my $sequence = "sequence.fa";
my @starts;

open (FASTA, "$sequence") || die "Cannot open $sequence: $!.\n";
chomp (my @seq = <FASTA>);
close FASTA;
shift @seq;
$sequence = join ('', @seq);
@seq = split ('', $sequence);

	for (my $i=0; $i<=$#seq-5; $i++){  ## -5 könnte man weglassen
		# start codon: ATG
		# stopp codon: TAG, TAA, TGA
		# multiple of 3 between start and stop
		if ($seq[$i] eq 'A' && $seq[$i+1] eq 'T' && $seq[$i+2] eq 'G'){
			push (@starts, $i);
			for (my $j=$i+3; $j<=$#seq-2; $j=$j+3){
				if (($seq[$j] eq 'T' && $seq[$j+1] eq 'A' && $seq[$j+2] eq 'A') ||
				($seq[$j] eq 'T' && $seq[$j+1] eq 'G' && $seq[$j+2] eq 'A') ||
				($seq[$j] eq 'T' && $seq[$j+1] eq 'A' && $seq[$j+2] eq 'G')){
					print "ORF: $i-", ($j+2), "\n";
					last;  ##lasts the j loop
				}
			}
		}
	}