TIMTOWTDI:

$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";
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