AU pairs:

+1 point in the interior of stacks

+0.5 points at end of stacks

GU pairs:

+1 point at end of stacks, when loop is 5’ of G

-1 point at end of stacks, when loop is 3’ of G

-1 point when inside of stack and adjacent to a GU pair

+0.5 points otherwise

GC pairs:

+2 points at end of stacks

+1 point in interior of stacks

Unpaired Bases:

+0.5 point for A

+0.5 point for G adjacent to stack

+0 points for G not adjacent to stack

+0 points for U

-1 point for C

Bonuses:

-2 points for each AU pair in excess of 60% AU content

-4 points for each GC pair in excess of 75% GC content

+2 points for every GNRA tetraloop

-0.25 points for each base, i, paired to another base, j, where i can pair to j+1 or j-1

Score = 100 * (total points) / (total number bases)