The Overview provides a way to navigate within the sequences, no matter what type of sequences or alignment is used. In the case of genomic alignments generated by Mauve, the Overview also allows you to explore the relationships between multiple aligned blocks. Selections and vertical ordering within this view are synchronized with other views in MegAlign Pro. Similarly, selections and ordering done elsewhere are reflected in the Overview.

To access the view, click on the Overview tab.

By default, the Overview displays a header, followed by one or more sequences with labels to their left. Each sequence is depicted as a “sequence/alignment block,” and the length is proportional to other sequences in the group. Each sequence row can display a variety of optional data tracks.

The Overview displays information in different ways, depending on the alignment stage and the workflow. In all cases, sequences are represented as either gray or colored blocks. Any sequence that is not part of an alignment is shown in solid gray. Sequences included in an alignment are usually drawn in dark green, although multi-block alignments, such as those generated by Mauve, are drawn in up to seven colors.

See the following topics for images and details of the Overview in different situations:


Information bar:

The blue/gray bar at the top of the view shows information pertaining to the current selection.

Selection Example Information displayed
Nothing, and sequences have not been aligned (blank) (blank)
Nothing, and at least some sequences have been aligned The name of the alignment.
One sequence The sequence name and its length in bp.
Multiple sequences

The number of sequences selected, the total number of sequences, and the alignment status.
A feature or any portion of one sequence The sequence name and selected range.
A portion of multiple sequences (selected in the Sequences view) The selected range and length in bp.


Tasks pertaining to the Overview:

Task How to…
Change settings for this view To change settings, including showing/hiding connecting lines and changing spacing between rows, use the Overview section of the Style panel.
Customize the look and layout of the view, zoom in or split the view See Customize the look and layout.
Set an unselected alignment block in the Overview as the active block Double-click on an inactive alignment block, or right-click on an inactive alignment block and choose Set As Active Block. The corresponding sequence blocks will line up vertically. The alignment block containing the sequence block will become active.
Change settings related to the Overview use the Overview section of the Style panel.
Make an alignment block the active block and move it to the left of the Overview Make a block active by double-clicking a sequence block. Then choose Overview > Set Start of Sequences to Active Block or the context (right-click) option of the same name. The blocks in each sequence are rotated so that the active sequence block is leftmost.
Center the Overview display over the active block Choose Overview > Show Active Block.
Return alignment blocks to their default order Choose Overview > Reset Start of Sequences or the context (right-click) option of the same name. In the Overview, the individual sequence ruler coordinates are updated to reflect the change.Note that resetting the start of sequences presumes that alignment consists of circular genomic sequences.
Search for a sequence by name Click the Search tool () on the right of the header area to open a search area. See Search for a sequence using a text query for details.
Export data from the view Click the Export Data tool (), a shortcut to the File > Export Data subcommands. See Export data to a file.
Save an image of the view Click the Export Image tool (), a shortcut to the File > Export Image subcommands. See Export an image of the view.
Print the view Click the Print tool (). See Print Images for details.

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