Please correct me if my assumptions are wrong: Basically, what you want is to find the start and end position of subsequences of same characters that aren't "-".

A straightforward way to do that is to inspect each character in sequence and compare it to the previous one. But that would be slow and annoying. It's easier to use a regex: 

#!/usr/bin/perl -w
use strict;
$_ = "-----MMMMM------IIIII----MMM---OOOO---I---MMMM-----";
while (/(\w)(\1*)/g) {
  print "$1:".(1+pos()-length "$1$2")."-".pos."\n";
}

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In reply to Re: group things? by Joost
in thread group things? by Anonymous Monk

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