Illustration of the difference between RNAdistance and DoPloCompare. An example of the difference between RNAdistance and DoPloCompare, illustrated on three structure comparisons. In each case, the compared structure appears next to its representing dot-plot diagram and its dot-bracket notation. The comparisons are relative to the original structure depicted in (A). While RNAdistance = 4 remains the same in (B), (C), and (D), DotPloCompare values increase as the structure visually diverts from the original structure.