Fig. 8.

Annotated secondary structures of query motif (a) and two candidate motifs for the seven-base sarcin/ricin motif search reported in Table 2. Yellow letters indicate the bases of the query motif used for the geometric search and the corresponding bases of the candidate motifs. The bold red box shows the constrained basepair. Candidate motifs obtained by the search include a bona fide composite sarcin/ricin motif (b) and a redundant motif (c) in which base A2703 in the query motif is mismatched to base C478 in the candidate motif. The higher-scoring version of this candidate, in which A477 is matched with A2703, had discrepancy 0.2161