Using a look-ahead with pos can save having to do the sums.

knoppix@Microknoppix:~$ perl -E '
> $s1 = q{ACTGGACGTATGCA};
> $s2 = q{AGTG-ACGC-CGCA};
> $m  = $s1 ^ $s2;
> push @pos, pos( $m ) while $m =~ m{(?=([^\x00]))}g;
> $m  =~ tr{[\x01-\xfe]}{\xff};
> $c1 = $s1 & $m;
> @p1 = $c1 =~ m{([^\x00])}g;
> $c2 = $s2 & $m;
> @p2 = $c2 =~ m{([^\x00])}g;
> printf qq{%-2s%-2s%6d\n}, $p1[ $_ ], $p2[ $_ ], $pos[ $_ ]
>    for 0 .. $#pos;'
C G      1
G -      4
T C      8
A -      9
T C     10
knoppix@Microknoppix:~$
[download]

I hope this is of interest.