I have noticed that other colored nucleotides in triloops than yellow, generally jam things up. Actually it was one glance at lab design a player posted in lab to get an oppinion on it, that made me realize what I already knew. I checked through lab to conform my suspision.
I would like a strategy that says:
No red nucleotides in triloops, give -1 pr each nucleotide other than yellow. Red almost seem to give trouble, if placed in triloop.
No green nucleotide in triloops. Sometime one is allowed without mispairing. But they are rare. So until we figure out the pattern for this, give -1 pr. each green nucleotide.
No blue nucleotides in triloops. Sometimes one is allowed without mispairing. Give -0,75 for the first blue nucleotide and -1 pr. extra.
Exception:
If two different colors (others than yellow) end up in the triloop together, this for unknown reason sometimes work better, than single nucleotides other than yellow is alone in the triloop. So give -1 if two nucleotides other than yellow ends up in a triloop together. For three nucleotides other than yellow, give -2.