use strict;
use warnings;

my $one= "AGCTGATCGAGCTAGTACCCTAGCTC";
my $two= "AGCTGATCGAGCTAGTACCCTATCTC";
my $diff = $one ^ $two;

$diff =~ tr/\0/x/c;

my $start = -1;

while (-1 < ($start = index $diff, 'x', ++$start)) {
    print "Difference at $start\n";
}