After reviewing my older strategy Numbers of yellow nucleotides pr. lengt of string, I realise there is situations it does not take into account. It don’t neccesarily penalize yellow from being in line after each other. Only for having too many or too few pr. string
This is not either the same as the related strategy Blue line as a long blue line can be opposite both yellow and red.
I have made a strategy that penalize two sameturning double AU-pairs. But that only sort of penalizes having two yellow in line, if more than two of such blocks present.
Our energy model allows for up to 4 yellow nucleotides in line after each other. Maybe even more, in longer strings. Like this shot taken from lab puzzle the star.
Therefore there is no strategy taking care of too long lines of yellow. So this should be banned as it will not allow the string to bind to it selves. The two strands will not pair up correct, or in other words the two lines of nucleotides wil not connect well enough to each other to pair up.
So I would like a strategy that says:
For each extra yellow nucleotide more than two in line after each other, penalize with -1
Neckarea will be excepted from this strategy for lines of 3 yellow nucleotides in line. For more than three yellow in line, give -1 pr each yellow nucleotide extra.