Figure 2.

An example of the different stages of the alignment process within CRWAlign-1. a) a single unaligned RNA sequence; b) three aligned sequences in the template alignment at the bacillales node and the average scores for each of the six blocks; c) query sequence has a unique match for block 4 that is aligned against the template; d) matches for blocks 2 and 4 are identified; e) no matches for block 5; f) seven sequences in the template alignment at the bacilli node (three red - bacillales, four blue - other bacilli), and the average block scores; g) block 5 has a unique match (see Methods section for details).