As Marshall has said, it is difficult to divine your intent. Perhaps you want to find the character offsets where you have matching letters in each string?

knoppix@Microknoppix:~$ perl -E '
$seq1 = q{AAAAACCCGGGTTTTTAAA};
$seq2 = q{AAAAACGGGTTTCCCAGAGA};
$same = $seq1 ^ $seq2;
push @posn, pos( $same ) while $same =~ m{(?=\x00)}g;
say for @posn;'
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knoppix@Microknoppix:~$
[download]

Please explain again what you are trying to achieve.