I had a strategy on the way, when something Dicey said changed my mind: 4 G in a row and 4 C’s in a row seem to cause problems when near loops.
Notice the two red nucleotides beside each other. I think two red nucleotides in line, when in connection with a multi loop weakens the puzzle. Brourd said the C wants to pair up else where. I think this will be the case when this pattern shows up in connections to hairpin loops and internal loops too.
There is already a strategy banning 3 red in line
But it does not something about positioning of that line. I say that a line red (sometimes only even two nucleotides long) if in connection with loop, will worsen things.
So far I had been planning to ban that specific problem pattern I mention here. Check the bottom of this section of the post. Here I say that 2 G’s near loop is trouble. Trouble is that the pattern is sometimes allowed. But Dicey’s input made me realise how this could be done.
I would like a strategy that says:
Give -0,5 if two G’s are in line in connection with loop
Give -1 if 3 G’s are in line in connection with loop
Give -2 if 4 G’s are in line in conection with loop
This will be no matter loop type, multiloop, hairpin loop or internal loop.