954223633 y:-7.88700008392334 z:57.22200012207031
- atom: CD x: -13.293000221252441 y:-6.72599983215332 z:57.652000427246094
- atom: OE1 x: -13.357000350952148 y:-5.650000095367432 z:57.01900100708008
- atom: OE2 x: -12.512999534606934 y:-6.883999824523926 z:58.62099838256836
- residue TYR has 12 atoms
- atom: N x: -14.315999984741211 y:-9.883000373840332 z:52.895999908447266
- atom: CA x: -13.588000297546387 y:-10.373000144958496 z:51.72700119018555
- atom: C x: -12.331000328063965 y:-9.508000373840332 z:51.678001403808594
- atom: O x: -12.291000366210938 y:-8.444000244140625 z:52.292999267578125
- atom: CB x: -14.402000427246094 y:-10.159000396728516 z:50.44300079345703
- atom: CG x: -15.472000122070312 y:-11.201000213623047 z:50.17599868774414
- atom: CD1 x: -15.234999656677246 y:-12.276000022888184 z:49.31800079345703
- atom: CD2 x: -16.729000091552734 y:-11.105999946594238 z:50.7760009765625
- atom: CE1 x: -16.225000381469727 y:-13.22700023651123 z:49.064998626708984
- atom: CE2 x: -17.722999572753906 y:-12.048999786376953 z:50.52899932861328
- atom: CZ x: -17.465999603271484 y:-13.100000381469727 z:49.67599868774414
- atom: OH x: -18.458999633789062 y:-14.013999938964844 z:49.433998107910156
- residue PRO has 7 atoms
- atom: N x: -11.282999992370605 y:-9.958999633789062 z:50.972999572753906
- atom: CA x: -10.079999923706055 y:-9.125 z:50.917999267578125
- atom: C x: -10.451000213623047 y:-7.831999778747559 z:50.20899963378906
- atom: O x: -11.345000267028809 y:-7.835000038146973 z:49.35900115966797
- atom: CB x: -9.114999771118164 y:-9.960000038146973 z:50.07699966430664
- atom: CG x: -9.54699993133545 y:-11.354000091552734 z:50.3380012512207
- atom: CD x: -11.050999641418457 y:-11.258999824523926 z:50.32500076293945
- residue HIS has 10 atoms
- atom: N x: -9.805000305175781 y:-6.724999904632568 z:50.560001373291016
- atom: CA x: -10.095000267028809 y:-5.4710001945495605 z:49.867000579833984
- atom: C x: -9.428000450134277 y:-5.605000019073486 z:48.49399948120117
- atom: O x: -8.277999877929688 y:-6.047999858856201 z:48.395999908447266
- atom: CB x: -9.512999534606934 y:-4.267000198364258 z:50.619998931884766
- atom: CG x: -10.348999977111816 y:-3.796999931335449 z:51.77000045776367
- atom: ND1 x: -10.534000396728516 y:-4.544000148773193 z:52.91400146484375
- atom: CD2 x: -11.008000373840332 y:-2.631999969482422 z:51.97100067138672
- atom: CE1 x: -11.263999938964844 y:-3.8559999465942383 z:53.77299880981445
- atom: NE2 x: -11.564000129699707 y:-2.691999912261963 z:53.224998474121094
- residue ARG has 11 atoms
- atom: N x: -10.140999794006348 y:-5.234000205993652 z:47.4370002746582
- atom: CA x: -9.592000007629395 y:-5.364999771118164 z:46.08599853515625
- atom: C x: -9.380000114440918 y:-4.051000118255615 z:45.33399963378906
- atom: O x: -10.031000137329102 y:-3.0390000343322754 z:45.611000061035156
- atom: CB x: -10.51200008392334 y:-6.256999969482422 z:45.25899887084961
- atom: CG x: -10.968999862670898 y:-7.511000156402588 z:45.96200180053711
- atom: CD x: -9.836999893188477 y:-8.48799991607666 z:46.11199951171875
- atom: NE x: -10.319000244140625 y:-9.800999641418457 z:46.51900100708008
- atom: CZ x: -9.5600004196167 y:-10.888999938964844 z:46.54499816894531
- atom: NH1 x: -8.28499984741211 y:-10.8100004196167 z:46.19200134277344
- atom: NH2 x: -10.07699966430664 y:-12.057000160217285 z:46.902000427246094
- residue ARG has 11 atoms
- atom: N x: -8.461999893188477 y:-4.076000213623047 z:44.375
- atom: CA x: -8.197999954223633 y:-2.8940000534057617 z:43.558998107910156
- atom: C x: -9.196999549865723 y:-2.7960000038146973 z:42.402000427246094
- atom: O x: -9.545999526977539 y:-3.7890000343322754 z:41.75600051879883
- atom: CB x: -6.775000095367432 y:-2.9260001182556152 z:42.994998931884766
- atom: CG x: -5.702000141143799 y:-2.631999969482422 z:44.012001037597656
- atom: CD x: -5.521999835968018 y:-1.1480000019073486 z:44.24100112915039
- atom: NE x: -4.9710001945495605 y:-0.4950000047683716 z:43.0629997253418
- atom: CZ x: -5.703999996185303 y:0.11400000005960464 z:42.13800048828125
- atom: NH1 x: -7.0279998779296875 y:0.16500000655651093 z:42.25899887084961
- atom: NH2 x: -5.113999843597412 y:0.652999997138977 z:41.07899856567383
- residue ILE has 8 atoms
- atom: N x: -9.649999618530273 y:-1.5729999542236328 z:42.15399932861328
- atom: CA x: -10.597000122070312 y:-1.2949999570846558 z:41.0880012512207
- atom: C x: -10.175000190734863 y:-0.020999999716877937 z:40.34199905395508
- atom: O x: -9.767999649047852 y:0.9660000205039978 z:40.95800018310547
- atom: CB x: -12.017999649047852 y:-1.1380000114440918 z:41.68000030517578
- atom: CG1 x: -13.008999824523926 y:-0.7609999775886536 z:40.59199905395508
- atom: CG2 x: -12.031000137329102 y:-0.08799999952316284 z:42.75
- atom: CD1 x: -14.376999855041504 y:-0.5450000166893005 z:41.137001037597656
- residue ASP has 8 atoms
- atom: N x: -10.21500015258789 y:-0.07400000095367432 z:39.01499938964844
- atom: CA x: -9.883000373840332 y:1.069000005722046 z:38.1619987487793
- atom: C x: -11.109000205993652 y:1.2790000438690186 z:37.2760009765625
- atom: O x: -11.706999778747559 y:0.3100000023841858 z:36.80699920654297
- atom: CB x: -8.668000221252441 y:0.7850000262260437 z:37.270999908447266
- atom: CG x: -7.4070000648498535 y:0.503000020980835 z:38.064998626708984
- atom: OD1 x: -7.235000133514404 y:1.093000054359436 z:39.1510009765625
- atom: OD2 x: -6.578999996185303 y:-0.30000001192092896 z:37.5890007019043
- residue ILE has 8 atoms
- atom: N x: -11.487000465393066 y:2.5350000858306885 z:37.05500030517578
- atom: CA x: -12.64799976348877 y:2.8480000495910645 z:36.23400115966797
- atom: C x: -12.291999816894531 y:4.013000011444092 z:35.319000244140625
- atom: O x: -11.878999710083008 y:5.072000026702881 z:35.79499816894531
- atom: CB x: -13.845999717712402 y:3.256999969482422 z:37.12300109863281
- atom: CG1 x: -14.107999801635742 y:2.1679999828338623 z:38.16699981689453
- atom: CG2 x: -15.086999893188477 y:3.505000114440918 z:36.266998291015625
- atom: CD1 x: -15.119000434875488 y:2.562000036239624 z:39.233001708984375
- residue ARG has 11 atoms
- atom: N x: -12.4399995803833 y:3.8239998817443848 z:34.01100158691406
- atom: CA x: -12.133000373840332 y:4.89300012588501 z:33.064998626708984
- atom: C x: -13.319999694824219 y:5.24399995803833 z:32.17399978637695
- atom: O x: -13.930999755859375 y:4.36899995803833 z:31.548999786376953
- atom: CB x: -10.928000450134277 y:4.513000011444092 z:32.202999114990234
- atom: CG x: -9.746000289916992 y:4.109000205993652 z:33.055999755859375
- atom: CD x: -8.42300033569336 y:4.166999816894531 z:32.321998596191406
- atom: NE x: -7.381999969482422 y:3.446000099182129 z:33.055999755859375
- atom: CZ x: -6.118000030517578 y:3.3529999256134033 z:32.65599822998047
- atom: NH1 x: -5.738999843597412 y:3.947000026702881 z:31.527999877929688
- atom: NH2 x: -5.239999771118164 y:2.6530001163482666 z:33.36800003051758
- residue LEU has 8 atoms
- atom: N x: -13.649999618530273 y:6.5329999923706055 z:32.150001525878906
- atom: CA x: -14.743000030517578 y:7.039999961853027 z:31.347000122070312
- atom: C x: -14.180999755859375 y:7.448999881744385 z:29.990999221801758
- atom: O x: -13.451000213623047 y:8.435999870300293 z:29.905000686645508
- atom: CB x: -15.355999946594238 y:8.258999824523926 z:32.018001556396484
- atom: CG x: -16.48200035095215 y:8.942999839782715 z:31.2450008392334
- atom: CD1 x: -17.711000442504883 y:8.062999725341797 z:31.25
- atom: CD2 x: -16.80299949645996 y:10.270000457763672 z:31.878000259399414
- residue ILE has 8 atoms
- atom: N x: -14.506999969482422 y:6.693999767303467 z:28.940000534057617
- atom: CA x: -14.029000282287598 y:7.00600004196167 z:27.59600067138672
- atom: C x: -15.149999618530273 y:7.5229997634887695 z:26.711000442504883
- atom: O x: -16.299999237060547 y:7.142000198364258 z:26.871999740600586
- atom: CB x: -13.437999725341797 y:5.7779998779296875 z:26.885000228881836
- atom: CG1 x: -14.513999938964844 y:4.703999996185303 z:26.7549991607666
- atom: CG2 x: -12.199999809265137 y:5.271999835968018 z:27.624000549316406
- atom: CD1 x: -14.071999549865723 y:3.513000011444092 z:25.937999725341797
- residue PRO has 7 atoms
- atom: N x: -14.821000099182129 y:8.404000282287598 z:25.766000747680664
- atom: CA x: -15.810999870300293 y:8.979000091552734 z:24.83799934387207
- atom: C x: -16.490999221801758 y:7.840000152587891 z:24.062999725341797
- atom: O x: -15.810999870300293 y:6.901000022888184 z:23.624000549316406
- atom: CB x: -14.961999893188477 y:9.873000144958496 z:23.937999725341797
- atom: CG x: -13.824999809265137 y:10.289999961853027 z:24.843000411987305
- atom: CD x: -13.48900032043457 y:8.99899959564209 z:25.56800079345703
- residue LYS has 9 atoms
- atom: N x: -17.80900001525879 y:7.921999931335449 z:23.8799991607666
- atom: CA x: -18.554000854492188 y:6.8480000495910645 z:23.209999084472656
- atom: C x: -18.02199935913086 y:6.297999858856201 z:21.886999130249023
- atom: O x: -17.986000061035156 y:5.081999778747559 z:21.684999465942383
- atom: CB x: -20.007999420166016 y:7.251999855041504 z:22.993000030517578
- atom: CG x: -20.899999618530273 y:6.093999862670898 z:22.548999786376953
- atom: CD x: -21.552000045776367 y:5.38100004196167 z:23.746000289916992
- atom: CE x: -22.51300048828125 y:4.2829999923706055 z:23.280000686645508
- atom: NZ x: -23.47800064086914 y:3.8610000610351562 z:24.336000442504883
- residue ASP has 8 atoms
- atom: N x: -17.625999450683594 y:7.181000232696533 z:20.983999252319336
- atom: CA x: -17.1200008392334 y:6.754000186920166 z:19.68600082397461
- atom: C x: -15.680000305175781 y:6.251999855041504 z:19.711999893188477
- atom: O x: -15.003000259399414 y:6.2179999351501465 z:18.670000076293945
- atom: CB x: -17.22599983215332 y:7.90500020980835 z:18.687000274658203
- atom: CG x: -16.69099998474121 y:9.199000358581543 z:19.2450008392334
- atom: OD1 x: -15.991000175476074 y:9.913999557495117 z:18.503999710083008
