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

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

for (my $i=0;$i<600000;$i++){
        #choose one of the two methods
        #hd($s1,$s2); # real    0m1.401s
        hd2($s1,$s2); # real    0m0.405s
}

sub hd{
     my ($k,$l) = @_;
     my $len = length ($k);
     my $num_mismatch = 0;

     for (my $i=0; $i<$len; $i++)
     {
      ++$num_mismatch if substr($k, $i, 1) ne substr($l, $i, 1);
     }
     return $num_mismatch;
}

sub hd2 {
    return ($_[0] ^ $_[1]) =~ tr/\001-\255//;
}