To move the RNA, you can click on the blue background and move the mouse.
You can use left and right arrows from the control palette at the bottom to undo and redo. You can zoom in and out using the magnifying glasses, mousewheel, or + and - keys.
You can change bases by painting them with the corresponding color from the bottom palette. You can also change color by using the keyboard shortcuts 1, 2, 3, and 4.
You can view your RNA in two modes:
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Natural Mode - In this mode, your RNA will fold into the most stable shape, as in the natural world. Use natural mode to check how your RNA actually folds. To select this mode, click the button on the left in the image above.
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Target Mode - You can freeze your RNA in the target shape. To select this mode, click the button on the right in the image above. Use target mode to check which stacks you have to make.
You can toggle between mode by clicking on them or hitting the space bar.