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. 2012 Mar;18(3):402–411. doi: 10.1261/rna.031385.111

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FIGURE 2. — Selected guide alignments from each of the sequenced Pyrobaculum. sR202 (panel A), sR203 (B), sR206 (C), sR207 (D), and sR210 (E) shown. Target RNA sequence shown in top sequence row of each panel. Predicted Watson-Crick and G-U base-pairing between target and sRNA guide regions shown (red). Stem-pairing of the lower stem (aqua, nested square brackets), intermediate stem (dark blue, nested arrows), and upper apical stem (purple, nested parentheses) are indicated. Lower stem/guide base-pairing is uncertain for sR202 (panel A) in region where target sequence (red) overlaps lower stem (aqua). Base-pairing of stems and kink-turn (orange) indicated with bracket notation (panel A, bottom row). Uncertain terminal base pair of intermediate stem (panels D,E) is indicated with lighter shading. RNA sequences are shown in uppercase for sequences recovered in RNA sequencing and in lowercase when sequence is inferred by conservation of aligned features in genome sequence.