#
# Any line starting with '#' is a comment.
#
# Needs a row for the alphabet.  First column is a repeat of the
# alphabet and assumed to be identical in order to the first alphabet row.
#
# Last row and column *must* be a non-alphabet character to represent
# any input sequence character that is outside of the alphabet.
#
A   T   G   C   S   W   R   Y   K   M   B   V   H   D   N   U   *
A   5  -4  -4  -4  -4   1   1  -4  -4   1  -4  -1  -1  -1  -2  -4  -5
T  -4   5  -4  -4  -4   1  -4   1   1  -4  -1  -4  -1  -1  -2   5  -5
G  -4  -4   5  -4   1  -4   1  -4   1  -4  -1  -1  -4  -1  -2  -4  -5
C  -4  -4  -4   5   1  -4  -4   1  -4   1  -1  -1  -1  -4  -2  -4  -5
S  -4  -4   1   1  -1  -4  -2  -2  -2  -2  -1  -1  -3  -3  -1  -4  -5
W   1   1  -4  -4  -4  -1  -2  -2  -2  -2  -3  -3  -1  -1  -1   1  -5
R   1  -4   1  -4  -2  -2  -1  -4  -2  -2  -3  -1  -3  -1  -1  -4  -5
Y  -4   1  -4   1  -2  -2  -4  -1  -2  -2  -1  -3  -1  -3  -1   1  -5
K  -4   1   1  -4  -2  -2  -2  -2  -1  -4  -1  -3  -3  -1  -1   1  -5
M   1  -4  -4   1  -2  -2  -2  -2  -4  -1  -3  -1  -1  -3  -1  -4  -5
B  -4  -1  -1  -1  -1  -3  -3  -1  -1  -3  -1  -2  -2  -2  -1  -1  -5
V  -1  -4  -1  -1  -1  -3  -1  -3  -3  -1  -2  -1  -2  -2  -1  -4  -5
H  -1  -1  -4  -1  -3  -1  -3  -1  -3  -1  -2  -2  -1  -2  -1  -1  -5
D  -1  -1  -1  -4  -3  -1  -1  -3  -1  -3  -2  -2  -2  -1  -1  -1  -5
N  -2  -2  -2  -2  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -2  -5
U  -4   5  -4  -4  -4   1  -4   1   1  -4  -1  -4  -1  -1  -2   5  -5
*  -5  -5  -5  -5  -5  -5  -5  -5  -5  -5  -5  -5  -5  -5  -5  -5  -5