Stack nt’s of each non-A type (U,G,C) should be strictly alternating from 3’ to 5’ to 3’ etc. as you follow down the stack. Penalize each repeated violation in an exponential manner if they are in adjacent base pairs, linear penalty otherwise.
So, GG, UUU, CCCC in adjacent base pairs = 4, 9, 16 point penalty while G-G, U-U-U, C-C-C-C with some intervening base pairs between get 2,3,4 point penalty respectively.