Figure 15

Fold-alignment dotplot of nanos translational control elements (see Figure 13 for key). From a range of potential stems (faint red diagonal lines, plots a-b), the Pair SCFG resolves the three true stems sharply using the comparative signal (white diagonal lines, plots d-e). Some uncertainty in the primary sequence alignment (parallel blurred red lines, plot c) is resolved by including structural information, including a deletion in the outermost stem (broken diagonal line, plot f).