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

my @starts = ();

while (<>) {
    chomp;
    next if $. < 2; # Skip first line
    my @seq = split '', $_;
    for (0..$#seq-5){
	if ($seq[$_] eq 'A' && $seq[$_+1] eq 'T' && $seq[$_+2] eq 'G') {
	    push (@starts, $_);
	    for (my $j=$_+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: $_-", ($j+2), "\n";
		    last;  ##lasts the j loop
		}
	    }
	}
    }
} continue {
    close ARGV if eof; # reset $.
}

__END__

$ perl bio_test.pl sequence.fa
ORF: 16-75
ORF: 50-136
ORF: 133-357
ORF: 232-357
ORF: 252-290
ORF: 287-334
ORF: 305-334
ORF: 363-380
ORF: 394-450
ORF: 489-623
ORF: 575-724
ORF: 651-797
ORF: 689-724
ORF: 724-936
ORF: 854-859
ORF: 859-936
ORF: 954-959
ORF: 1051-1200
ORF: 1145-1255
ORF: 1228-1275
ORF: 1249-1275