This strategy is similar to Aldo’s Repetition, but it only focuses on triplets, ignores sequences that are unlikely to be problematic, and also penalizes sequences that can form small bulges and loops.
Look at every group of three consecutive nucleotides in the sequence. For each group of three nucleotides, search for its complement (include GU pairing).
Penalize the sequence in the following ways:
1 point for completely complementary sequences with 0 or 1 GU pairs
0.5 points for completely complementary sequences with 2 or more GU pairs
0.5 points for sequences that can create a 11 loop
0.25 points for partially complementary sequences formed by bulging 1 nucleotide out of the complementary strand
Ignore complementarity between bases that are supposed to be paired in the target structure.
Ignore complementary regions that are separated by fewer than 3 nt.
Ignore sequences that would form 11 loops and bulges with more than 1 GU pair
Ex. Sequence Examined: AAA

1 penalty point for complements with 0 or 1 GU pairs: UUU

0.5 penalty points for complements with 2 or 3 GU pairs: none possible

0.5 penalty points for partially complementary sequences that can form a 11 loop with 0 or 1 GU pairs: UXU (X = A/C/G)

0.25 penalty points for partially complementary sequences that can form a 11 loop with 0 or 1 GU pairs: UUXU, UXUU (X = A/C/G)
Ex. Sequence Examined: GGG

1 penalty point for complements with 0 or 1 GU pairs: CCC, UCC, CUC, CCU

0.5 penalty points for complements with 2 or 3 GU pairs: UUC, UCU, CUU, UUU

0.5 penalty points for partially complementary sequences that form a 11 loop with 0 or 1 GU pairs: CRC, CRU, URC (R = A/G)

0.25 penalty points for partially complementary sequences that form a 1nt bulge with 0 or 1 GU pairs: CRCC, CCRC, URCC, UCRC, CRUC, CURC, CRCU, CCRU (R = A/G)