Figure 4.

Histograms of IDIs between actual base pairs in the 3D–3D alignment of E. coli and T. thermophilus 5S, 16S and 23S rRNAs. The IDIs used in these histograms were calculated before the revision of the 3D structures to correct syn-anti errors. The upper-left panel shows the IDI between all aligned base pairs, whether in the same geometric family or not. The base pairs with IDI > 6.0 are discussed in section ‘Base pair discrepancies between aligned positions in the rRNA 3D structural alignments’. The upper-right panel shows the IDI between aligned base pairs that belong to the same geometric family, and the lower panels subdivide these into two cases, those in which with identical base combinations (lower left) and those with different base combinations (lower right). All IDI values above 6 are placed in the rightmost bin in each histogram.