use warnings;
use strict;
use 5.010; # for say()

my $a='AAATGCCTT';
my $b='AAAAGCGTC';
my $c='AAAGGCGTC';

my $mask = chr(0) x length $a;
for ($b, $c) {
    $mask |= $a ^ $_;
}

# just to illustrate what the mask looks like:
use Data::Dumper;
$Data::Dumper::Useqq = 1;


# count number of 0-bytes
my $matches =()= $mask =~ /\0/g;
say "Matches:     ", $matches;
say "Non-matches: ", length($a) - $matches;