The Overview has different appearances, depending on the stage and workflow.
After aligning with a method other than Mauve, or after performing a Mauve alignment that results in a single aligned block, any blocks in the Overview will be green and will have the same lengths.
The interior of a sequence block displays a histogram of residue count, with gray areas representing gaps. These histograms reflect the proportion of non-gapped positions in a window corresponding to the number of positions spanned by a single pixel at a given zoom level.
After aligning sequences end-to-end (see Add Multi-Segment Sequences), vertical blue bars are used to show the beginnings and ends of the component sequences (i.e., the segments). These bars are displayed regardless of the type of alignment performed.
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