Hairpins with tetraloops and pentaloops mostly seem to be fine without boosting. (Strings 4 nts and longer) However hairpins with loops bigger than a pentaloop, some sort of boost seems to be necessary. (Strings 4 nts and longer) It appears a GC-pair at the end of a string is not enough to hold a loop of 6 nucleotides in spot, if they are all A’s. Often 1 or 2 of the nucleotides i the loop ring end up with a blue color dark enough to suggest they paired up somewhere - unwanted. I still don’t know what sort of boosting is correct here, just that some seem to be needed.
As I’m not sure which kind of boosting that is required, so I want a strategy that opens up for it in this special boosting, but not too much. I just want this situation penalized less, as I can see a potential need for boost here.
As we already have all A’s loop strategy and the boosting in bigger loops is what I’m after, I would like a strategy that says:
Give +1⁄2 if there is up to 2 different colors boosting, in loops 6 nts and longer (on strings 4 nt’s and longer.) I don’t know about position yet, so this strategy will need an addition.
This is related to the post I wrote earlier about Boost according to lenght of hairpin.