- atom: OD2 x: -16.976999282836914 y:9.498000144958496 z:20.422000885009766
- residue GLN has 9 atoms
- atom: N x: -15.208000183105469 y:5.869999885559082 z:20.895000457763672
- atom: CA x: -13.840999603271484 y:5.36899995803833 z:21.02899932861328
- atom: C x: -13.864999771118164 y:4.067999839782715 z:21.81100082397461
- atom: O x: -12.859999656677246 y:3.375 z:21.93899917602539
- atom: CB x: -12.97700023651123 y:6.406000137329102 z:21.72800064086914
- atom: CG x: -13.196000099182129 y:7.809000015258789 z:21.20599937438965
- atom: CD x: -11.937000274658203 y:8.630999565124512 z:21.261999130249023
- atom: OE1 x: -11.22599983215332 y:8.621999740600586 z:22.266000747680664
- atom: NE2 x: -11.645999908447266 y:9.350000381469727 z:20.18199920654297
- residue TYR has 12 atoms
- atom: N x: -15.048999786376953 y:3.755000114440918 z:22.316999435424805
- atom: CA x: -15.3100004196167 y:2.546999931335449 z:23.077999114990234
- atom: C x: -14.543000221252441 y:1.3359999656677246 z:22.562999725341797
- atom: O x: -13.607999801635742 y:0.8619999885559082 z:23.190000534057617
- atom: CB x: -16.804000854492188 y:2.242000102996826 z:23.031999588012695
- atom: CG x: -17.19499969482422 y:1.00600004196167 z:23.79199981689453
- atom: CD1 x: -17.104999542236328 y:0.9660000205039978 z:25.180999755859375
- atom: CD2 x: -17.6299991607666 y:-0.13699999451637268 z:23.121000289916992
- atom: CE1 x: -17.437999725341797 y:-0.1850000023841858 z:25.889999389648438
- atom: CE2 x: -17.964000701904297 y:-1.2970000505447388 z:23.815000534057617
- atom: CZ x: -17.865999221801758 y:-1.319000005722046 z:25.20199966430664
- atom: OH x: -18.17799949645996 y:-2.4670000076293945 z:25.902000427246094
- residue TYR has 12 atoms
- atom: N x: -14.942999839782715 y:0.8270000219345093 z:21.410999298095703
- atom: CA x: -14.288000106811523 y:-0.3409999907016754 z:20.8700008392334
- atom: C x: -12.777999877929688 y:-0.21400000154972076 z:20.922000885009766
- atom: O x: -12.097000122070312 y:-1.1469999551773071 z:21.32200050354004
- atom: CB x: -14.779999732971191 y:-0.5960000157356262 z:19.445999145507812
- atom: CG x: -16.284000396728516 y:-0.7670000195503235 z:19.385000228881836
- atom: CD1 x: -16.902000427246094 y:-1.9190000295639038 z:19.878999710083008
- atom: CD2 x: -17.097999572753906 y:0.25699999928474426 z:18.899999618530273
- atom: CE1 x: -18.301000595092773 y:-2.0450000762939453 z:19.89900016784668
- atom: CE2 x: -18.493999481201172 y:0.1469999998807907 z:18.916000366210938
- atom: CZ x: -19.089000701904297 y:-1.0019999742507935 z:19.420000076293945
- atom: OH x: -20.4689998626709 y:-1.069000005722046 z:19.485000610351562
- residue CYS has 6 atoms
- atom: N x: -12.243000030517578 y:0.9359999895095825 z:20.545000076293945
- atom: CA x: -10.789999961853027 y:1.1050000190734863 z:20.573999404907227
- atom: C x: -10.241999626159668 y:1.0920000076293945 z:22.003999710083008
- atom: O x: -9.145000457763672 y:0.6069999933242798 z:22.257999420166016
- atom: CB x: -10.390999794006348 y:2.4019999504089355 z:19.875999450683594
- atom: SG x: -9.300999641418457 y:2.1089999675750732 z:18.48900032043457
- residue GLY has 4 atoms
- atom: N x: -11.019000053405762 y:1.6349999904632568 z:22.93199920654297
- atom: CA x: -10.604000091552734 y:1.6460000276565552 z:24.31800079345703
- atom: C x: -10.835000038146973 y:0.289000004529953 z:24.96299934387207
- atom: O x: -10.050999641418457 y:-0.16200000047683716 z:25.792999267578125
- residue VAL has 7 atoms
- atom: N x: -11.920000076293945 y:-0.36800000071525574 z:24.582000732421875
- atom: CA x: -12.220999717712402 y:-1.6660000085830688 z:25.134000778198242
- atom: C x: -11.131999969482422 y:-2.628000020980835 z:24.66900062561035
- atom: O x: -10.866999626159668 y:-3.63700008392334 z:25.305999755859375
- atom: CB x: -13.607000350952148 y:-2.1589999198913574 z:24.66699981689453
- atom: CG1 x: -13.576000213623047 y:-2.502000093460083 z:23.184999465942383
- atom: CG2 x: -14.036999702453613 y:-3.3519999980926514 z:25.479999542236328
- residue LEU has 8 atoms
- atom: N x: -10.487000465393066 y:-2.309999942779541 z:23.559999465942383
- atom: CA x: -9.4399995803833 y:-3.1710000038146973 z:23.065000534057617
- atom: C x: -8.232999801635742 y:-2.9670000076293945 z:23.94700050354004
- atom: O x: -7.6620001792907715 y:-3.9210000038146973 z:24.485000610351562
- atom: CB x: -9.074000358581543 y:-2.805999994277954 z:21.634000778198242
- atom: CG x: -7.961999893188477 y:-3.6480000019073486 z:21.007999420166016
- atom: CD1 x: -8.39900016784668 y:-5.107999801635742 z:20.95599937438965
- atom: CD2 x: -7.644999980926514 y:-3.119999885559082 z:19.613000869750977
- residue TYR has 12 atoms
- atom: N x: -7.855000019073486 y:-1.7059999704360962 z:24.0939998626709
- atom: CA x: -6.703000068664551 y:-1.3450000286102295 z:24.893999099731445
- atom: C x: -6.7870001792907715 y:-1.8880000114440918 z:26.312999725341797
- atom: O x: -5.877999782562256 y:-2.578000068664551 z:26.77199935913086
- atom: CB x: -6.550000190734863 y:0.17399999499320984 z:24.950000762939453
- atom: CG x: -5.408999919891357 y:0.6000000238418579 z:25.836000442504883
- atom: CD1 x: -4.098999977111816 y:0.5410000085830688 z:25.382999420166016
- atom: CD2 x: -5.636000156402588 y:0.9879999756813049 z:27.158000946044922
- atom: CE1 x: -3.0409998893737793 y:0.8510000109672546 z:26.216999053955078
- atom: CE2 x: -4.584000110626221 y:1.2960000038146973 z:28.003999710083008
- atom: CZ x: -3.2880001068115234 y:1.222000002861023 z:27.525999069213867
- atom: OH x: -2.2260000705718994 y:1.49399995803833 z:28.360000610351562
- residue PHE has 11 atoms
- atom: N x: -7.882999897003174 y:-1.565000057220459 z:26.993999481201172
- atom: CA x: -8.121000289916992 y:-1.968999981880188 z:28.378000259399414
- atom: C x: -8.307999610900879 y:-3.4790000915527344 z:28.600000381469727
- atom: O x: -8.409000396728516 y:-3.937999963760376 z:29.736000061035156
- atom: CB x: -9.335000038146973 y:-1.2009999752044678 z:28.913999557495117
- atom: CG x: -9.093999862670898 y:-0.5210000276565552 z:30.23200035095215
- atom: CD1 x: -7.830999851226807 y:-0.009999999776482582 z:30.555999755859375
- atom: CD2 x: -10.133000373840332 y:-0.37299999594688416 z:31.152999877929688
- atom: CE1 x: -7.607999801635742 y:0.6340000033378601 z:31.783000946044922
- atom: CE2 x: -9.920999526977539 y:0.27399998903274536 z:32.38800048828125
- atom: CZ x: -8.659000396728516 y:0.7749999761581421 z:32.70100021362305
- residue THR has 7 atoms
- atom: N x: -8.368000030517578 y:-4.252999782562256 z:27.52199935913086
- atom: CA x: -8.527000427246094 y:-5.695000171661377 z:27.659000396728516
- atom: C x: -7.127999782562256 y:-6.291999816894531 z:27.558000564575195
- atom: O x: -6.834000110626221 y:-7.348999977111816 z:28.125
- atom: CB x: -9.447999954223633 y:-6.2870001792907715 z:26.538000106811523
- atom: OG1 x: -10.755999565124512 y:-5.709000110626221 z:26.632999420166016
- atom: CG2 x: -9.590999603271484 y:-7.790999889373779 z:26.69499969482422
- residue GLY has 4 atoms
- atom: N x: -6.26200008392334 y:-5.583000183105469 z:26.841999053955078
- atom: CA x: -4.89900016784668 y:-6.0329999923706055 z:26.658000946044922
- atom: C x: -4.8379998207092285 y:-7.366000175476074 z:25.944000244140625
- atom: O x: -5.651000022888184 y:-7.636000156402588 z:25.055999755859375
- residue SER has 6 atoms
- atom: N x: -3.8940000534057617 y:-8.215999603271484 z:26.344999313354492
- atom: CA x: -2.950000047683716 y:-7.925000190734863 z:27.43899917602539
- atom: C x: -1.9830000400543213 y:-6.807000160217285 z:27.10099983215332
- atom: O x: -1.75600004196167 y:-6.502999782562256 z:25.93000030517578
- atom: CB x: -2.1080000400543213 y:-9.154000282287598 z:27.775999069213867
- atom: OG x: -1.0529999732971191 y:-9.291999816894531 z:26.840999603271484
- residue ASP has 8 atoms
- atom: N x: -1.3969999551773071 y:-6.228000164031982 z:28.145000457763672
- atom: CA x: -0.42899999022483826 y:-5.145999908447266 z:28.013999938964844
- atom: C x: 0.6370000243186951 y:-5.468999862670898 z:26.96299934387207
- atom: O x: 0.9330000281333923 y:-4.64900016784668 z:26.097000122070312
- atom: CB x: 0.22100000083446503 y:-4.900000095367432 z:29.3700008392334
- atom: CG x: 0.7870000004768372 y:-6.170000076293945 z:29.974000930786133
- atom: OD1 x: 1.9320000410079956 y:-6.541999816894531 z:29.61400032043457
- atom: OD2 x: 0.07400000095367432 y:-6.804999828338623 z:30.790000915527344
- residue ILE has 8 atoms
- atom: N x: 1.215999960899353 y:-6.6620001792907715 z:27.04199981689453
- atom: CA x: 2.2239999771118164 y:-7.057000160217285 z:26.06999969482422
- atom: C x: 1.5240000486373901 y:-7.189000129699707 z:24.72800064086914
- atom: O x: 2.115000009536743 y:-6.8979997634887695 z:23.695999145507812
- atom: CB x: 2.88700008392334 y:-8.416000366210938 z:26.416000366210938
- atom: CG1 x: 3.5199999809265137 y:-8.373000144958496 z:27.809999465942383
- atom: CG2 x: 3.9570000171661377 y:-8.734999656677246 z:25.385000228881836
- atom: CD1 x: 4.730000019073486 y:-7.460999965667725 z:27.913000106811523
- residue PHE has 11 atoms
- atom: N x: 0.27000001072883606 y:-7.638999938964844 z:24.740999221801758
- atom: CA x: -0.4909999966621399 y:-7.76800012588501 z:23.500999450683594
- atom: C x: -0.550000011920929 y:-6.389999866485596 z:22.841999053955078
- atom: O x: -0.3019999861717224 y:-6.252999782562256 z:21.641000747680664
- atom: CB x: -1.9140000343322754 y:-8.26200008392334 z:23.777000427246094
- atom: CG x: -2.802999973297119 y:-8.269000053405762 z:22.55900001525879
- atom: CD1 x: -4.051000118255615 y:-7.645999908447266 z:22.586000442504883
- atom: CD2 x: -2.3959999084472656 y:-8.892999649047852 z:21.381999969482422
- atom: CE1 x: -4.880000114440918 y:-7.64300012588501 z:21.461000442504883
- atom: CE2 x: -3.2209999561309814 y:-8.895000457763672 z:20.25200080871582
- atom: CZ x: -4.4629998207092285 y:-8.267000198364258 z:20.29599952697754
- residue ASN has 8 atoms
- atom: N x: -0.8730000257492065 y:-5.379000186920166 z:23.64900016784668
- atom: CA x: -0.9649999737739563 y:-3.994999885559082 z:23.198999404907227
- atom: C x: 0.36899998784065247 y:-3.4709999561309814 z:22.68199920654297
- atom: O x: 0.4090000092983246 y:-2.625 z:21.791000366210938
- atom: CB x: -1.4759999513626099 y:-3.121000051498413 z:24.334999084472656
- atom: CG x: -2.9230000972747803 y:-3.3919999599456787 z:24.648000717163086
- atom: OD1 x: -3.4649999141693115 y:-4.428999900817871 z:24.25200080871582
- atom: ND2 x: -3.565000057220459 y:-2.4709999561309814 z:25.361000061035156
- residue LYS has 9 atoms
- atom: N x: 1.4589999914169312 y:-3.9660000801086426 z:23.25200080871582
- atom: CA x: 2.7829999923706055 y:-3.575000047683716 z:22.798999786376953
- atom: C x: 2.8970000743865967 y:-4.184000015258789 z:21.39900016784668
- atom: O x: 3.390000104904175 y:-3.553999900817871 z:20.46500015258789
- atom: CB x: 3.865000009536743 y:-4.192999839782715 z:23.691999435424805
- atom: CG x: 4.803999900817871 y:-3.2190001010894775 z:24.374000549316406
- atom: CD x: 4.2220001220703125 y:-2.7219998836517334 z:25.68199920654297
- atom: CE x: 5.249000072479248 y:-1.906999945640564 z:26.447999954223633
- atom: NZ x: 4.71999979019165 y:-1.440000057220459 z:27.759000778198242
- residue ASN has 8 atoms
- atom: N x: 2.4240000247955322 y:-5.421000003814697 z:21.270999908447266
- atom: CA x: 2.4730000495910645 y:-6.144999980926514 z:20.006000518798828
- atom: C x: 1.680999994277954 y:-5.458000183105469 z:18.91900062561035
- atom: O x: 2.183000087738037 y:-5.236999988555908 z:17.82200050354004
- atom: CB x: 1.9279999732971191 y:-7.566999912261963 z:20.170000076293945
- atom: CG x: 2.819000005722046 y:-8.437000274658203 z:21.020999908447266
- atom: OD1 x: 4.0329999923706055 y:-8.473999977111816 z:20.822999954223633
- atom: ND2 x: 2.2230000495910645 y:-9.152000427246094 z:21.969999313354492
- residue MET has 8 atoms
- atom: N x: 0.43299999833106995 y:-5.135000228881836 z:19.23699951171875
- atom: CA x: -0.46299999952316284 y:-4.486000061035156 z:18.29400062561035
- atom: C x: -0.013000000268220901 y:-3.0759999752044678 z:17.910999298095703
- atom: O x: 0.13500000536441803 y:-2.7690000534057617 z:16.731000900268555
- atom: CB x: -1.8730000257492065 y:-4.451000213623047 z:18.875
- atom: CG x: -2.9140000343322754 y:-3.936000108718872 z:17.91699981689453
- atom: SD x: -4.511000156402588 y:-3.989000082015991 z:18.68199920654297
- atom: CE x: -5.236000061035156 y:-5.382999897003174 z:17.812000274658203
- residue ARG has 11 atoms
- atom: N x: 0.20499999821186066 y:-2.2179999351501465 z:18.899999618530273
- atom: CA x: 0.6489999890327454 y:-0.8560000061988831 z:18.618000030517578
- atom: C x: 2.0329999923706055 y:-0.8849999904632568 z:17.986000061035156
- atom: O x: 2.75600004196167 y:0.10899999737739563 z:18.027000427246094
- atom: CB x: 0.7039999961853027 y:-0.02199999988079071 z:19.905000686645508
- atom: CG x: -0.6389999985694885 y:0.16200000047683716 z:20.607999801635742
- atom: CD x: -0.546999990940094 y:1.11899995803833 z:21.801000595092773
- atom: NE x: 0.36800000071525574 y:0.6430000066757202 z:22.839000701904297
- atom: CZ x: 1.690000057220459 y:0.8040000200271606 z:22.823999404907227
- atom: NH1 x: 2.2869999408721924 y:1.440999984741211 z:21.822999954223633
- atom: NH2 x: 2.4210000038146973 y:0.3109999895095825 z:23.812000274658203
- residue ALA has 5 atoms
- atom: N x: 2.3959999084472656 y:-2.0299999713897705 z:17.41200065612793
- atom: CA x: 3.694999933242798 y:-2.2079999446868896 z:16.777000427246094
- atom: C x: 3.558000087738037 y:-2.7639999389648438 z:15.357999801635742
- atom: O x: 4.267000198364258 y:-2.3389999866485596 z:14.446999549865723
- atom: CB x: 4.560999870300293 y:-3.131999969482422 z:17.625
- residue HIS has 10 atoms
- atom: N x: 2.6530001163482666 y:-3.7170000076293945 z:15.168000221252441
- atom: CA x: 2.447000026702881 y:-4.2870001792907715 z:13.842000007629395
- atom: C x: 1.50600004196167 y:-3.38100004196167 z:13.050000190734863
- atom: O x: 1.3990000486373901 y:-3.496000051498413 z:11.829999923706055
- atom: CB x: 1.8489999771118164 y:-5.692999839782715 z:13.930999755859375
- atom: CG x: 2.2960000038146973 y:-6.5980000495910645 z:12.826000213623047
- atom: ND1 x: 3.5880000591278076 y:-7.076000213623047 z:12.737000465393066
- atom: CD2 x: 1.6419999599456787 y:-7.076000213623047 z:11.741000175476074
- atom: CE1 x: 3.7090001106262207 y:-7.809999942779541 z:11.645000457763672
- atom: NE2 x: 2.5429999828338623 y:-7.827000141143799 z:11.02299976348877
- residue ALA has 5 atoms
- atom: N x: 0.828000009059906 y:-2.4809999465942383 z:13.76200008392334
- atom: CA x: -0.10000000149011612 y:-1.5369999408721924 z:13.149999618530273
- atom: C x: 0.6909999847412109 y:-0.40799999237060547 z:12.517999649047852
- atom: O x: 0.12399999797344208 y:0.5239999890327454 z:11.958000183105469
- atom: CB x: -1.0499999523162842 y:-0.9750000238418579 z:14.199999809265137
- residue LEU has 8 atoms
- atom: N x: 2.009999990463257 y:-0.4959999918937683 z:12.625
- atom: CA x: 2.8910000324249268 y:0.5099999904632568 z:12.059000015258789
- atom: C x: 3.50600004196167 y:-0.03500000014901161 z:10.78499984741211
- atom: O x: 3.7899999618530273 y:0.7179999947547913 z:9.859999656677246
- atom: CB x: 3.9809999465942383 y:0.875 z:13.062000274658203
- atom: CG x: 3.4670000076293945 y:1.5980000495910645 z:14.305000305175781
- atom: CD1 x: 4.455999851226807 y:1.4429999589920044 z:15.440999984741211
- atom: CD2 x: 3.243000030517578 y:3.062999963760376 z:13.977999687194824
- residue GLU has 9 atoms
- atom: N x: 3.7119998931884766 y:-1.3480000495910645 z:10.744999885559082
- atom: CA x: 4.270999908447266 y:-2.0 z:9.562999725341797
- atom: C x: 3.1630001068115234 y:-2.0859999656677246 z:8.519000053405762
- atom: O x: 3.4089999198913574 y:-2.381999969482422 z:7.3460001945495605
- atom: CB x: 4.775000095367432 y:-3.4110000133514404 z:9.897000312805176
- atom: CG x: 6.122000217437744 y:-3.4679999351501465 z:10.611000061035156
- atom: CD x: 6.538000106811523 y:-4.894000053405762 z:10.965999603271484
- atom: OE1 x: 5.827000141143799 y:-5.545000076293945 z:11.767999649047852
- atom: OE2 x: 7.573999881744385 y:-5.364999771118164 z:10.442000389099121
- residue LYS has 9 atoms
- atom: N x: 1.937000036239624 y:-1.8250000476837158 z:8.96399974822998
- atom: CA x: 0.7760000228881836 y:-1.8489999771118164 z:8.09000015258789
- atom: C x: 0.4650000035762787 y:-0.4359999895095825 z:7.625
- atom: O x: -0.1469999998807907 y:-0.23800000548362732 z:6.577000141143799
- atom: CB x: -0.42500001192092896 y:-2.430999994277954 z:8.829000473022461
- atom: CG x: -0.34700000286102295 y:-3.931999921798706 z:9.03600025177002
- atom: CD x: -0.3109999895095825 y:-4.669000148773193 z:7.701000213623047
- atom: CE x: -0.36899998784065247 y:-6.182000160217285 z:7.88100004196167
- atom: NZ x: -0.4009999930858612 y:-6.886000156402588 z:6.570000171661377
- residue GLY has 4 atoms
- atom: N x: 0.8970000147819519 y:0.5450000166893005 z:8.40999984741211
- atom: CA x: 0.6600000262260437 y:1.930999994277954 z:8.053999900817871
- atom: C x: -0.44699999690055847 y:2.5869998931884766 z:8.862000465393066
- atom: O x: -1.2719999551773071 y:3.318000078201294 z:8.3100004196167
- residue PHE has 11 atoms
- atom: N x: -0.4729999899864197 y:2.3239998817443848 z:10.166999816894531
- atom: CA x: -1.4789999723434448 y:2.8940000534057617 z:11.060999870300293
- atom: C x: -0.8289999961853027 y:3.25 z:12.390000343322754
- atom: O x: 0.3659999966621399 y:3.0260000228881836 z:12.576000213623047
- atom: CB x: -2.614000082015991 y:1.8949999809265137 z:11.293999671936035
- atom: CG x: -3.365000009536743 y:1.534999966621399 z:10.04699993133545
- atom: CD1 x: -2.7880001068115234 y:0.7170000076293945 z:9.079999923706055
- atom: CD2 x: -4.638999938964844 y:2.0510001182556152 z:9.812999725341797
- atom: CE1 x: -3.4639999866485596 y:0.42100000381469727 z:7.896999835968018
- atom: CE2 x: -5.323999881744385 y:1.7610000371932983 z:8.633999824523926
- atom: CZ x: -4.734000205993652 y:0.9449999928474426 z:7.675000190734863
- residue THR has 7 atoms
- atom: N x: -1.6059999465942383 y:3.812999963760376 z:13.309000015258789
- atom: CA x: -1.0820000171661377 y:4.171000003814697 z:14.621000289916992
- atom: C x: -2.1449999809265137 y:4.130000114440918 z:15.713000297546387
- atom: O x: -2.8350000381469727 y:5.118000030517578 z:15.982999801635742
- atom: CB x: -0.4440000057220459 y:5.560999870300293 z:14.616999626159668
- atom: OG1 x: -0.1979999989271164 y:5.96999979019165 z:15.970999717712402
- atom: CG2 x: -1.3569999933242798 y:6.568999767303467 z:13.937999725341797
- residue ILE has 8 atoms
- atom: N x: -2.260999917984009 y:2.9660000801086426 z:16.34000015258789
- atom: CA x: -3.2179999351501465 y:2.749000072479248 z:17.410999298095703
- atom: C x: -2.7730000019073486 y:3.4049999713897705 z:18.715999603271484
- atom: O x: -1.5839999914169312 y:3.5250000953674316 z:18.99799919128418
- atom: CB x: -3.384000062942505 y:1.25 z:17.70800018310547
- atom: CG1 x: -3.8320000171661377 y:0.5090000033378601 z:16.45400047302246
- atom: CG2 x: -4.36899995803833 y:1.0549999475479126 z:18.841999053955078
- atom: CD1 x: -3.9230000972747803 y:-0.9929999709129333 z:16.635000228881836
- residue ASN has 8 atoms
- atom: N x: -3.750999927520752 y:3.8329999446868896 z:19.49799919128418
- atom: CA x: -3.5160000324249268 y:4.416999816894531 z:20.804000854492188
- atom: C x: -4.771999835968018 y:3.9769999980926514 z:21.53499984741211
- atom: O x: -5.671000003814697 y:3.4179999828338623 z:20.91699981689453
- atom: CB x: -3.364000082015991 y:5.951000213623047 z:20.72800064086914
- atom: CG x: -4.677000045776367 y:6.679999828338623 z:20.570999145507812
- atom: OD1 x: -5.383999824523926 y:6.507999897003174 z:19.586000442504883
- atom: ND2 x: -5.002999782562256 y:7.520999908447266 z:21.547000885009766
- residue GLU has 9 atoms
- atom: N x: -4.8480000495910645 y:4.176000118255615 z:22.83799934387207
- atom: CA x: -6.034999847412109 y:3.7279999256134033 z:23.54800033569336
- atom: C x: -7.315999984741211 y:4.426000118255615 z:23.10700035095215
