#!/usr/bin/perl -slw
use strict;

my $s1 = 'AAAAA';
my $s2 = 'ATCAA';
my $s3 = 'AAAAA';

print "$s1:$s2 hd:", hd( $s1, $s2 ); # will give value 2
print "$s1:$s3 hd:", hd( $s1, $s3 ); # will give value 0

sub hd{ length( $_[ 0 ] ) - ( ( $_[ 0 ] ^ $_[ 1 ] ) =~ tr[\0][\0] ) }
__END__
P:\test>500235
AAAAA:ATCAA hd:2
AAAAA:AAAAA hd:0