plot_score = (number of white cells in the upper triangle of the pairwise probabilities plot) / (total number of cells in the upper triangle of the pairwise probabilities plot)

cap_score = ((number of GC pairs that are at the end of a stack) + 0.5 * (number of GC pairs that are 1 away from the end of a stack)) / (3 * total number of stacks)

gc_penalty = 2 if 80% or more of the design's pairs are GC pairs, 0 otherwise.

A design's total score is: (2 + plot_score + cap_score - gc_penalty) * 25

The +2 and *25 are just to make it come out to between 0 and 100.

cap_score = ((number of GC pairs that are at the end of a stack) + 0.5 * (number of GC pairs that are 1 away from the end of a stack)) / (3 * total number of stacks)

gc_penalty = 2 if 80% or more of the design's pairs are GC pairs, 0 otherwise.

A design's total score is: (2 + plot_score + cap_score - gc_penalty) * 25

The +2 and *25 are just to make it come out to between 0 and 100.