substr() is pretty fast, but I guess this will be faster. I think :-)

return map {tr/\0/\0/ / $len} $ref_seq ^ $test_seq;
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Update: If you are using the return value in scalar context, the above will yield 1, of course. Sorry about that.

Try this:

my($score) = map {tr/\0// / $len} $ref_seq ^ $test_seq;
return $score;
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... or even (might be faster with many short strings):

return +(map{tr/\0// / $len} $ref_seq ^ $test_seq)[0];
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The Sidhekin
print "Just another Perl ${\(trickster and hacker)},"