- atom: O x: -8.413999557495117 y:4.002999782562256 z:23.4689998626709
- atom: CB x: -5.839000225067139 y:3.9059998989105225 z:25.049999237060547
- atom: CG x: -5.285999774932861 y:5.250999927520752 z:25.452999114990234
- atom: CD x: -5.427000045776367 y:5.492000102996826 z:26.93899917602539
- atom: OE1 x: -6.584000110626221 y:5.568999767303467 z:27.41699981689453
- atom: OE2 x: -4.386000156402588 y:5.5960001945495605 z:27.628999710083008
- residue TYR has 12 atoms
- atom: N x: -7.186999797821045 y:5.4730000495910645 z:22.301000595092773
- atom: CA x: -8.359000205993652 y:6.21999979019165 z:21.871999740600586
- atom: C x: -8.829000473022461 y:6.129000186920166 z:20.430999755859375
- atom: O x: -10.012999534606934 y:6.314000129699707 z:20.163000106811523
- atom: CB x: -8.189000129699707 y:7.686999797821045 z:22.2549991607666
- atom: CG x: -8.407999992370605 y:7.910999774932861 z:23.726999282836914
- atom: CD1 x: -9.579999923706055 y:7.461999893188477 z:24.343000411987305
- atom: CD2 x: -7.442999839782715 y:8.538999557495117 z:24.511999130249023
- atom: CE1 x: -9.788999557495117 y:7.626999855041504 z:25.70400047302246
- atom: CE2 x: -7.639999866485596 y:8.711000442504883 z:25.878999710083008
- atom: CZ x: -8.817999839782715 y:8.24899959564209 z:26.469999313354492
- atom: OH x: -9.015999794006348 y:8.385000228881836 z:27.82900047302246
- residue THR has 7 atoms
- atom: N x: -7.926000118255615 y:5.84499979019165 z:19.503999710083008
- atom: CA x: -8.315999984741211 y:5.76200008392334 z:18.10300064086914
- atom: C x: -7.355000019073486 y:4.928999900817871 z:17.274999618530273
- atom: O x: -6.382999897003174 y:4.380000114440918 z:17.781999588012695
- atom: CB x: -8.359000205993652 y:7.159999847412109 z:17.450000762939453
- atom: OG1 x: -7.072000026702881 y:7.771999835968018 z:17.58099937438965
- atom: CG2 x: -9.40999984741211 y:8.045999526977539 z:18.10300064086914
- residue ILE has 8 atoms
- atom: N x: -7.651000022888184 y:4.840000152587891 z:15.984999656677246
- atom: CA x: -6.809999942779541 y:4.129000186920166 z:15.03600025177002
- atom: C x: -6.605000019073486 y:5.14300012588501 z:13.92300033569336
- atom: O x: -7.561999797821045 y:5.546000003814697 z:13.265999794006348
- atom: CB x: -7.505000114440918 y:2.8489999771118164 z:14.496000289916992
- atom: CG1 x: -6.677000045776367 y:2.243000030517578 z:13.366000175476074
- atom: CG2 x: -8.907999992370605 y:3.1640000343322754 z:14.024999618530273
- atom: CD1 x: -5.2870001792907715 y:1.8519999980926514 z:13.770000457763672
- residue ARG has 11 atoms
- atom: N x: -5.361999988555908 y:5.576000213623047 z:13.73900032043457
- atom: CA x: -5.0320000648498535 y:6.578000068664551 z:12.72599983215332
- atom: C x: -4.03000020980835 y:6.0970001220703125 z:11.682000160217285
- atom: O x: -3.0840001106262207 y:5.367000102996826 z:11.996000289916992
- atom: CB x: -4.446000099182129 y:7.829999923706055 z:13.387999534606934
- atom: CG x: -5.349999904632568 y:8.541000366210938 z:14.371999740600586
- atom: CD x: -4.564000129699707 y:9.571000099182129 z:15.16100025177002
- atom: NE x: -5.436999797821045 y:10.416000366210938 z:15.961999893188477
- atom: CZ x: -6.255000114440918 y:11.333999633789062 z:15.456000328063965
- atom: NH1 x: -6.309000015258789 y:11.53499984741211 z:14.142999649047852
- atom: NH2 x: -7.034999847412109 y:12.043000221252441 z:16.260000228881836
- residue PRO has 7 atoms
- atom: N x: -4.21999979019165 y:6.513000011444092 z:10.418999671936035
- atom: CA x: -3.3289999961853027 y:6.136000156402588 z:9.314000129699707
- atom: C x: -2.0810000896453857 y:7.013000011444092 z:9.279999732971191
- atom: O x: -2.1059999465942383 y:8.13700008392334 z:9.77299976348877
- atom: CB x: -4.203000068664551 y:6.354000091552734 z:8.08899974822998
- atom: CG x: -5.043000221252441 y:7.53000020980835 z:8.503999710083008
- atom: CD x: -5.443999767303467 y:7.158999919891357 z:9.90999984741211
- residue LEU has 8 atoms
- atom: N x: -0.9909999966621399 y:6.5 z:8.71500015258789
- atom: CA x: 0.23899999260902405 y:7.2820000648498535 z:8.612000465393066
- atom: C x: 0.4749999940395355 y:7.710999965667725 z:7.160999774932861
- atom: O x: 0.6140000224113464 y:6.875999927520752 z:6.260000228881836
- atom: CB x: 1.4550000429153442 y:6.493000030517578 z:9.128000259399414
- atom: CG x: 1.6330000162124634 y:6.239999771118164 z:10.633000373840332
- atom: CD1 x: 3.072000026702881 y:5.822000026702881 z:10.888999938964844
- atom: CD2 x: 1.3270000219345093 y:7.493000030517578 z:11.430999755859375
- residue GLY has 4 atoms
- atom: N x: 0.5199999809265137 y:9.02400016784668 z:6.947000026702881
- atom: CA x: 0.7110000252723694 y:9.560999870300293 z:5.611999988555908
- atom: C x: 2.055000066757202 y:9.293999671936035 z:4.956999778747559
- atom: O x: 2.5769999027252197 y:8.173999786376953 z:5.01200008392334
- residue VAL has 5 atoms
- atom: N x: 2.6010000705718994 y:10.335000038146973 z:4.326000213623047
- atom: CA x: 3.885999917984009 y:10.26200008392334 z:3.632999897003174
- atom: C x: 5.041999816894531 y:10.295999526977539 z:4.625999927520752
- atom: O x: 5.809000015258789 y:9.336999893188477 z:4.73799991607666
- atom: CB x: 4.046000003814697 y:11.435999870300293 z:2.6449999809265137
- residue THR has 7 atoms
- atom: N x: 5.1620001792907715 y:11.411999702453613 z:5.3379998207092285
- atom: CA x: 6.205999851226807 y:11.58899974822998 z:6.3429999351501465
- atom: C x: 5.745999813079834 y:10.847000122070312 z:7.5879998207092285
- atom: O x: 6.538000106811523 y:10.524999618530273 z:8.479999542236328
- atom: CB x: 6.401000022888184 y:13.09000015258789 z:6.693999767303467
- atom: OG1 x: 7.418000221252441 y:13.229000091552734 z:7.696000099182129
- atom: CG2 x: 5.10099983215332 y:13.690999984741211 z:7.216000080108643
- residue GLY has 4 atoms
- atom: N x: 4.451000213623047 y:10.559000015258789 z:7.620999813079834
- atom: CA x: 3.871999979019165 y:9.878999710083008 z:8.756999969482422
- atom: C x: 3.1549999713897705 y:10.939000129699707 z:9.560999870300293
- atom: O x: 3.7009999752044678 y:11.47599983215332 z:10.526000022888184
- residue VAL has 7 atoms
- atom: N x: 1.9320000410079956 y:11.253999710083008 z:9.142000198364258
- atom: CA x: 1.121000051498413 y:12.267000198364258 z:9.810999870300293
- atom: C x: -0.13600000739097595 y:11.644000053405762 z:10.413000106811523
- atom: O x: -0.7139999866485596 y:10.715999603271484 z:9.848999977111816
- atom: CB x: 0.6930000185966492 y:13.37600040435791 z:8.821000099182129
- atom: CG1 x: 0.11800000071525574 y:14.564000129699707 z:9.583999633789062
- atom: CG2 x: 1.8819999694824219 y:13.795000076293945 z:7.960999965667725
- residue ALA has 5 atoms
- atom: N x: -0.5550000071525574 y:12.157999992370605 z:11.562000274658203
- atom: CA x: -1.746000051498413 y:11.645999908447266 z:12.223999977111816
- atom: C x: -2.989000082015991 y:11.880000114440918 z:11.366999626159668
- atom: O x: -3.7219998836517334 y:12.854999542236328 z:11.567999839782715
- atom: CB x: -1.9160000085830688 y:12.317000389099121 z:13.588000297546387
- residue GLY has 4 atoms
- atom: N x: -3.2219998836517334 y:10.994000434875488 z:10.402999877929688
- atom: CA x: -4.394999980926514 y:11.140999794006348 z:9.5649995803833
- atom: C x: -5.603000164031982 y:11.170000076293945 z:10.477999687194824
- atom: O x: -5.493000030517578 y:10.807000160217285 z:11.645999908447266
- residue GLU has 9 atoms
- atom: N x: -6.754000186920166 y:11.597999572753906 z:9.97599983215332
- atom: CA x: -7.928999900817871 y:11.63700008392334 z:10.82699966430664
- atom: C x: -8.236000061035156 y:10.243000030517578 z:11.357999801635742
- atom: O x: -7.811999797821045 y:9.243000030517578 z:10.781999588012695
- atom: CB x: -9.128000259399414 y:12.204000473022461 z:10.067999839782715
- atom: CG x: -8.973999977111816 y:13.675999641418457 z:9.729000091552734
- atom: CD x: -8.668999671936035 y:14.520999908447266 z:10.954000473022461
- atom: OE1 x: -9.545999526977539 y:14.63599967956543 z:11.836999893188477
- atom: OE2 x: -7.546000003814697 y:15.064000129699707 z:11.038999557495117
- residue PRO has 7 atoms
- atom: N x: -8.956999778747559 y:10.168000221252441 z:12.486000061035156
- atom: CA x: -9.35099983215332 y:8.928999900817871 z:13.156000137329102
- atom: C x: -10.333999633789062 y:8.079000473022461 z:12.36299991607666
- atom: O x: -11.458999633789062 y:8.48799991607666 z:12.119999885559082
- atom: CB x: -9.963000297546387 y:9.427000045776367 z:14.458000183105469
- atom: CG x: -9.27299976348877 y:10.722000122070312 z:14.6899995803833
- atom: CD x: -9.281999588012695 y:11.329000473022461 z:13.32800006866455
- residue LEU has 8 atoms
- atom: N x: -9.914999961853027 y:6.882999897003174 z:11.980999946594238
- atom: CA x: -10.781000137329102 y:5.994999885559082 z:11.220000267028809
- atom: C x: -12.0 y:5.538000106811523 z:12.052000045776367
- atom: O x: -11.925000190734863 y:5.4029998779296875 z:13.284000396728516
- atom: CB x: -9.970000267028809 y:4.785999774932861 z:10.727999687194824
- atom: CG x: -8.637999534606934 y:5.125 z:10.034000396728516
- atom: CD1 x: -7.88100004196167 y:3.8529999256134033 z:9.711999893188477
- atom: CD2 x: -8.88599967956543 y:5.926000118255615 z:8.770999908447266
- residue PRO has 7 atoms
- atom: N x: -13.142999649047852 y:5.301000118255615 z:11.381999969482422
- atom: CA x: -14.369999885559082 y:4.864999771118164 z:12.055999755859375
- atom: C x: -14.175000190734863 y:3.4600000381469727 z:12.61299991607666
- atom: O x: -13.482000350952148 y:2.6470000743865967 z:12.015000343322754
- atom: CB x: -15.402999877929688 y:4.925000190734863 z:10.942999839782715
- atom: CG x: -14.595000267028809 y:4.534999847412109 z:9.737000465393066
- atom: CD x: -13.314000129699707 y:5.303999900817871 z:9.918000221252441
- residue VAL has 7 atoms
- atom: N x: -14.791000366210938 y:3.1710000038146973 z:13.751999855041504
- atom: CA x: -14.619999885559082 y:1.871999979019165 z:14.383999824523926
- atom: C x: -15.878000259399414 y:1.4279999732971191 z:15.11400032043457
