Perhaps this'll be of use?

#!/usr/bin/perl -w
use strict;
use warnings;

while (my $seq=<DATA>) {
        print $seq, ':';
        my $cnt=0;
        my $prev=undef;
        my @arr = split /|/,$seq;
        while (my $c = shift @arr) {
                ++ $cnt;
                if ($c eq 'N') {
                        $prev = $cnt;
                }
                else {
                        print( $prev, ' ') if $prev;
                        $prev = undef;
                }
        }
        print "\n";
}
__DATA__
GNNTCGANNTT
GAATCGNNNTT
GANNCGNNNNN
[download]

On my machine, this gives me:

roboticus@swill ~/PerlMonks
$ ./RevGap.pl
GNNTCGANNTT
:3 9
GAATCGNNNTT
:9
GANNCGNNNNN
:4 11
[download]

--roboticus