I twice caught out bot in a situation like this:
It’s a clear violation of the energy model and we players are not allowed to do so for good reasons. As I understand this, it is deemed to fail in synthesis. Even if it went through, I think this pattern will still mean trouble.
Two of my strategies normally will try to penalized similar situations. The strategy Red line goes after longer red sequences and Green line goes after longer green sequences. Here they didn’t succede repressing this unwanted pattern, as they only goes for their own half the pattern and a small penalty won’t be enough in this case. I thought this situation was banned by default, which was why I didn’t went directly at it before.
I would like to have a top strategy for our bot saying, that 4 sameturning GC-pairs is restricted area. There should be no weigths in this strategy, it should be one of those rare always rules. Be it a line of 4, 5 or whatever number of sameturning GC-pairs in a row.
Here is the data on design 9.
Secondary structure
…(((((((…(((((.((((…)))).((((…)))).)))))…(((((.((((…)))).((((…)))).)))))…)))))))…
RNA sequence
AAAAACAAUAUGAACUACCACAUGAAAACAUGAGAUGAAAACAUCAGGUAGAAGAAUGAGCUCAAAAGAGCAGGGGAAAACCCCACAUUCAACAUAUUGAAAAAAAAAAAAAAAAAAAA
Here is the link to my bot results: