Okay. Thanks for taking the time to clarify things for me.

It strikes me that with the possibilities of motifs as short as 4bp, combined with fuzziness; there must literally billions of places where repeats occur within a few dozens of bps. Without there being some additional information about either what to look for, or where to look, or both; this is just a brute force problem without the possibility for clever or interesting solutions.

I still have a copy of the human genome I downloaded, which I indexed the wazoo out of when trying out my novel indexer, and I still have the indexes (33gb of highly compressed dbs); but without some criteria upon which to start looking, the best I could do is produce another huge file of possibles that would serve no good purpose.