perldoc -f index will help with the where. One standard technique for counting instances that you could apply would be to create a $var in last your else clause and increment it each time you find a sequence that satisfies your intent. Since you're working with hashes, other approaches may work better.

Super Searching for nodes with include the words "count" and "hash" may lead you to numerous answers.

And please, most of us are NOT bioinformatics scholars -- I have no more than a rough idea from context or what an "oligo" or a "negative stand" is-- and many of us have rather draconian limits on how much time we can spend helping... which means triage of nodes that are "TL,DR" (Too long, didn't read). Your 134 lines is a tad longer than the recommendation (in PerlMonks FAQ particularly what you'll find in Posting on PerlMonks ) that you boil your code down to a self-contained, concise (20-30 Lns or less) example that illustrates your issue.