This strategy is the natural sibling of the strategy Green paired with red and Blue paired with yellow.
Here the strategy comes: For each red nucleotide not paired up with green (alone – placed in end loops, internal loops, multiloops, bulges and hookarea), give -1.
Ignore red nucleotides paired up with blue in GU-pairs, as there are other market strategies taking care of this. Or give -2 pr. each.
I have hold this strategy back for a long time, as there seemed to be other strategies taking care of this. But essential what this three strategies will do together, is actively making the loops all A ́s. This is why I would like to have added Mat’s name in the title of the two other strategies, in honor of him through all the time insisting that the end loops should be all A’s. A thing I took a much longer time of adopting when it came to boosting with red nucleotides in end loops.
These strategies is an all A’s strategy together, which there already is a strategy for, but they are so in a split up manner, that may be usefull if we are later to tweak one of the strategies a little.