my @allowed = qw[ AA AG GC GT CA CG TT TC ];
my $allowed = join "|", @allowed;
my $regex   = qr/ N+ | (?: (?=$allowed) . )*  . /x;

my $data = "CTGTCAGCNNNCCGGTTTTCAAGNNGAGCACACACCAAAAATGCACCAAAGCTTNACATCCATACAAA";

print "$_\n" for $data =~ m/$regex/g;