my $str = $Genome; my $match = "ATCGACTACGACTCGACT"; my $len = length($match); for my $i ( 0 .. length($str) - $len ) { my $s = substr $str, $i, $len; my $x = $s ^ $match; $x =~ tr/\0//d; # equal characters xor to \0 print "'$s' at offset $i matched\t".length($x)."\n" unless length($x) > 5; }