Automated layout of multistem junctions. Raw R2R output is shown for the manA motif , a pseudoknot (lower right) and a "skeleton"-style drawing (upper right). The layout of the central multistem junction was determined using R2R's solver functions. This motif presents an atypical case where it is not possible to direct all stems horizontally or vertically. The directions of the stems were chosen manually to promote symmetry, the lowest two stems on the junction were constrained to be aligned vertically, and the midpoint of these two stems was aligned horizontally with the upper-most stem. Subject to these constraints, R2R's solver chose a layout that best approximated a circle. The layout was used in a previously published figure . A finished drawing would require assembling the pseudoknot (as in Figure 1), and moving text. Modular structures present in some manA RNAs are not shown. Note: the text "0-6 nt" was moved inward manually to fit the column width.