[Market strategy] Max number of GC-pairs next to each other in strings 4 NT's long

Strategy Market Strategy Market - Single State
1

I have noticed that the good designs don’t have more than max 2 GC-pairs in a row, in a string 4 nucleotides long. I would like a strategy specificly for strings 4 nucleotides long that says:

Max. 2 GC-pairs next to each other in a string 4 NT’s long. (their direction compared to each other, does not matter in this strategy)

If 3 GC-pairs are connected with each other, give -1

If 4 GC-pairs are connected with each other, give -2

Neck area is excluded from this strategy. The neckarea behaves differently. 4 GC-pairs in row have been seen working.

(It won’t matter if there is 3 GC-pairs in the 4 Nt’s string all in all, as long as there is an other base pair than GC between one of the GC-pairs and the other two GC-pairs.)

2

Dear Eli,

Your strategy has been added to our implementation queue with task id 116. You can check the schedule of the implementation here.

Thanks for sharing your idea!

EteRNA team