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

my $file = shift @ARGV;

die "no dna file specified!\n" if !defined $file;

open my $fh, '<', $file or die "$file: $!\n";
my $data = do { local $/; <$fh> };
close $fh;

$data =~ s/n([nN\n]+)n/^$1^/gm;

print $data, "\n";

__END__