The top window is a two dimensional figure. The bottom window is an alignment of E.coli with your sequence. Click on a base in either window to highlight it. The diagram is based on the canoncial E.coli structure. All SSU rRNA structures are shown as mutations, insertions, and deletions from this structure.
Colors give information about the type of deviation in structure.
These colors allow you to quickly see how your structure differs from the canonical E.coli structure.