Ok, with some minor corrections it works just fine!
Thanks!

$first= "AAAAXXXXAAAAXXXXXXXXXXXAAAA"; 
$second="AXXXAXXAAXXXXXAAAAXXXXXAAAA";

$matches=0;
for $i (0..length($first)-1) 
{
  if (substr($first,$i,1) eq substr($second,$i,1)) { $matches++; }
}
print $matches."\n";
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