Using index would look something like the following:

sub using_index {
   our $seq; *seq = \$_[0];
   my @groups;

   my $pos = -1;
   my $start = -1;

   for (;;) {
      my $new_pos = index($seq, 'M', $pos+1);

      if ($new_pos < 0) {
         if (defined($start)) {
            push(@groups, [ $start, $pos ]);
         }
         last;
      }

      if ($start < 0) {
         $start = $new_pos;
      }
      elsif ($new_pos - $pos > 1) {
         push(@groups, [ $start, $pos ]);
         $start = $new_pos;
      }

      $pos = $new_pos;
   }

   return @groups;
}
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It would be simpler if there was a function that returned the next character which isn't 'M'.

As you can guess, it's much slower than the regexp approach. The regexp approach is 170% faster than (i.e. 2.7 times the speed of) the index method on the input you provided.

Benchmark code:

Benchmark results: