As an example, consider the S15 mRNA pseudoknot that binds to specific proteins in the autoregulation mechanism of ribosomal protein S15 synthesis (Philippe et al., 1995) . For the reference sequence S15 and 10 support sequences from the corresponding RFAM family, DotKnot-PW returns pairwise predictions ordered by the combined free energy and similarity score. The top two pairwise predictions with the highest scores are shown in Figure 3 .