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)