Here is another thing I have seen not working in 2-2 loop.
If all 4 nucleotides in a 2-2 loop is all A’s. Yellow seem to be too weak to hold the loop open in it self.
I haven’t seen it work so far.
Also I tried fill a 2-2 loop with blue in an otherwise great design, Mat – Things to test, from round 1 scoring 94%.
Here is the result
More testing of cause needs to be done. But so far having blue in a loop almost always seem to be a bad idea.
I would like a strategy for 2-2 loops that says:
Give -1 if 4 A’s inside
Give -1 if 4 U’s inside