FIGURE 3.
RNAalifold base-pairing probability matrix of the CRE and VR region, based on 96 isolates. The upper half of the matrix shows all base pair probabilities <10−6. The lower half shows the base pair probabilities of the MFE structure. (Oval) The interaction of the internal bulge of 5BSL3.2 with basal region of 5BSL2 (Fig. 7, No. 15), described previously in Diviney et al. (2008) and Tuplin et al. (2012). Dotplot and structure of CRE, VR, and X-tail region (19 isolates) without constraints are available in the Supplemental Material (Supplemental Fig. 3A,B).
