use strict; use warnings; my $seq="IIIIIMMMMMMMMMMMOOOOOOOOOOOOOOOOMMMMMMMMMMMMMIIIIIMMMMMMMMMOOOOO +OOOOOOOOOMMMMMMMMMMMMMIIIMMMMMMMMMMMOOOOOOOOOOOOOOOMMMMMMMMMMMIIIIIIM +MMMMMMMMMMMMOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMIIIMMMMMMMMMOOOOOOOOOOOOOOO +OOOOOOOOOOOOMMMMMMMIIIIMMMMMMMMMMMOOOOOOOOOOOOOOOOOOOOOMMMMMMMIIIMMMM +MMMMMOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMIIIMMMMMMMMMMMOOOOOOOOOOOOOOOO +OMMMMMMMMI"; while ($seq=~/(M+)/g) { my $l = pos($seq); print $l-length($&)+1," to ",$l,$/; }