my $s1 = "ACTGGA";
    my $s2 = "AGTG-A";

   # Note the string can be longer than this.
   # But they are always of the same length.

##</code><code>##

#String Position 0-based
# First col = Base in S1
# Second col = Base in S2
# Third col = Position in S1 where they differ
C G 1
G - 4