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    • org.biojava.bio.alignment.PAM80 Maven / Gradle / Ivy

    There is a newer version: 1.9.7
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    #
# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
#
# PAM 80 substitution matrix, scale = ln(2)/2 = 0.346574
#
# Expected score = -2.55, Entropy = 1.44 bits
#
# Lowest score = -11, Highest score = 13
#
    A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V   B   Z   X   *
A   4  -4  -1  -1  -4  -2  -1   0  -4  -2  -4  -4  -3  -5   0   1   1  -8  -5   0  -1  -1  -1 -11
R  -4   7  -2  -5  -5   0  -4  -6   0  -3  -5   2  -2  -6  -2  -1  -3   0  -7  -5  -3  -1  -3 -11
N  -1  -2   5   3  -6  -1   0  -1   2  -3  -5   0  -4  -5  -3   1   0  -5  -3  -4   4   0  -1 -11
D  -1  -5   3   6  -9   0   4  -1  -1  -4  -7  -2  -6  -9  -4  -1  -2 -10  -7  -5   5   2  -3 -11
C  -4  -5  -6  -9   9  -9  -9  -6  -5  -4  -9  -9  -8  -8  -5  -1  -4 -10  -2  -3  -7  -9  -5 -11
Q  -2   0  -1   0  -9   7   2  -4   2  -4  -3  -1  -2  -8  -1  -3  -3  -8  -7  -4   0   5  -2 -11
E  -1  -4   0   4  -9   2   6  -2  -2  -3  -6  -2  -4  -9  -3  -2  -3 -11  -6  -4   2   5  -2 -11
G   0  -6  -1  -1  -6  -4  -2   6  -5  -6  -7  -4  -5  -6  -3   0  -2 -10  -8  -3  -1  -2  -3 -11
H  -4   0   2  -1  -5   2  -2  -5   8  -5  -4  -3  -5  -3  -2  -3  -4  -4  -1  -4   0   1  -2 -11
I  -2  -3  -3  -4  -4  -4  -3  -6  -5   7   1  -4   1   0  -5  -4  -1  -8  -3   3  -4  -4  -2 -11
L  -4  -5  -5  -7  -9  -3  -6  -7  -4   1   6  -5   2   0  -4  -5  -4  -3  -4   0  -6  -4  -3 -11
K  -4   2   0  -2  -9  -1  -2  -4  -3  -4  -5   6   0  -9  -4  -2  -1  -7  -6  -5  -1  -1  -3 -11
M  -3  -2  -4  -6  -8  -2  -4  -5  -5   1   2   0   9  -2  -5  -3  -2  -7  -6   1  -5  -3  -2 -11
F  -5  -6  -5  -9  -8  -8  -9  -6  -3   0   0  -9  -2   8  -7  -4  -5  -2   4  -4  -7  -8  -5 -11
P   0  -2  -3  -4  -5  -1  -3  -3  -2  -5  -4  -4  -5  -7   7   0  -2  -9  -8  -3  -3  -2  -2 -11
S   1  -1   1  -1  -1  -3  -2   0  -3  -4  -5  -2  -3  -4   0   4   2  -3  -4  -3   0  -2  -1 -11
T   1  -3   0  -2  -4  -3  -3  -2  -4  -1  -4  -1  -2  -5  -2   2   5  -8  -4  -1  -1  -3  -1 -11
W  -8   0  -5 -10 -10  -8 -11 -10  -4  -8  -3  -7  -7  -2  -9  -3  -8  13  -2 -10  -7  -9  -7 -11
Y  -5  -7  -3  -7  -2  -7  -6  -8  -1  -3  -4  -6  -6   4  -8  -4  -4  -2   9  -5  -4  -6  -4 -11
V   0  -5  -4  -5  -3  -4  -4  -3  -4   3   0  -5   1  -4  -3  -3  -1 -10  -5   6  -4  -4  -2 -11
B  -1  -3   4   5  -7   0   2  -1   0  -4  -6  -1  -5  -7  -3   0  -1  -7  -4  -4   5   2  -2 -11
Z  -1  -1   0   2  -9   5   5  -2   1  -4  -4  -1  -3  -8  -2  -2  -3  -9  -6  -4   2   5  -2 -11
X  -1  -3  -1  -3  -5  -2  -2  -3  -2  -2  -3  -3  -2  -5  -2  -1  -1  -7  -4  -2  -2  -2  -3 -11
* -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11   1




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