Strategy
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Two UU’s in a row are usually no problem. But if they are close like 1 and 2 bases apart, they can be trouble. Start penalizing mildly.
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Give a small penalty to designs that has 3 UUU’s in a row. Increase penalty if there are more of these repeats.
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Penalize if there 4 UUUU’s or more in a design and increase penalty the longer the U repeat is. Penalize exponentially if there are more long U repeats.
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Similar if longer repeats than UU’s are close together - penalize also and hard.
Background article
Long and multiple repeat U’s being problematic