The base pair similarity score calculated in the previous sections might not be powerful enough to distinguish true positive conserved structure element pairs from false-positive structure element pairs due to the finite lengths of stems and exclusion of loop sequences in the alignment. Therefore, a dissimilarity score is also used to confirm whether a pair is significant. The dissimilarity for two given structure elements s i (x) and s j (y) in sequences Seq x and Seq y is defined as: