Below the annotation and sequence viewer is the 2D display, where genes and directions are drawn, below which are the energies of structures generated by Rnall. To the right lets you focus on a particular color with given spread and brightness variables, all set by the scroll bars. When you mouse over energies and genes in the display it shows some basic information.
The black lines indicate the "sequence path" and reads like a book. At the top-left is the start position being displayed, and at the bottom right is the last position being displayed. It snakes between them going left to right, then moving down to the next row (see display customization). When you mouse over a structure it displays the energy, window size, and location of that structure. When you select it, that information gets piped to Rnall again where the pipeline takes over (see tools section below).
When you select a gene, as mentioned in the Annotation and Sequence Viewer section, RnallViewer displays a list of information about that gene at the bottom of the display, lining up highlighted and selected genes to the same categories if possible. Also, as mentioned in the tutorial, you can adjust the structure energy focus using controls at the right. The long color bar selects which color (energy) to focus on. Energies are assigned color based on the high and low energies selected in the general preferences (see display customization).