# all five kinds of bases need to be included
# do not forget to set gap-open/extension penalty with -O/-E
    A       C       G       T       N
A   91      -114    -31     -123    0
C   -114    100     -125    -31     0
G   -31     -125    100     -114    0
T   -123    -31     -144    91      0
N   0       0       0       0       0