Based on how I understand your question, this is how I would do it.

#!/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.atg
+actagca/atgactagcaaggtaaggtaaggtaaggtaaggtatgatgatgannnn./atgatgactag
+actgacaaggtaaggtaaggtatgatgatgatcgatgacgat
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