[Strategy market] End basepair in neck/hook

I have found that C tends to be most prevalent at a specific spot in the neck area in the lab data. Like the marked nucleotide in the picture.

As Mat added when I discussed my forum post with him in chat: Eli - I do like my C there on most designs.

I won’t severly penalize the GC-pairs that turn opposite the most prevalent pattern, as they occour in good designs in 20-25% of the time. Mat added: Eli - yep - I have two 97% with “GC-pairs that turn opposite the most prevalent pattern”

So I will not rule them totally out as it would be a shame, just push the algorithm in the way that has highest success rate.

For theory behind see this post. Energy in neck aligned with energy spots in the design

I would like a strategy that says:

Give + 2 if marked base is a C (it’s basepair partner should be G)

Give +1 if marked base is a G (it’s basepair partner should be C)

Give 0 if end basepair is GU and AU basepairs. I know that a few time GU and AU- closing pairs will fly, but so far they are very rare.