[Market strategy] Red line near multiloop, Fisker + Dicey

Strategy Market Strategy Market - Single State
1

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.

2

This definitely is a Fisker strategy with a hint, at best, from me. The penalties seem solid to me.

I wonder if there is a possibility to crunch the numbers once without, and on a re-run with a penalty for multiple Guanine lines as closing stacks/quads to loops. I would propose a -1 penalty too for the case of two lines of 2 reds in connection to loops. -2 penalty for 3x 2G-lines in connection to a loop. However, seeing how multiloops occur only in more complex molecules, feel free not to attempt this re-run if you believe the harder-to-fold (bigger and more sophisticated) puzzles this would apply to, would lead to scientifically unsound conclusions (due to designs not reds).