use strict;
use warnings;

while (my $line = <DATA>) {
chomp $line;
# The below regex tells perl to look for
# any of A,T,G,C followed by a string of 
# one or more Ns, followed by A,T,G,C.
my @info = split /[ATGC]N+[ATGC]/, $line;
print join(", ", @info), "\n";
}

__DATA__
NNNAAAATATGACAAAGGGGTTNNNNNNNNNNNNNNGATGTCTGGTCAATAGGAT
CGCAGCCATTAACATCTCAACAAGCCAAAAATTCCTTCTCAGAAATTCGGNNN
AAAATATGACAAAGGGGTTNNNNNNNNNNNNNNGATGTCTGGTCAATAGGAT