or download this
$seq="IIIIIMMMMMMMMMMMOOOOOOOOOOOOOOOOMMMMMMMMMMMMMIIIIIMMMMMMMMMOOOOO
+OOOOOOOOOMMMMMMMMMMMMMIIIMMMMMMMMMMMOOOOOOOOOOOOOOOMMMMMMMMMMMIIIIIIM
+MMMMMMMMMMMMOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMIIIMMMMMMMMMOOOOOOOOOOOOOOO
+OOOOOOOOOOOOMMMMMMMIIIIMMMMMMMMMMMOOOOOOOOOOOOOOOOOOOOOMMMMMMMIIIMMMM
+MMMMMOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMIIIMMMMMMMMMMMOOOOOOOOOOOOOOOO
+OMMMMMMMMI";
$i=0;
$_= $seq;
s/([^M]*)(M*)/{ my $j=$i+length($1); $i=$j+length($2); $j==$i ? "" :
+"pos $j-$i\n" }/ge;
print $seq, "\n", $_, "\n";