Strategy for turn on labs (Same State)
For when MS2 sequence is in between the FMN sequences
Give bonus if there are 11 single bases or less at the shortest side between the aptamer on either side and the MS2 sequence. Add more bonus if the shortest side is like 5-6 bases long. Penalize for single bases stretches longer than 11 bases on either side and if shorter than 6 bases away.
For MS2 on the outside of the FMN sequences
Reverse the strategy. So best bonus is given to distance 11 bases apart and decreasing towards 6 bases. (Same state 1) Penalize for single base stretches that are shorter or longer than 6-11 bases.
http://eterna.cmu.edu/game/browse/5736176/?filter1=Id&filter1_arg2=5742236&filter1_arg1=5742ā¦
Strategy for turnoff labs (Exclusion)
Give +3 for MS2 being next to FMN and decrease the bonus by one for each base the MS2 moves away from the one FMN it is closest to.
Perspective
A popular strategy to achieve a shortening of the space between MS2 and FMN is to abbreviate the stretch of single bases by making them form a stem with themselves. But before I make a strategy for it, I wish to know if the trick can be done by simply cutting the bases out (We should get those data with the NG labs where we could vary distance between MS2 and FMN) or if the Static stem play an active and positive role in itself.
Background
https://docs.google.com/document/d/1uvcHNX0CTY6dWQnqu9pisSgxG54QuqbMx60TsoV53XQ/edit#heading=h.2ec4vā¦https://getsatisfaction.com/eternagame/topics/switch-scores-for-eterna-switch-puzzles?page3#reply_15ā¦