- atom: O x: -16.320999145507812 y:2.0989999771118164 z:16.045000076293945
- atom: CB x: -13.45199966430664 y:1.9279999732971191 z:15.414999961853027
- atom: CG1 x: -13.395000457763672 y:0.6629999876022339 z:16.229000091552734
- atom: CG2 x: -12.142000198364258 y:2.13700008392334 z:14.706000328063965
- residue ASP has 8 atoms
- atom: N x: -16.44499969482422 y:0.29499998688697815 z:14.708000183105469
- atom: CA x: -17.641000747680664 y:-0.2070000022649765 z:15.37600040435791
- atom: C x: -17.44300079345703 y:-1.562000036239624 z:16.04199981689453
- atom: O x: -18.38599967956543 y:-2.1410000324249268 z:16.584999084472656
- atom: CB x: -18.812000274658203 y:-0.27399998903274536 z:14.397000312805176
- atom: CG x: -19.378000259399414 y:1.090999960899353 z:14.090999603271484
- atom: OD1 x: -19.974000930786133 y:1.7089999914169312 z:15.01099967956543
- atom: OD2 x: -19.208999633789062 y:1.5449999570846558 z:12.937000274658203
- residue SER has 6 atoms
- atom: N x: -16.21299934387207 y:-2.056999921798706 z:16.011999130249023
- atom: CA x: -15.904000282287598 y:-3.3350000381469727 z:16.624000549316406
- atom: C x: -14.416999816894531 y:-3.440999984741211 z:16.860000610351562
- atom: O x: -13.630000114440918 y:-2.6700000762939453 z:16.297000885009766
- atom: CB x: -16.336000442504883 y:-4.482999801635742 z:15.71399974822998
- atom: OG x: -15.477999687194824 y:-4.5929999351501465 z:14.583999633789062
- residue GLU has 9 atoms
- atom: N x: -14.02299976348877 y:-4.389999866485596 z:17.70199966430664
- atom: CA x: -12.605999946594238 y:-4.583000183105469 z:17.94700050354004
- atom: C x: -12.114999771118164 y:-5.175000190734863 z:16.631000518798828
- atom: O x: -11.086999893188477 y:-4.754000186920166 z:16.094999313354492
- atom: CB x: -12.359999656677246 y:-5.572000026702881 z:19.093000411987305
- atom: CG x: -12.958000183105469 y:-5.177999973297119 z:20.433000564575195
- atom: CD x: -12.744000434875488 y:-6.241000175476074 z:21.503000259399414
- atom: OE1 x: -11.678000450134277 y:-6.239999771118164 z:22.149999618530273
- atom: OE2 x: -13.63700008392334 y:-7.091000080108643 z:21.690000534057617
- residue LYS has 9 atoms
- atom: N x: -12.881999969482422 y:-6.133999824523926 z:16.10300064086914
- atom: CA x: -12.550999641418457 y:-6.808000087738037 z:14.845000267028809
- atom: C x: -12.190999984741211 y:-5.770999908447266 z:13.795000076293945
- atom: O x: -11.251999855041504 y:-5.955999851226807 z:13.017000198364258
- atom: CB x: -13.72700023651123 y:-7.6579999923706055 z:14.350000381469727
- atom: CG x: -13.319999694824219 y:-8.717000007629395 z:13.312999725341797
- atom: CD x: -14.470999717712402 y:-9.666000366210938 z:12.951000213623047
- atom: CE x: -13.95300006866455 y:-10.96500015258789 z:12.319999694824219
- atom: NZ x: -13.071999549865723 y:-10.746999740600586 z:11.128999710083008
- residue ASP has 8 atoms
- atom: N x: -12.949999809265137 y:-4.681000232696533 z:13.784000396728516
- atom: CA x: -12.708999633789062 y:-3.5869998931884766 z:12.864999771118164
- atom: C x: -11.27299976348877 y:-3.0889999866485596 z:12.994000434875488
- atom: O x: -10.62399959564209 y:-2.819999933242798 z:11.98799991607666
- atom: CB x: -13.6850004196167 y:-2.4489998817443848 z:13.14900016784668
- atom: CG x: -15.019000053405762 y:-2.638000011444092 z:12.45199966430664
- atom: OD1 x: -15.416999816894531 y:-3.799999952316284 z:12.22700023651123
- atom: OD2 x: -15.673999786376953 y:-1.6230000257492065 z:12.137999534606934
- residue ILE has 8 atoms
- atom: N x: -10.767000198364258 y:-2.9700000286102295 z:14.220000267028809
- atom: CA x: -9.394000053405762 y:-2.506999969482422 z:14.414999961853027
- atom: C x: -8.388999938964844 y:-3.507999897003174 z:13.859999656677246
- atom: O x: -7.361000061035156 y:-3.1089999675750732 z:13.307999610900879
- atom: CB x: -9.074000358581543 y:-2.252000093460083 z:15.904000282287598
- atom: CG1 x: -9.920999526977539 y:-1.0920000076293945 z:16.42300033569336
- atom: CG2 x: -7.604000091552734 y:-1.9160000085830688 z:16.07200050354004
- atom: CD1 x: -9.934000015258789 y:-0.9750000238418579 z:17.92300033569336
- residue PHE has 11 atoms
- atom: N x: -8.67199993133545 y:-4.802999973297119 z:13.996999740600586
- atom: CA x: -7.755000114440918 y:-5.816999912261963 z:13.468000411987305
- atom: C x: -7.697000026702881 y:-5.741000175476074 z:11.954000473022461
- atom: O x: -6.613999843597412 y:-5.801000118255615 z:11.366000175476074
- atom: CB x: -8.1850004196167 y:-7.229000091552734 z:13.838000297546387
- atom: CG x: -8.031000137329102 y:-7.553999900817871 z:15.281000137329102
- atom: CD1 x: -8.97599983215332 y:-7.142000198364258 z:16.200000762939453
- atom: CD2 x: -6.9629998207092285 y:-8.329000473022461 z:15.71399974822998
- atom: CE1 x: -8.86400032043457 y:-7.50600004196167 z:17.531999588012695
- atom: CE2 x: -6.8420000076293945 y:-8.699000358581543 z:17.04400062561035
- atom: CZ x: -7.793000221252441 y:-8.289999961853027 z:17.95400047302246
- residue ASP has 8 atoms
- atom: N x: -8.868000030517578 y:-5.627999782562256 z:11.32800006866455
- atom: CA x: -8.956000328063965 y:-5.539999961853027 z:9.875
- atom: C x: -7.9770002365112305 y:-4.494999885559082 z:9.343000411987305
- atom: O x: -7.117000102996826 y:-4.798999786376953 z:8.513999938964844
- atom: CB x: -10.378999710083008 y:-5.177999973297119 z:9.451000213623047
- atom: CG x: -11.38599967956543 y:-6.243000030517578 z:9.824000358581543
- atom: OD1 x: -11.04800033569336 y:-7.438000202178955 z:9.717000007629395
- atom: OD2 x: -12.520000457763672 y:-5.888000011444092 z:10.206999778747559
- residue TYR has 12 atoms
- atom: N x: -8.109999656677246 y:-3.2669999599456787 z:9.835000038146973
- atom: CA x: -7.236000061035156 y:-2.171999931335449 z:9.430000305175781
- atom: C x: -5.750999927520752 y:-2.553999900817871 z:9.388999938964844
- atom: O x: -5.015999794006348 y:-2.0889999866485596 z:8.51200008392334
- atom: CB x: -7.4120001792907715 y:-0.9829999804496765 z:10.37600040435791
- atom: CG x: -8.711999893188477 y:-0.2290000021457672 z:10.222999572753906
- atom: CD1 x: -8.961999893188477 y:0.5600000023841858 z:9.097999572753906
- atom: CD2 x: -9.673999786376953 y:-0.26100000739097595 z:11.227999687194824
- atom: CE1 x: -10.13700008392334 y:1.3040000200271606 z:8.98799991607666
- atom: CE2 x: -10.85200023651123 y:0.4740000069141388 z:11.125
- atom: CZ x: -11.074000358581543 y:1.253999948501587 z:10.008000373840332
- atom: OH x: -12.22599983215332 y:1.99399995803833 z:9.934000015258789
- residue ILE has 8 atoms
- atom: N x: -5.306000232696533 y:-3.385999917984009 z:10.331999778747559
- atom: CA x: -3.9000000953674316 y:-3.7909998893737793 z:10.378999710083008
- atom: C x: -3.6470000743865967 y:-5.202000141143799 z:9.848999977111816
- atom: O x: -2.5460000038146973 y:-5.744999885559082 z:9.998000144958496
- atom: CB x: -3.3369998931884766 y:-3.7060000896453857 z:11.810999870300293
- atom: CG1 x: -4.114999771118164 y:-4.64900016784668 z:12.734999656677246
- atom: CG2 x: -3.4070000648498535 y:-2.2730000019073486 z:12.29800033569336
- atom: CD1 x: -3.5190000534057617 y:-4.806000232696533 z:14.109000205993652
- residue GLN has 9 atoms
- atom: N x: -4.672999858856201 y:-5.791999816894531 z:9.23799991607666
- atom: CA x: -4.566999912261963 y:-7.129000186920166 z:8.661999702453613
- atom: C x: -3.9079999923706055 y:-8.130999565124512 z:9.602999687194824
- atom: O x: -2.7799999713897705 y:-8.581999778747559 z:9.387999534606934
- atom: CB x: -3.802999973297119 y:-7.051000118255615 z:7.3420000076293945
- atom: CG x: -4.520999908447266 y:-6.198999881744385 z:6.308000087738037
- atom: CD x: -3.6029999256134033 y:-5.708000183105469 z:5.218999862670898
- atom: OE1 x: -2.9730000495910645 y:-6.502999782562256 z:4.520999908447266
- atom: NE2 x: -3.515000104904175 y:-4.388000011444092 z:5.065999984741211
- residue TRP has 14 atoms
- atom: N x: -4.6479997634887695 y:-8.468000411987305 z:10.651000022888184
- atom: CA x: -4.2129998207092285 y:-9.406999588012695 z:11.666000366210938
- atom: C x: -5.4029998779296875 y:-10.319000244140625 z:11.925000190734863
- atom: O x: -6.546999931335449 y:-9.857000350952148 z:11.963000297546387
- atom: CB x: -3.867000102996826 y:-8.654000282287598 z:12.949999809265137
- atom: CG x: -2.4119999408721924 y:-8.647000312805176 z:13.345000267028809
- atom: CD1 x: -1.3270000219345093 y:-8.75100040435791 z:12.519000053405762
- atom: CD2 x: -1.8910000324249268 y:-8.4350004196167 z:14.666000366210938
- atom: NE1 x: -0.164000004529953 y:-8.61299991607666 z:13.244999885559082
- atom: CE2 x: -0.4819999933242798 y:-8.416000366210938 z:14.562999725341797
- atom: CE3 x: -2.4809999465942383 y:-8.253999710083008 z:15.925999641418457
- atom: CZ2 x: 0.34700000286102295 y:-8.222999572753906 z:15.670999526977539
- atom: CZ3 x: -1.6579999923706055 y:-8.062000274658203 z:17.027000427246094
- atom: CH2 x: -0.257999986410141 y:-8.04800033569336 z:16.891000747680664
- residue LYS has 9 atoms
- atom: N x: -5.131999969482422 y:-11.611000061035156 z:12.079999923706055
- atom: CA x: -6.172999858856201 y:-12.593999862670898 z:12.36400032043457
- atom: C x: -6.895999908447266 y:-12.119000434875488 z:13.630999565124512
- atom: O x: -6.25 y:-11.840999603271484 z:14.640000343322754
- atom: CB x: -5.515999794006348 y:-13.961000442504883 z:12.612000465393066
- atom: CG x: -6.453999996185303 y:-15.081999778747559 z:13.057999610900879
- atom: CD x: -5.710000038146973 y:-16.18600082397461 z:13.833000183105469
- atom: CE x: -4.585000038146973 y:-16.8439998626709 z:13.029000282287598
- atom: NZ x: -3.36299991607666 y:-15.994999885559082 z:12.892999649047852
- residue TYR has 12 atoms
- atom: N x: -8.222000122070312 y:-12.010000228881836 z:13.583000183105469
- atom: CA x: -8.960000038146973 y:-11.565999984741211 z:14.760000228881836
- atom: C x: -8.760000228881836 y:-12.576000213623047 z:15.869999885559082
- atom: O x: -8.963000297546387 y:-13.774999618530273 z:15.677000045776367
- atom: CB x: -10.458000183105469 y:-11.418999671936035 z:14.470000267028809
