Thanks greatly for the start on this... All *possible* combinations are important - certainly over 20K sequences they'll likely all appear at least a couple of times. Overlapping instances are important - so "AGCTGT" would need to be scored; 
         AGCT    GCTG   CTGT    TGTA   etc.
AGCTGT     1      1       1      0

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and so on...

In reply to Re^3: Find number of short words in long word by sedm1000
in thread Find number of short words in long word by sedm1000

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