my $x = "EKFCNSVVDLYSNLSKPFLDIVLYIFKLTSAIGAQGPA----SMMAYLVV"; my $y = "ERFCRQLSSMASKLI-------ISPFTLVYYTYQCFQSTGWPVSIFGYFI"; my $z = $x^$y; my $score = ($z =~ tr/\0//); return $score/length($x)