1
2
3
4
5
6
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8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
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#
# This matrix was created by Todd Lowe 12/10/92
#
# Uses ambiguous nucleotide codes, probabilities rounded to
# nearest integer
#
# Lowest score = -4, Highest score = 5
#
A T G C S W R Y K M B V H D N
A 5 -4 -4 -4 -4 1 1 -4 -4 1 -4 -1 -1 -1 -2
T -4 5 -4 -4 -4 1 -4 1 1 -4 -1 -4 -1 -1 -2
G -4 -4 5 -4 1 -4 1 -4 1 -4 -1 -1 -4 -1 -2
C -4 -4 -4 5 1 -4 -4 1 -4 1 -1 -1 -1 -4 -2
S -4 -4 1 1 -1 -4 -2 -2 -2 -2 -1 -1 -3 -3 -1
W 1 1 -4 -4 -4 -1 -2 -2 -2 -2 -3 -3 -1 -1 -1
R 1 -4 1 -4 -2 -2 -1 -4 -2 -2 -3 -1 -3 -1 -1
Y -4 1 -4 1 -2 -2 -4 -1 -2 -2 -1 -3 -1 -3 -1
K -4 1 1 -4 -2 -2 -2 -2 -1 -4 -1 -3 -3 -1 -1
M 1 -4 -4 1 -2 -2 -2 -2 -4 -1 -3 -1 -1 -3 -1
B -4 -1 -1 -1 -1 -3 -3 -1 -1 -3 -1 -2 -2 -2 -1
V -1 -4 -1 -1 -1 -3 -1 -3 -3 -1 -2 -1 -2 -2 -1
H -1 -1 -4 -1 -3 -1 -3 -1 -3 -1 -2 -2 -1 -2 -1
D -1 -1 -1 -4 -3 -1 -1 -3 -1 -3 -2 -2 -2 -1 -1
N -2 -2 -2 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
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