#!/usr/bin/perl

use strict;

my $count = 0;
while (<DATA>) {
    while ( /(aaggt)/g ) {
        $count++;
        print "$1 - Count: $count\n";
        print "Found at position : " . pos(), "\n";
        pos() += 100;
    }
}

__DATA__
aatgatgataaggtaaggtatgatgatgatgatgatagtagannnnnnnnnatgcatga'/atgca.atgactagca/atgactagcaaggtaaggtaaggtaaggtaaggtatgatgatgannnn./atgatgactagactgacaaggtaaggtaaggtatgatgatgatcgatgacgat