Secondary structure patterns of IRs. (A) Dot-plot similarity analysis of IRX-69.83, which contains smaller, less homologous IRs in each arm. Internal IRs detected by IRF and percent identity are indicated (Supplemental data S1 and S2). Below each dot-plot are the RepeatMasker and TRF (Benson 1999) tracks from the UCSC Genome Browser, where the IR and internal secondary structures can be observed visually as mirror symmetries. (B) Dot-plot similarity analysis of IRX-150.52. The spacer of this IR is homologous to a region in the arms. (C) Analysis of IR7-143.36 and IR7-143.41. One arm of both of these IRs is found in the spacer of the other. IRs with similar secondary structure to A, B, and C are indicated in Table 1. Internal IRs detected in these regions were eliminated from the final data set (Supplemental data S1 and S2). The dot-plot similarity analysis was performed with a window size of 50 bp and mimimum identity of 85%. (D) Possible double cruciform structure suggested by IRs that contain internal IRs, for example, in A and Figure 2C. (Black and gray DNA strands) outside of IR region; (blue and red DNA strands) large, high homology IR; (purple and orange DNA strands) internal, lower homology IRs.
