A weight is assigned to a significant pair, which is a combination of the free energy, covariation and dissimilarity. The overall weight s of a significant structure element pair [s i (x), s j (y)] in sequences Seq x and Seq y is a combination of the free energy weights w[s i (x)] and w[s j (y)], base pair similarity score sim[s i (x), s j (y)] and dissimilarity dissim[s i (x), s j (y)]: s½s i ðxÞ, s j ðyÞ ¼ Â sim½s i ðxÞ, s j ðyÞ À Â fw½s i ðxÞ þ w½s j ðyÞg À Â dissim½s i ðxÞ, s j ðyÞ Only structure element pairs with positive score s are allowed in the following dynamic programming algorithm. Here, and are set to 0.5 and is set to 1.