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.
Give a small penalty to designs that has 3 UUU’s in a row. Increase penalty if there are more of these repeats.
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.
Similar if longer repeats than UU’s are close together - penalize also and hard.
Long and multiple repeat U’s being problematic