1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
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#
# This matrix is in Blast format.
#
# We expect all the characters required by Gap4 to be in this list, but the
# order is not important.
#
A C G T U R Y M W S K D H V B - *
A 4 -8 -8 -8 -8 2 -3 2 2 -3 -3 1 1 1 -4 2 -10
C -8 4 -8 -8 -8 -3 2 2 -3 2 -3 -4 1 1 1 2 -10
G -8 -8 4 -8 -8 2 -3 -3 -3 2 2 1 -4 1 1 2 -10
T -8 -8 -8 4 4 -3 2 -3 2 -3 2 1 1 -4 1 2 -10
U -8 -8 -8 4 4 -3 2 -3 2 -3 2 1 1 -4 1 2 -10
R 2 -3 2 -3 -3 2 -4 0 1 1 1 1 0 1 0 0 0
Y -3 2 -3 2 2 -4 2 0 1 1 1 0 1 0 1 0 0
M 2 2 -3 -3 -3 0 0 2 1 1 -3 0 1 1 0 0 0
W 2 -3 -3 2 2 1 1 1 2 -3 1 1 1 0 0 0 0
S -3 2 2 -3 -3 1 1 1 -3 2 1 0 0 1 1 0 0
K -3 -3 2 2 2 1 1 -3 1 1 2 1 0 0 1 0 0
D 1 -4 1 1 1 1 0 0 1 0 1 1 0 0 0 0 0
H 1 1 -4 1 1 0 1 1 1 0 0 0 1 0 0 0 0
V 1 1 1 -4 -4 1 0 1 0 1 0 0 0 1 0 0 0
B -4 1 1 1 1 0 1 0 0 1 1 0 0 0 1 0 0
- 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 3 1
* -10 -10 -10 -10 -10 0 0 0 0 0 0 0 0 0 0 1 4
|
