I'd guess that the xor method is probably quicker but you could benchmark these as well:

    # Method 1
    
    my @a1 = split //, $ref_seq; 
    my @a2 = split //, $test_seq; 

    $score += ($a1[$_] eq $a2[$_]) for 0 .. $#a1;


    # Method 2, Destructive

    $score += (chop $ref_seq eq chop $test_seq) while $ref_seq;
[download]

--
John.