I would like a strategy for placement of GU-pairs that say:
Give +1 if all the first GU-pairs, have the blue nucleotide to the left side
Give +1 if the last GU-pair, the red nucleotide turn to the left side.
Give +1 if there is only one GU-pair and blue nucleotide is to the left.
Give +1 if the there is only one GU-pair and the blue nucleotide sits to the right (the first blue is also the last blue)
For theory see my post on GU-challenges and The watch theory.