Identify each terminal mismatch in the structure, and award points as follows:
External Loops and Multiloops:
1 point for AA
0 points for all others
Internal Loops other than 1-1, 2-1, or 2-2:
2 points for GA or AA
1 point for UU
0 points for all others
Hairpins:
2 points for AA or GA when G is 5’ of A
1 point for UU
0 points for all others
Score = 100 * (Evaluated Score / Maximum Possible Score)