[strategy market] pairs and stacks

-2 for every consecutive GU pair (so three consecutive GU pairs would be -4 points)

-2 for every consecutive GC pair, starting with the fourth consecutive GC

+1 for each instance in a stack where there is a UA pair between two GC pairs (so, a stack of 5 pairs that runs GC, AU, GC, AU, GC would be worth two points)

+1 for each stack that puts two alternating UA pairs between two GC pairs (for example, a stack that runs GC, AU, UA, CG)

+1 for each GC pair that ends a stack

  • 2 for each GU pair that ends a stack

+1 for every unpaired A or G where the loop is bordered by GC pairs

-1 for every unpaired C

-1 point for every 5% of the design that is GU pairs, starting at 5% (so 16% would be -3 points)

Dear robu-san,

Your strategy has been added to our implementation queue with task id 82. You can check the schedule of the implementation here.

Thanks for sharing your idea!

EteRNA team