Yes, the direct matches are not a problem. I am glad you could confirm the code. For the mismatch code I mean: I have a hash value which is a DNA sequence, example:
TGATTGAA

If my % threshold was .75 for example, and if I was searching for TGAT, I would like for the program to tell me that there able for the program to find the identical match at position 1, AND identify the second match at position 5 as an "acceptable mismatch".

With respect to your suggestion of regexp...Is it possible to type those in on the command line? Currently I use @ARGV[0] as my $search query, typically something like "ATC".
Thanks! ER

In reply to Re^2: Pattern searching allowing for mis-matches... by MaroonBalloon
in thread Pattern searching allowing for mis-matches... by MaroonBalloon

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