Thanks for the link, but from what I can tell, I have already independently coded everything found on that page....

Based on the other replies to my OP, it looks like the better thing to do for me would be to find a way to compare the Hemming distance of $string to subsets of the overall sequence, each of the same length as string.

Whether or not I can implement that in the context of the program I've already devised, without a major overhaul is the main question. So, in the meantime, I'll be reading up and playing around withit.

Thanks to all who answered though,
Matt