If you want a regex-only solution:

#!/usr/bin/perl

use strict;
use warnings;

my @strings = qw(
  GNNTCGANNTT
  GAATCGNNNTT
  GANNCGNNNNN
);

my @found;

for my $string( @strings ){
  my $revstring = reverse $string;
    
  $revstring =~ m<
                    (?:
                        .*?
                        (?{ [ $^R ? @{ $^R } : () , pos ] })
                        NN+
                    )+
                    (?{ @found = @{ $^R }; })
                 >x;

  print "String: $string     Positions: ", join( ', ', @found ), "\n";
}
[download]

Prints:

String: GNNTCGANNTT     Positions: 2, 8
String: GAATCGNNNTT     Positions: 2
String: GANNCGNNNNN     Positions: 0, 7
[download]

$,=42;for(34,0,-3,9,-11,11,-17,7,-5){$*.=pack'c'=>$,+=$_}for(reverse s
+plit//=>$*
){$%++?$ %%2?push@C,$_,$":push@c,$_,$":(push@C,$_,$")&&push@c,$"}$C[$#
+C]=$/;($#C
>$#c)?($ c=\@C)&&($ C=\@c):($ c=\@c)&&($C=\@C);$%=$|;for(@$c){print$_^
+$$C[$%++]}
[download]