my @allowed = qw[ AA AG GC GT CA CG TT TC NN ];
my %allowed = map { $_ => 1 } @allowed;

my $buf;
while ( get next input character as $c ) {
    if ($allowed{ substr($buf,-1).$c }) {
        $buf .= $c;
    } else {
        print "$buf\n";
        $buf = $c;
    }
}
print "$buf\n"; # don't forget last one