The trick is to reverse the string being searched:

use strict;
use warnings;

my @strs = qw(GNNTCGANNTT GAATCGNNNTT GANNCGNNNNN);

for my $str (@strs) {
    my $rstr = reverse $str;
    my @starts;

    push @starts, $-[1] while $rstr =~ /(N+)/g;
    
    if (1 == @starts) {
        print "$str: One N found at @starts\n";
    } elsif (@starts) {
        print "$str: Ns found at @starts\n";
    } else {
        print "No N found in $str\n";
    }
}
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Prints:

GNNTCGANNTT: Ns found at 2 8
GAATCGNNNTT: One N found at 2
GANNCGNNNNN: Ns found at 0 7
[download]

Note too that the special array @- is used to get the index of the first match for each run of Ns.