Please see How do I post a question effectively? Once you have a discrete test case that you have run through Devel::NYTProf, and as well run test cases with Benchmark for versions both including and excluding study, we can help you understand your results.
in reply to Re^2: counting the number of 16384 pattern matches in a large DNA sequence
in thread counting the number of 16384 pattern matches in a large DNA sequence
You may also want to check out index, since you the regex engine is more power than you really need.
#11929 First ask yourself `How would I do this without a computer?' Then have the computer do it the same way.