Figure 3

Sequence/structure model for Yfr1 RNA based on a structural alignment created from a ClustalW multiple sequence alignment and an RNAlishapes consensus secondary structure from 31 cyanobacteria. Sequence is given in IUPAC-notation (R: A or G; Y: C or U; M: A or C; S: G or C; B: G, U or C; V: G, C or A; D: G, T or A). Base pair colors indicate the number of different base pairs which occur in the different sequences at this position (red = 1, yellow = 2, green = 3 and blue = 4) and their shading resembles the frequency of base pairing, i.e. the number of sequences where this base pair is not present. The unpaired sequence is given as a sequence logo prepared using WebLogo [23].