- atom: CG x: -11.286999702453613 y:-11.11299991607666 z:15.708000183105469
- atom: CD1 x: -10.930999755859375 y:-10.07800006866455 z:16.576000213623047
- atom: CD2 x: -12.423999786376953 y:-11.857999801635742 z:16.016000747680664
- atom: CE1 x: -11.687000274658203 y:-9.791999816894531 z:17.722999572753906
- atom: CE2 x: -13.187000274658203 y:-11.57800006866455 z:17.160999298095703
- atom: CZ x: -12.8100004196167 y:-10.543999671936035 z:18.007999420166016
- atom: OH x: -13.557000160217285 y:-10.265999794006348 z:19.131999969482422
- residue ARG has 11 atoms
- atom: N x: -8.35099983215332 y:-12.07800006866455 z:17.030000686645508
- atom: CA x: -8.109999656677246 y:-12.918000221252441 z:18.19099998474121
- atom: C x: -9.045999526977539 y:-12.545000076293945 z:19.327999114990234
- atom: O x: -9.180000305175781 y:-11.371999740600586 z:19.68600082397461
- atom: CB x: -6.64300012588501 y:-12.793999671936035 z:18.628999710083008
- atom: CG x: -5.697000026702881 y:-13.623000144958496 z:17.770999908447266
- atom: CD x: -4.306000232696533 y:-13.03600025177002 z:17.694000244140625
- atom: NE x: -3.683000087738037 y:-12.902999877929688 z:19.003999710083008
- atom: CZ x: -2.4519999027252197 y:-12.432999610900879 z:19.19300079345703
- atom: NH1 x: -1.718999981880188 y:-12.057999610900879 z:18.14900016784668
- atom: NH2 x: -1.9579999446868896 y:-12.322999954223633 z:20.422000885009766
- residue GLU has 9 atoms
- atom: N x: -9.708999633789062 y:-13.553999900817871 z:19.881999969482422
- atom: CA x: -10.630000114440918 y:-13.32800006866455 z:20.979999542236328
- atom: C x: -9.880999565124512 y:-12.907999992370605 z:22.240999221801758
- atom: O x: -8.704000473022461 y:-13.222000122070312 z:22.416000366210938
- atom: CB x: -11.458000183105469 y:-14.58899974822998 z:21.243000030517578
- atom: CG x: -12.715999603271484 y:-14.678000450134277 z:20.395999908447266
- atom: CD x: -13.70300006866455 y:-13.559000015258789 z:20.702999114990234
- atom: OE1 x: -14.116000175476074 y:-13.442999839782715 z:21.875999450683594
- atom: OE2 x: -14.069000244140625 y:-12.795999526977539 z:19.7810001373291
- residue PRO has 7 atoms
- atom: N x: -10.557000160217285 y:-12.173999786376953 z:23.131999969482422
- atom: CA x: -9.939000129699707 y:-11.720000267028809 z:24.371000289916992
- atom: C x: -9.152999877929688 y:-12.814000129699707 z:25.082000732421875
- atom: O x: -8.093999862670898 y:-12.553000450134277 z:25.649999618530273
- atom: CB x: -11.133000373840332 y:-11.241999626159668 z:25.18000030517578
- atom: CG x: -11.991999626159668 y:-10.654999732971191 z:24.128000259399414
- atom: CD x: -11.949000358581543 y:-11.706999778747559 z:23.049999237060547
- residue LYS has 9 atoms
- atom: N x: -9.663999557495117 y:-14.041000366210938 z:25.042999267578125
- atom: CA x: -8.987000465393066 y:-15.14900016784668 z:25.709999084472656
- atom: C x: -7.636000156402588 y:-15.522000312805176 z:25.11199951171875
- atom: O x: -6.769999980926514 y:-16.047000885009766 z:25.81800079345703
- atom: CB x: -9.890999794006348 y:-16.393999099731445 z:25.76099967956543
- atom: CG x: -10.576000213623047 y:-16.767000198364258 z:24.45599937438965
- atom: CD x: -11.342000007629395 y:-18.08099937438965 z:24.591999053955078
- atom: CE x: -12.46399974822998 y:-18.19700050354004 z:23.55500030517578
- atom: NZ x: -11.987000465393066 y:-18.033000946044922 z:22.152999877929688
- residue ASP has 8 atoms
- atom: N x: -7.442999839782715 y:-15.236000061035156 z:23.82699966430664
- atom: CA x: -6.190999984741211 y:-15.576000213623047 z:23.158000946044922
- atom: C x: -5.249000072479248 y:-14.38599967956543 z:23.02199935913086
- atom: O x: -4.289000034332275 y:-14.437000274658203 z:22.250999450683594
- atom: CB x: -6.478000164031982 y:-16.13599967956543 z:21.766000747680664
- atom: CG x: -7.806000232696533 y:-16.85700035095215 z:21.69099998474121
- atom: OD1 x: -7.918000221252441 y:-17.975000381469727 z:22.240999221801758
- atom: OD2 x: -8.744000434875488 y:-16.29400062561035 z:21.08300018310547
- residue ARG has 11 atoms
- atom: N x: -5.5269999504089355 y:-13.3100004196167 z:23.753000259399414
- atom: CA x: -4.684999942779541 y:-12.119999885559082 z:23.701000213623047
- atom: C x: -3.753000020980835 y:-12.059000015258789 z:24.905000686645508
- atom: O x: -2.9630000591278076 y:-11.131999969482422 z:25.038000106811523
- atom: CB x: -5.535999774932861 y:-10.854000091552734 z:23.65399932861328
- atom: CG x: -6.466000080108643 y:-10.753000259399414 z:22.45599937438965
- atom: CD x: -7.349999904632568 y:-9.517000198364258 z:22.576000213623047
- atom: NE x: -8.53499984741211 y:-9.595999717712402 z:21.73699951171875
- atom: CZ x: -9.552000045776367 y:-8.748000144958496 z:21.80900001525879
- atom: NH1 x: -9.529999732971191 y:-7.751999855041504 z:22.68600082397461
- atom: NH2 x: -10.593000411987305 y:-8.897000312805176 z:21.003000259399414
- residue SER has 6 atoms
- atom: N x: -3.8580000400543213 y:-13.041000366210938 z:25.791000366210938
- atom: CA x: -2.989000082015991 y:-13.07699966430664 z:26.95599937438965
- atom: C x: -1.5839999914169312 y:-13.416000366210938 z:26.474000930786133
- atom: O x: -1.284999966621399 y:-14.574000358581543 z:26.16699981689453
- atom: CB x: -3.4690001010894775 y:-14.126999855041504 z:27.961000442504883
- atom: OG x: -4.433000087738037 y:-13.57800006866455 z:28.847000122070312
- residue GLU has 10 atoms
- atom: N x: -0.7360000014305115 y:-12.394000053405762 z:26.395999908447266
- atom: CA x: 0.6309999823570251 y:-12.565999984741211 z:25.93899917602539
- atom: C x: 1.6269999742507935 y:-11.968999862670898 z:26.92799949645996
- atom: O x: 2.7279999256134033 y:-12.541000366210938 z:27.077999114990234
- atom: CB x: 0.7960000038146973 y:-11.9399995803833 z:24.552000045776367
- atom: CG x: -0.11400000005960464 y:-12.574999809265137 z:23.51099967956543
- atom: CD x: 0.17499999701976776 y:-12.116999626159668 z:22.09000015258789
- atom: OE1 x: 0.09000000357627869 y:-10.902999877929688 z:21.815000534057617
- atom: OE2 x: 0.4819999933242798 y:-12.97700023651123 z:21.23900032043457
- atom: OXT x: 1.3029999732971191 y:-10.935999870300293 z:27.54400062561035
- residue MN has 1 atoms
- atom: MN x: -6.214000225067139 y:-5.52400016784668 z:35.61399841308594
- residue MN has 1 atoms
- atom: MN x: -6.142000198364258 y:-2.124000072479248 z:36.37300109863281
- residue MN has 1 atoms
- atom: MN x: 13.84000015258789 y:-1.5140000581741333 z:61.231998443603516
- residue MN has 1 atoms
- atom: MN x: 8.105999946594238 y:-25.408000946044922 z:15.770000457763672
- residue NA has 1 atoms
- atom: NA x: 4.251999855041504 y:-0.11299999803304672 z:43.87799835205078
- residue NA has 1 atoms
- atom: NA x: 16.698999404907227 y:-13.654000282287598 z:18.052000045776367
- residue F2A has 30 atoms
- atom: PA x: -3.8420000076293945 y:-3.880000114440918 z:34.38800048828125
- atom: O1A x: -5.063000202178955 y:-3.622999906539917 z:35.20000076293945
- atom: O2A x: -2.5329999923706055 y:-3.359999895095825 z:34.85300064086914
- atom: C3A x: -3.6730000972747803 y:-5.749000072479248 z:34.435001373291016
- atom: O5' x: -4.066999912261963 y:-3.2890000343322754 z:32.92499923706055
- atom: PB x: -4.76800012588501 y:-7.072999954223633 z:33.6879997253418
- atom: O1B x: -4.315000057220459 y:-7.23199987411499 z:32.28099822998047
- atom: O2B x: -6.175000190734863 y:-6.676000118255615 z:33.970001220703125
- atom: O3B x: -4.465000152587891 y:-8.342000007629395 z:34.42300033569336
- atom: PG x: -4.432000160217285 y:-8.357000350952148 z:35.915000915527344
- atom: O1G x: -2.990999937057495 y:-8.444000244140625 z:36.2599983215332
- atom: O2G x: -5.375 y:-9.385000228881836 z:36.42900085449219
- atom: O3G x: -4.946000099182129 y:-7.052999973297119 z:36.409000396728516
- atom: C5' x: -5.205999851226807 y:-3.6419999599456787 z:32.145999908447266
- atom: C4' x: -4.960000038146973 y:-3.3380000591278076 z:30.687000274658203
- atom: O4' x: -4.2230000495910645 y:-2.0969998836517334 z:30.54800033569336
- atom: C1' x: -3.4019999504089355 y:-2.1610000133514404 z:29.38800048828125
- atom: N9 x: -2.00600004196167 y:-1.9320000410079956 z:29.775999069213867
- atom: C4 x: -1.0019999742507935 y:-1.4759999513626099 z:28.95199966430664
- atom: N3 x: -1.1009999513626099 y:-1.1349999904632568 z:27.658000946044922
- atom: C2 x: 0.08100000023841858 y:-0.7540000081062317 z:27.180999755859375
- atom: N1 x: 1.2619999647140503 y:-0.6800000071525574 z:27.80299949645996
- atom: C6 x: 1.3289999961853027 y:-1.0219999551773071 z:29.106000900268555
- atom: N6 x: 2.506999969482422 y:-0.9359999895095825 z:29.729999542236328
- atom: C5 x: 0.14499999582767487 y:-1.4479999542236328 z:29.731000900268555
- atom: N7 x: -0.12700000405311584 y:-1.8680000305175781 z:31.024999618530273
- atom: C8 x: -1.4129999876022339 y:-2.138000011444092 z:31.003999710083008
- atom: C2' x: -3.621999979019165 y:-3.5390000343322754 z:28.760000228881836
- atom: C3' x: -4.086999893188477 y:-4.3429999351501465 z:29.964000701904297
- atom: O3' x: -4.868000030517578 y:-5.460000038146973 z:29.570999145507812
- residue HOH has 1 atoms
- atom: O x: -2.4089999198913574 y:8.484999656677246 z:43.20899963378906
- residue HOH has 1 atoms
- atom: O x: -0.14300000667572021 y:-1.7710000276565552 z:48.332000732421875
- residue HOH has 1 atoms
- atom: O x: -16.437999725341797 y:-4.840000152587891 z:18.80699920654297
- residue HOH has 1 atoms
- atom: O x: 16.079999923706055 y:1.4079999923706055 z:30.270999908447266
- residue HOH has 1 atoms
- atom: O x: 21.016000747680664 y:-1.5190000534057617 z:33.81999969482422
- residue HOH has 1 atoms
- atom: O x: -6.730999946594238 y:0.6259999871253967 z:20.711999893188477
- residue HOH has 1 atoms
- atom: O x: 20.124000549316406 y:-7.186999797821045 z:32.66400146484375
- residue HOH has 1 atoms
- atom: O x: -12.125 y:5.327000141143799 z:17.954999923706055
- residue HOH has 1 atoms
- atom: O x: -13.345999717712402 y:10.083999633789062 z:45.89799880981445
- residue HOH has 1 atoms
- atom: O x: -8.428000450134277 y:6.59499979019165 z:30.35300064086914
