For two interrupted stems, the base pair similarity score is calculated by deleting bulges and internal loops and scoring stems as consecutive base pairs. Base pair similarity scores for regular and interrupted stems are also calculated if the difference in number of base pairs is less than 5. For example, a stem with one bulge might be a conserved match with a regular stem. A stem s i (x) in sequence Seq x and a stem s j (y) in sequence Seq y are a significant pair if the score sim[s i (x), s j (y)] has an estimated P-value less than .