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

my $substring = 'ATG';

while (<>) {
    chomp;
    next if $. < 2; # Skip first line
    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.pl sequence.fa
Found ATG at 16
Found ATG at 50
Found ATG at 133
Found ATG at 232
Found ATG at 252
Found ATG at 287
Found ATG at 305
Found ATG at 363
Found ATG at 394
Found ATG at 489
Found ATG at 575
Found ATG at 651
Found ATG at 689
Found ATG at 724
Found ATG at 854
Found ATG at 859
Found ATG at 954
Found ATG at 1014
Found ATG at 1044
Found ATG at 1051
Found ATG at 1145
Found ATG at 1228
Found ATG at 1249
Found ATG at 1272