#!usr/bin/perl
use strict;
use warnings;
use Data::Dumper;

my $substring = 'ATG';

while (<>) {
    chomp;
    next if $. < 2; # Skip first line
    my @seq = split ' ', $_;
    # print Dumper \@seq; # Remove hashtag and see how the input looks
    for (@seq) {
	my $found = index($_, $substring);
	while ($found != -1) { # check for multiple occurrences in the same string
	    print "Found $substring at $found\n"; # Do your calculations here
	    my $offset = $found + 1; # keep track of offset in your counter as you do on your primary script and should have it
	    $found = index($_, $substring, $offset);
	}
    }
} continue {
    close ARGV if eof; # reset $.
}

__END__

$ perl bio_test.pl sequence.fa
Found 'ATG' at 16
Found 'ATG' at 50
Found 'ATG' at 62
Found 'ATG' at 19
Found 'ATG' at 39
Found 'ATG' at 3
Found 'ATG' at 21
Found 'ATG' at 8
Found 'ATG' at 39
Found 'ATG' at 63
Found 'ATG' at 7
Found 'ATG' at 12
Found 'ATG' at 50
Found 'ATG' at 14
Found 'ATG' at 2
Found 'ATG' at 7
Found 'ATG' at 31
Found 'ATG' at 20
Found 'ATG' at 50
Found 'ATG' at 57
Found 'ATG' at 9
Found 'ATG' at 21
Found 'ATG' at 42
Found 'ATG' at 65