Consensus sequences and structures for the four RNA motifs identified. (A) rpsB motif, (B) rpsL motif, (C) ffh motif, (D) SAM-V riboswitch. See Additional files 4, 5, 6, 7 for alignments of all representatives. Calculations for conservation of nucleotide identity are described in the Methods section. Proposed base pairs with more than 5% non-canonical Watson-Crick pairings or missing nucleotides are not classified as covarying.