while ($sequence=<FILE>){
    
    foreach($sequence =~ /$substring/g) { 
   #print "malakas\n";
            $count += () = /$substring/g;
[download]

Hmmm, copy-and-paste is too hard? I did not write a double loop. And your result just doesn't make much sense. In fact, it doesn't make any sense.

Considering that spoon-feeding isn't working for you, I don't know what else to do.