- residue HOH has 1 atoms
- atom: O x: -18.88599967956543 y:7.940000057220459 z:27.29599952697754
- residue HOH has 1 atoms
- atom: O x: -12.711000442504883 y:-14.880000114440918 z:25.305999755859375
- residue HOH has 1 atoms
- atom: O x: 13.637999534606934 y:-8.12399959564209 z:24.416000366210938
- residue HOH has 1 atoms
- atom: O x: -4.113999843597412 y:-2.135999917984009 z:36.98699951171875
- residue HOH has 1 atoms
- atom: O x: 12.25 y:-8.463000297546387 z:47.82099914550781
- residue HOH has 1 atoms
- atom: O x: 13.711000442504883 y:2.4779999256134033 z:60.03499984741211
- residue HOH has 1 atoms
- atom: O x: 13.440999984741211 y:-24.489999771118164 z:30.077999114990234
- residue HOH has 1 atoms
- atom: O x: -1.406000018119812 y:-12.001999855041504 z:50.17599868774414
- residue HOH has 1 atoms
- atom: O x: -18.986000061035156 y:-14.868000030517578 z:32.553001403808594
- residue HOH has 1 atoms
- atom: O x: -10.734000205993652 y:-14.918000221252441 z:48.27399826049805
- residue HOH has 1 atoms
- atom: O x: 11.635000228881836 y:-24.492000579833984 z:31.9689998626709
- residue HOH has 1 atoms
- atom: O x: 3.058000087738037 y:-2.069999933242798 z:43.28900146484375
- residue HOH has 1 atoms
- atom: O x: 1.7419999837875366 y:-11.512999534606934 z:49.70600128173828
- residue HOH has 1 atoms
- atom: O x: -25.611000061035156 y:13.20199966430664 z:33.939998626708984
- residue HOH has 1 atoms
- atom: O x: -29.035999298095703 y:5.309000015258789 z:24.209999084472656
- residue HOH has 1 atoms
- atom: O x: 0.3100000023841858 y:-5.184999942779541 z:48.196998596191406
- residue HOH has 1 atoms
- atom: O x: -13.279000282287598 y:3.0230000019073486 z:18.819000244140625
- residue HOH has 1 atoms
- atom: O x: -23.634000778198242 y:-16.91900062561035 z:58.840999603271484
- residue HOH has 1 atoms
- atom: O x: -2.9119999408721924 y:-6.1479997634887695 z:54.277000427246094
- residue HOH has 1 atoms
- atom: O x: -1.1610000133514404 y:10.043000221252441 z:47.38800048828125
- residue HOH has 1 atoms
- atom: O x: 29.593000411987305 y:-14.854999542236328 z:40.95399856567383
- residue HOH has 1 atoms
- atom: O x: -12.48900032043457 y:5.578999996185303 z:53.430999755859375
- residue HOH has 1 atoms
- atom: O x: 12.057000160217285 y:2.822999954223633 z:36.19300079345703
- residue HOH has 1 atoms
- atom: O x: 27.393999099731445 y:-13.095000267028809 z:37.10499954223633
- residue HOH has 1 atoms
- atom: O x: -28.520000457763672 y:9.92199993133545 z:38.66999816894531
- residue HOH has 1 atoms
- atom: O x: -5.872000217437744 y:10.038999557495117 z:19.493999481201172
- residue HOH has 1 atoms
- atom: O x: 25.288000106811523 y:-19.02199935913086 z:24.20199966430664
- residue HOH has 1 atoms
- atom: O x: -3.128999948501587 y:-4.6519999504089355 z:39.78499984741211
- residue HOH has 1 atoms
- atom: O x: -15.873000144958496 y:-9.145000457763672 z:20.726999282836914
- residue HOH has 1 atoms
- atom: O x: -5.986999988555908 y:-5.311999797821045 z:55.07600021362305
- residue HOH has 1 atoms
- atom: O x: -22.631999969482422 y:-11.35200023651123 z:32.91999816894531
- residue HOH has 1 atoms
- atom: O x: 15.930000305175781 y:-11.468000411987305 z:48.625
- residue HOH has 1 atoms
- atom: O x: 10.845999717712402 y:10.20199966430664 z:45.08700180053711
- residue HOH has 1 atoms
- atom: O x: -1.7580000162124634 y:-6.790999889373779 z:39.04999923706055
- residue HOH has 1 atoms
- atom: O x: 0.8429999947547913 y:1.375 z:59.32500076293945
- residue HOH has 1 atoms
- atom: O x: -23.67099952697754 y:9.42199993133545 z:51.630001068115234
- residue HOH has 1 atoms
- atom: O x: -7.863999843597412 y:-7.434000015258789 z:35.81700134277344
- residue HOH has 1 atoms
- atom: O x: -14.73900032043457 y:-2.5480000972747803 z:57.404998779296875
- residue HOH has 1 atoms
- atom: O x: -12.61299991607666 y:-3.4010000228881836 z:56.3650016784668
- residue HOH has 1 atoms
- atom: O x: -12.157999992370605 y:14.347999572753906 z:9.017999649047852
- residue HOH has 1 atoms
- atom: O x: -10.178999900817871 y:16.46299934387207 z:7.783999919891357
- residue HOH has 1 atoms
- atom: O x: -26.187999725341797 y:1.3630000352859497 z:32.53200149536133
- residue HOH has 1 atoms
- atom: O x: -19.97100067138672 y:13.097999572753906 z:46.61899948120117
- residue HOH has 1 atoms
- atom: O x: 24.52400016784668 y:-18.415000915527344 z:41.80699920654297
- residue HOH has 1 atoms
- atom: O x: -18.277999877929688 y:-7.002999782562256 z:31.499000549316406
- residue HOH has 1 atoms
- atom: O x: -17.966999053955078 y:-11.64799976348877 z:31.121000289916992
- residue HOH has 1 atoms
- atom: O x: 19.69499969482422 y:-9.303000450134277 z:57.77000045776367
- residue HOH has 1 atoms
- atom: O x: 20.47800064086914 y:-7.195000171661377 z:55.983001708984375
- residue HOH has 1 atoms
- atom: O x: -20.400999069213867 y:-4.622000217437744 z:26.72800064086914
- residue HOH has 1 atoms
- atom: O x: -23.23699951171875 y:-3.7679998874664307 z:26.531999588012695
- residue HOH has 1 atoms
- atom: O x: -21.20199966430664 y:0.3619999885559082 z:21.589000701904297
- residue HOH has 1 atoms
- atom: O x: -1.5870000123977661 y:-0.9639999866485596 z:42.207000732421875
- residue HOH has 1 atoms
- atom: O x: -24.679000854492188 y:-1.2269999980926514 z:32.99100112915039
- residue HOH has 1 atoms
- atom: O x: -27.02199935913086 y:10.708000183105469 z:33.94599914550781
- residue HOH has 1 atoms
- atom: O x: 11.821000099182129 y:-2.0350000858306885 z:62.28200149536133
- residue HOH has 1 atoms
- atom: O x: 13.04800033569336 y:-3.318000078201294 z:60.446998596191406
- residue HOH has 1 atoms
- atom: O x: -16.23699951171875 y:-0.24300000071525574 z:10.319000244140625
- residue HOH has 1 atoms
- atom: O x: -18.378000259399414 y:4.208000183105469 z:55.77299880981445
- residue HOH has 1 atoms
- atom: O x: -17.55299949645996 y:3.2249999046325684 z:51.25199890136719
- residue HOH has 1 atoms
- atom: O x: 9.491000175476074 y:-6.734000205993652 z:43.38999938964844
- residue HOH has 1 atoms
- atom: O x: 23.27199935913086 y:-28.881000518798828 z:39.137001037597656
- residue HOH has 1 atoms
- atom: O x: -13.192999839782715 y:17.964000701904297 z:19.21299934387207
- residue HOH has 1 atoms
- atom: O x: 21.905000686645508 y:-4.89900016784668 z:35.422000885009766
- residue HOH has 1 atoms
- atom: O x: 2.9800000190734863 y:-5.75 z:44.49599838256836
- residue HOH has 1 atoms
- atom: O x: 4.548999786376953 y:-9.392000198364258 z:42.6619987487793
- residue HOH has 1 atoms
- atom: O x: 4.017000198364258 y:-12.059000015258789 z:46.9379997253418
- residue HOH has 1 atoms
- atom: O x: 6.761000156402588 y:-12.234000205993652 z:47.72800064086914
- residue HOH has 1 atoms
- atom: O x: 5.676000118255615 y:-16.034000396728516 z:45.32099914550781
- residue HOH has 1 atoms
- atom: O x: -7.611999988555908 y:-15.508000373840332 z:46.83700180053711
- residue HOH has 1 atoms
- atom: O x: 10.524999618530273 y:-10.456999778747559 z:40.52899932861328
- residue HOH has 1 atoms
- atom: O x: 6.034999847412109 y:-0.2840000092983246 z:30.01300048828125
- residue HOH has 1 atoms
- atom: O x: 7.501999855041504 y:-17.215999603271484 z:20.152000427246094
- residue HOH has 1 atoms
- atom: O x: 7.015999794006348 y:-19.85099983215332 z:17.801000595092773
- residue HOH has 1 atoms
- atom: O x: 10.140999794006348 y:-20.489999771118164 z:16.503999710083008
- residue HOH has 1 atoms
- atom: O x: -28.062999725341797 y:-9.74899959564209 z:39.11600112915039
- residue HOH has 1 atoms
- atom: O x: -13.135000228881836 y:6.835000038146973 z:48.64500045776367
- residue HOH has 1 atoms
- atom: O x: -12.461000442504883 y:13.706000328063965 z:21.788999557495117
- residue HOH has 1 atoms
- atom: O x: -21.52199935913086 y:-11.213000297546387 z:47.9640007019043
- residue HOH has 1 atoms
- atom: O x: -22.802000045776367 y:-13.795999526977539 z:49.27899932861328
- residue HOH has 1 atoms
- atom: O x: 17.39699935913086 y:-18.308000564575195 z:38.902000427246094
- residue HOH has 1 atoms
- atom: O x: 13.23799991607666 y:-16.785999298095703 z:38.619998931884766
- residue HOH has 1 atoms
- atom: O x: 11.210000038146973 y:-8.220000267028809 z:18.395999908447266
- residue HOH has 1 atoms
- atom: O x: -1.9579999446868896 y:10.479000091552734 z:54.09700012207031
- residue HOH has 1 atoms
- atom: O x: 18.85700035095215 y:-12.720999717712402 z:17.263999938964844
Once we have the coordinates of an atom we can compute distances between atoms or angles. We can also align two structures rototranslating the two to minimize their distance. We will not cover this and many other features that are provided by Biopython, such as Pyhlogentic analysis tools, interface towards pathways in KEGG, clustering, etc. If you are interested, you can read about all the features available in the Biopython tutorial.
Exercises¶
Write a python script that retrieves all the information present in SRA regarding PacBio sequencing performed on E.coli strain K12 (query term is “E.coli K12 wgs PacBio”). Print the number of results and for each id report the title, the accession id, the total number of spots and total number of bases sequenced.
Sample output:
Entries found: 11
Results for id: 9966072
WGS of E. coli K12 with PacBio HiFi
- acc="SRR10971019"
- total_spots="95514"
- total_bases="1389500381"
Results for id: 6705337
PacBio RSII sequencing of E. coli K12
- acc="SRR8154667"
- total_spots="163482"
- total_bases="1561717136"
Results for id: 6705336
PacBio RSII sequencing of E. coli K12
- acc="SRR8154668"
- total_spots="163482"
- total_bases="897324802"
...
...
Show/Hide Solution
Write a python function that reads all the entries of a blast alignment file in .xml format (like blast_res_apple.xml and outputs all the HSPs (see example below) having bitscore > B, alignment length > A and minimum percentage of identity > I, where B, A and I are input thresholds. Hint: implement a filtering function: filterHSPs(align, minBitscore = 0, minAlignLen = 0, minPercIdent = 0.1).
