>perl -wMstrict -le "my $seq = 'xxxTATAATGyyyTatAtAtzzz'; my $box = qr{ (?i) TATA [TA] [TA] [TAG] }xms; ;; my @TATAs; while ($seq =~ m{ ($box) }xmsg) { push @TATAs, [ $1, $-[1], ]; } ;; print qq{matched '$_->[0]' at pos $_->[1]} for @TATAs; " matched 'TATAATG' at pos 3 matched 'TatAtAt' at pos 13