[Strategy Market] [Switch] Penalize repeat repeat repeats bases

While I’m a big fan of repeats in riboswitches, too much can be too much.


Penalize when there are more than two set of repeat bases in a row.

  • No to penalize: AAUU or CCAA
  • To penalize: AAUUAA or GGCCAA

The more of this, the higher the penalty. And the longer the individual repeats, the worse.

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