Here is a strategy for our little bot, as I can see he is not sure what to do when around adjacent multiloops.
I would like a strategy for adjacent multiloops (4 basepairs) that says:
At least 2 of the basepairs should be GC-pairs.
Give -1 if there is only 1 GC-pair
Give -2 if there is 0 GC-pairs.
This is probably not as strict as it should be, but I don’t want to restrain him too much, as I have seen bots succede with less than 4 GC-pairs and Quasispecies made me aware that nature don’t always have 4 GC-pairs in a adjacent multiloop with 8 nt’s long in his post Use RNase P Multiloop Sequences to Create “Cross” Designs. Go see the bacterial sequence.