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I built a script to detect microsatellites in a FASTA file. However, there are thousands of possibilities. So, my question is:

what are the markers of a "good" or "useful" microsatellite? - How many base pairs, how many repetitions?

And, are there any other heuristics that can be run to further detect usefulness of the microsatellite?

thanks.

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Try running software like Censor. If checks in the reference repeat databases and detects microsatellites. So, you can most probably be sure of the microsatellites generated. Moreover, the microsatellites have their information present in the GIRI database. So, you can get more information, if you find the microsatellite in your sequences. Hope this helps.

~Rama.

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