From DPAT3 penalize designs that have any of the following list of stacks in R96 Same State NG 2 since they are only predicted by Vienna 2 to exist in the MFE structure of poor performing designs only ( designs scoring bellow 80 only). Here is an explanation from DPAT3’s documentation of the way the stacks are written)
’ If you wanted to look at a stack in the 2nd State with 3 pairs in it and the nucleotide pairs are 22 paired with 50, 23 paired with 49, and 24 paired with 48 then it would be written, “2ndState-22:50,23:49,24:48" ’
And here are the 2060 unique stacks predicted only in designs scoring under 80 in R96 Same State NG 2
(i tried posting this with all the stacks but it did not seam to like 2000 lines of text so here is a link to the source text file)
https://dl.dropboxusercontent.com/u/87351147/R96SameStateNG2_SNuPP_Pickstacks_range0-80.TXT