I've looked at the Needleman-Wunsch information and I can probably get what I want by using high gap, gap extention, and mismatch penalties. The problem I see is that I can't specify a lower limit for the length of the match string found by Needleman-Wunsch.

In reply to Re^2: Search for identical substrings by bioMan
in thread Search for identical substrings by bioMan

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