Fig. 2.

Illustration of the input conformations of the dinucleotides for aligning RNA Sequence 1 and Sequence 2. a The illustration of RNA Sequence 1 with a stem-loop structure motif. The stem consists of consecutive stacked base pairs, while the loop represents unpaired segments enclosed by the base pairs. b The illustration of RNA Sequence 2 with a stem-loop structure motif. c The corresponding contact matrix for the AU dinucleotide. d The corresponding contact matrix for the GU dinucleotide. e The corresponding contact matrix for the AA dinucleotide. f The corresponding contact matrix for the GG dinucleotide