Evidence for secondary structure in cluster 3. (a) Multiple alignment of a subset (for clarity) of repeats in cluster 3. Numbers 1 to 7 and 7 to 1 indicate the residues involved in stem base-pairing, some compensatory mutations in the stem are highlighted with circles. Note G:U base pairing at position 5 in Xanthomonas oryzae and relaxed conservation of loop residues typical of RNA secondary structure in which the structure is functional rather than the sequence. (b) Sequence logo for all repeats in cluster 3. (c) Predicted secondary structure of Syntrophus acidotrophicus repeat using RNAfold. Stem positions are numbered in accordance with the alignment.