>perl -wMstrict -le "my $dna = 'xxpecbcbccrlxxxPeeeerlxxpLxxxPeRLxx'; ;; my $perl = qr{ [Pp] [^x]* [Ll] }xms; ;; my @matches = $dna =~ m{ $perl }xmsg; printf qq{'$_' } for @matches; " 'pecbcbccrl' 'Peeeerl' 'pL' 'PeRL'