where dissim 1 is the difference in the stem lengths and dissim 2 is the difference in the number of loop lengths. As an example, consider the pseudoknot pair p 1 (x) and p 1 (y) in sequences Seq x and Seq y , respectively, with stems S 1 , S 2 and loops L 1 , L 2 , L3. The pseudoknot pair has dissimilarity of 6. [[[[[[.) )))))) [.[[[[[[[.) ))))). .