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Potential interactions in RNA molecules. (A) Possible base-pairing of nucleotides. (B) cis-only RRI (intramolecular base-pairing) within a single RNA molecule. (C) Trans RRI (intermolecular base-pairing) between two identical RNA molecules. (D) Situation in concatenation-based prediction tool, where both RRI types are involved. Inter- and intramolecular base pairs are indicated by vertical pipe symbols and arches, respectively (adapted from [25]).
