For two given stems s i (x) and s j (y) with fixed lengths in sequences Seq x and Seq y , respectively, the base pair similarity score sim[s i (x), s j (y)] is calculated using an ungapped local structure alignment of the base pairs with the RIBOSUM85-60 matrix. As an example, consider the following optimal ungapped local structure alignment of the two stems with base pair similarity score of sim[s 1 (x), s 2 (y)] ¼ 22.04 using the RIBOSUM85-60 matrix.