"a solution to the bigger problem rather than a solution to a small part of it."

Dear Monk, you are exactly correct. the reason for this work is to do with a biological context. In the context of DNA there are different types of repeat families (ya we do have families of repeats) such as tandem repeats are one type, where the repeats are in tandem eg) AATAAT,(AAT is repeated in tandem) next is palindromic repeat where a palindrome is repeated eg) AATTAAATCGACTAATTAA (AATTAA, a palindrome is repeated with some spacer in between)and so on..these repeats regions associates to various diseases and they also act as marker or as landmark to hunt down particular regions.(there are certain regions, that are flanked by certain repeat families)

So if i have the informations such as the positions and the frequencies of the a particular repeat family, one could hunt down certain regions which are flanked by these repeats and with the number of frequencies of the certain repeats one could estimate how likely is this DNA (i.e. the string in our scripting context) mutated

I hope i am clear this time, if not plz let me know

system information RAM: 4 GB, Processor: Intel® Core™2 Quad CPU Q8300 @ 2.50GHz × 4, 64 bit machine, perl-v5.14.1 built for x86_64-linux, OS - Fedora 15