#
# 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




