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

my %hash;
my $substring = 'ATG';
my @tags = ('TAG', 'TAA', 'TGA');

while (<>) {
    chomp;
    next if $. < 2; # Skip first line
    my $found = index($_, $substring);
    while ($found != -1) {
	foreach my $tag (@tags) {
	    my $position = index($_, $tag, $found + 2);
	    $hash{$position} = $tag if ($position != -1);
	}
	my $offset = $found + 1;
	$found = index($_, $substring, $offset);
    }
} continue {
    close ARGV if eof; # reset $.
}

foreach my $position (sort {$a <=> $b} keys %hash) {
    print "Position: $position String: $hash{$position}\n";
}

__END__

$ perl bio.pl sequence.fa
Position: 29 String: TAA
Position: 48 String: TGA
Position: 73 String: TAA
Position: 134 String: TGA
Position: 201 String: TAA
Position: 221 String: TGA
Position: 248 String: TAA
Position: 288 String: TGA
Position: 309 String: TAG
Position: 324 String: TGA
Position: 332 String: TAA
Position: 378 String: TAA
Position: 381 String: TAG
Position: 395 String: TGA
Position: 408 String: TGA
Position: 448 String: TAA
Position: 505 String: TGA
Position: 512 String: TAA
Position: 621 String: TGA
Position: 700 String: TGA
Position: 722 String: TAA
Position: 743 String: TAA
Position: 752 String: TGA
Position: 857 String: TAA
Position: 864 String: TAA
Position: 957 String: TAG
Position: 974 String: TAA
Position: 1002 String: TGA
Position: 1019 String: TAA
Position: 1052 String: TGA
Position: 1198 String: TGA
Position: 1210 String: TAG
Position: 1253 String: TGA
Position: 1265 String: TAA