Alignments of MDC020656.85
MDC020656.85: 1939-2593
gi|125995253|dbj|AB270792.1|: 201263-201917
Score:820.917 AlignLen:579 Id/Len:0.8812785388127854
MDC020656.85: 1446-1935
gi|125995253|dbj|AB270792.1|: 306490-306017
Score:582.873 AlignLen:428 Id/Len:0.8629032258064516
....
....
that is reporting the HSP with query start-end position, subject start-end position, score, alignment length and number of identities / alignment length.
Show/Hide Solution
Write a python function
retrieve_sequences(search_term, number, outfile)that retrieves the firstnumberof sequences from NCBI’s “nucleotide” database having a search termterm(hint: use term and retmax parameters of Entrez.esearch) and stores them in a fasta fileoutfile(hint: use SeqIO.write). Test your code retrieving the first 5 entries having search term “starch AND Malus Domestica [Organism]”
Show/Hide Solution
Write a python function that aligns the sequences in the file created in exercise 3. (here you can find mine) against the NCBI nr database limiting the hits to the Malus Domestica organism (parameter entrez_query=‘“Malus Domestica” [Organism]’ in qblast)and prints to screen the following info for each hsp:
The title;
Score and e-value;
The number of alignments on the same subject, the number of identities and positives and the alignment length;
The number of mismatches and the list of their positions (hint: you can use the match string and look for ” “).
Show/Hide Solution
Write a python function
getPublicationInfo(title_term,other_term)that retrieves the first 20 pubmed publications having thetitle_termin the title andother_termsomewhere else in the text (hint use: “Title” and “[Other Term]” as esearch parameter term). For each publication print:the title
authors
journal
year of publication (hint: get and split properly the “PubDate” entry)
a link to the pubmed entry (hint: it is the string “https://www.ncbi.nlm.nih.gov/pubmed/” followed by the pubmed id (“eid” entry of the dictionary “ArticleIds”). es: https://www.ncbi.nlm.nih.gov/pubmed/26919684
Hint: to see how to combine search terms test them here: https://www.ncbi.nlm.nih.gov/pubmed/advanced.
Test your code calling getPublicationInfo("apple","drought")
Show/Hide Solution
Write some python code to retrieve the structure of two forms of the aspartate transcarbamoylase (PDB ids: 4FYW and 1D09). If you are interested, read more about the Aspartate Transcarbamoylase here. Write a function that gets the .cif file name and prints:
the number of chains, residues and atoms present in the file;
a histogram of the residues (plotting it with matplotlib) that are not water (encoded as “HOH”);
a link to an online tool to visualize the 3D structure. The link will be “http://www.rcsb.org/pdb/ngl/ngl.do?pdbid=” followed by the PDB id of the protein (e.g. 1d09).
Show/Hide Solution
Material available for midterms and exams¶
The course notes can be used as the slides of the theory and practicals. Documentation on the libraries are here (check the midterm simulation page to download them):
You can download all of them here: archive
Midterm test¶
Before you start¶
Please write one single python script.
IMPORTANT: Add your name and ID (matricola) on top of each .py file!
Problem 1¶
Given a list of positive integers (possibly repeated and unsorted) in the range [1,N], write a function that finds the missing values and returns them as a list. Note that the function should not crash if the list is empty. A warning should also be printed in case the user by mistake had negative numbers in the list.
Ex.
S = [1,9,7, 7, 4, 3, 3, 3]
S1 = list(range(10))
print(find_missing(S))
print(find_missing(S1))
print(find_missing([]))
S2 = [1, -72, 4, -3, -3, 3,10]
M = find_missing(S2)
print(M)
should return:
[2, 5, 6, 8]
[]
Warning: list is empty. Returning None
None
Warning -72 is <0. Ignoring it.
Warning -3 is <0. Ignoring it.
Warning -3 is <0. Ignoring it.
[2, 5, 6, 7, 8, 9]
Problem 2¶
The .agp file data_reduced.agp available here is a compact representation on how a set of assembled contigs made it into the scaffolds. The first few lines are reported below:
ScaffID s_start s_end type contig c_start c_end c_strand
scaffold_1 1 120953 W scf7180000021845 1 120953 -
scaffold_1 120954 121453 N 500 scaffold yes na
scaffold_1 121454 1026498 W scf7180000018491_2 1 905045 +
scaffold_1 1026499 1026998 N 500 scaffold yes na
In particular, the first row states that scaffold_1 from position 1 to 120953 has been built using the sequence of the contig scf7180000021845 from position 1 to 120953 in reverse strand (-) which means that the sequence has to be reverse-complemented. The second row states that in scaffold_1 positions 120954 to 121453 are a gap made of 500 N (note the 4th column is N rather W that stands for whole genome sequence).
Let’s suppose to have three sequences \(s1="ATAATA"\), \(s2="AAA"\) and \(s3="CCAAA"\), the following agp-formatted entries can be used to create a sequence my_scaff:
my_scaff 1 6 W s1 1 6 +
my_scaff 7 9 N 3 scaffold yes na
my_scaff 10 12 W s2 1 3 -
my_scaff 13 15 N 3 scaffold yes na
my_scaff 16 17 W s3 1 2 +
this would represent a fasta-formatted sequence:
>my_scaff
ATAATANNNTTTNNNCC
where basically the sequence is composed by s1 as it is, followed by three N, followed by the reverse complement of s2, three N and the first two characters of s3.
The file small_seq.fasta stores sequence information in .fasta format. A mock entry is the following:
>Chr01
AGGCCTAGGTCTTCCAGAGTCGCTTTTTCCAGCTCCAGACCGATCTCTTCAG
AGGCCAATCGCCAGTTTACCACATACACCCAGACCGATCTCTTCAG
where the first line is the identifier of the read and starts with a “>”. The sequence follows the line with the identifier and can be on multiple lines.
Implement the following python functions:
computeStats(filename, show_output = True): gets thefilenameof a .agp file as explained above, stores its content in a suitable data structure of your choice (hint: pandas might help here). Ifshow_outputisFalsethe function only returns the data structure. Otherwise, it counts (and prints) the total number of entries, the total number of scaffolds (hint: you can use DataFrame[column].unique()), total number of contigs (and their total size note that you might have to convert the c_start and c_end column to int with .astype(int)) and total number of gaps (and their total size). The function should also produce a box plot of the number of contigs per scaffold.
Note: The function should return the data structure containing all the data.
Calling:
fn = "data_reduced.agp"
scaffDF = computeStats(fn)
should give:
The file contains 7898 entries
... 1958 scaffolds
... 4928 contigs (tot. size: 873,456,804 bases)
... and 2970 gaps (tot. size: 1,485,000 bases)
printSequence(scaffInfo, scafID, sequenceFile): gets thescaffInfodata structure created by computeStats, a scaffold identifierscaffInfoand the filename of a fasta formatted filesequenceFileand ifscafIDis present inscaffInfoit prints a fasta-formatted string reporting the sequence of the scaffold built as discussed above.
Hint: you can use biophtyon to read the fasta file.
Calling:
scaffDF = computeStats("small.agp", show_output = False)
printSequence(scaffDF,"my_scaff","small_seq.fasta")
print("")
printSequence(scaffDF,"my_scaff2","small_seq.fasta")
print("")
printSequence(scaffDF,"my_other_scaff","small_seq.fasta")
print("")
printSequence(scaffDF,"scaffold3","small_seq.fasta")
should give:
>my_scaff
ATAATANNNTTTNNNCC
>my_scaff2
TATTTTTATATGTATGTAATNNNNNNNNNNTTTATATATA
Warning: scaffold my_other_scaff not present
>scaffold3
NNNNNNNNNNNNNNNNNNNNCCCCGGAGGTACCTCCGGGGCCCCGGAGGT
Available material for exams¶
The course notes can be used as the slides of the theory and practicals. Documentation on the libraries are here (check the midterm simulation page to download them):
You can download all of them here: archive
Download the data¶
Create a “qcbsciprolab-MT1-NAME-SURNAME-ID” folder on the desktop. Download the following data to the folder that you just created.
The big .agp file: data_reduced.agp, the small .agp file small.agp and the fasta file with the sequences: small_seq.fasta.
A possible solution¶
[1]:
"""Solution to exercise1"""
def find_missing(S):
if len(S) > 0:
m = max(S)
vals = [ 0 for i in range(m)]
for x in S:
if x < 0:
print("Warning {} is <0. Ignoring it.".format(x))
else:
vals[x-1] += 1
return [x+1 for x in range(m) if vals[x] == 0]
else:
print("Warning: list is empty. Returning None")
if __name__ == "__main__":
S = [1,9,7, 7, 4, 3, 3, 3]
S1 = list(range(10))
print(find_missing(S))
print(find_missing(S1))
print(find_missing([]))
S2 = [1, -72, 4, -3, -3, 3,10]
M = find_missing(S2)
print(M)
[2, 5, 6, 8]
[]
Warning: list is empty. Returning None
None
Warning -72 is <0. Ignoring it.
Warning -3 is <0. Ignoring it.
Warning -3 is <0. Ignoring it.
[2, 5, 6, 7, 8, 9]
[4]:
"""Solution exercise2"""
import matplotlib.pyplot as plt
import pandas as pd
import numpy as np
from Bio import SeqIO
def computeStats(filename, show_output = True):
sInfo = pd.read_csv(filename, sep="\t", header = 0)
if show_output:
print("The file contains {} entries".format(sInfo.shape[0]))
scaffolds = sInfo["ScaffID"].unique()
print("... {} scaffolds".format(scaffolds.shape[0]))
contigs = sInfo[sInfo["type"] == "W"]
c_sizes = contigs["c_end"].astype(int) - contigs["c_start"].astype(int)
print("... {} contigs (tot. size: {:,} bases)".format(contigs.shape[0],
np.sum(c_sizes)))
gaps = sInfo[sInfo["type"] == "N"]
print("... and {} gaps (tot. size: {:,} bases)".format(gaps.shape[0],
np.sum(gaps["contig"].astype(int))))
cont_by_scaff = contigs.groupby("ScaffID").aggregate(pd.DataFrame.count)['contig']
#print(cont_by_scaff)
cont_by_scaff.plot(kind = 'box')
plt.ylabel("# contigs per scaffold")
plt.show()
return sInfo
def printSequence(scaffInfo, scafID, sequenceFile):
scaff = scaffInfo[scaffInfo["ScaffID"] == scafID]
hdr = ">" + scafID
seq = ""
if len(scaff) > 0:
seqDict = SeqIO.to_dict(SeqIO.parse(sequenceFile, "fasta"))
for entry in range(len(scaff)):
entry_data = scaff.iloc[entry]
if entry_data["type"] == "N":
seq += "N" * int(entry_data["contig"])
elif entry_data["type"] == "W":
ctg = entry_data["contig"]
if not ctg in seqDict:
print("Warning: contig {} not present. Exiting...".format(ctg))
break
else:
c_s = int(entry_data["c_start"])
c_e = int(entry_data["c_end"])
c_strand = entry_data["c_strand"]
t_s = seqDict[ctg][c_s -1: c_e ]
if c_strand == "-":
t_s = t_s.reverse_complement()
seq += t_s.seq
if len(seq) > 0:
print(hdr)
print(seq)
else:
print("Warning: scaffold {} not present".format(scafID))
if __name__ == "__main__":
fn = "MTsim/data_reduced.agp"
scaffDF = computeStats(fn)
scaffDF = computeStats("MTsim/small.agp", show_output = False)
printSequence(scaffDF,"my_scaff","MTsim/small_seq.fasta")
print("")
printSequence(scaffDF,"my_scaff2","MTsim/small_seq.fasta")
print("")
printSequence(scaffDF,"my_other_scaff","MTsim/small_seq.fasta")
print("")
printSequence(scaffDF,"scaffold3","MTsim/small_seq.fasta")
The file contains 7898 entries
... 1958 scaffolds
... 4928 contigs (tot. size: 873,456,804 bases)
... and 2970 gaps (tot. size: 1,485,000 bases)
>my_scaff
ATAATANNNTTTNNNCC
>my_scaff2
TATTTTTATATGTATGTAATNNNNNNNNNNTTTATATATA
Warning: scaffold my_other_scaff not present
>scaffold3
NNNNNNNNNNNNNNNNNNNNCCCCGGAGGTACCTCCGGGGCCCCGGAGGT