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

my $substring = 'TAA';

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";
	my $offset = $found + 1;
	$found = index($_, $substring, $offset);
    }
} continue {
    close ARGV if eof; # reset $.
}

__END__

$ perl bio_2.pl sequence.fa
Found TAA at 29
Found TAA at 73
Found TAA at 106
Found TAA at 201
Found TAA at 248
Found TAA at 332
Found TAA at 378
Found TAA at 385
Found TAA at 448
Found TAA at 480
Found TAA at 512
Found TAA at 722
Found TAA at 743
Found TAA at 857
Found TAA at 864
Found TAA at 870
Found TAA at 934
Found TAA at 974
Found TAA at 1008
Found TAA at 1019
Found TAA at 1265