The Sequences View displays added sequences and aligned sequences. Sequence names selected in this view are simultaneously selected all other views in MegAlign Pro. Similarly, sequence names selected elsewhere will be highlighted in the Sequences View.

To access the view, click on the Sequences tab.

By default, the Sequences view consists of three sections: the header, the footer, and sequences area, the last of which consists of nucleotide or amino acid codes for each sequence on the right, and their labels on the left. Each section can display a variety of optional data tracks. The Sequences view has a different appearance depending on the zoom level.

When viewing a multi-block alignment produced by Mauve and using a minimal horizontal zoom, the currently-selected alignment block will appear the same color as in the Overview. Flanking sequences in adjacent blocks will appear gray. At higher zoom levels, the residues for the active block will be shown in bright colors, while flanking sequence residues are represented by “dimmed” (dull) colors.

The dimmed residues are displayed as unaligned sequences, and therefore appear ungapped and without a consensus. To view the dimmed residues as aligned sequences, select the corresponding block in the Overview.

The following table describes ways to control the appearance of the Sequences view:

Task How to…
To change settings related to the Sequences view Use the Sequences section of the Style panel. The Sequences > Color Sequence Foreground (Background) commands act as alternatives to checking/unchecking the Color foreground (background) boxes in the that section.
To control the portion of sequence displayed in the view The Overview’s “viewport indicator” highlights the portion of sequence displayed in the displayed in the Sequences View. You can drag the indicator to scroll the Sequences view along the sequence. If you split the Sequences view, there will be more than one viewport indicator in the Overview. If you split the Overview, a viewport indicator may appear in more than one of the sub-panes.

To show/hide a vertical guideline The guideline is displayed, by default, and is a navigational aid to help in guiding your eye between the sequences and the rulers. To hide the guideline in all open projects, click Sequences > Show Guideline to remove the checkmark. Even after hiding the guideline, an abbreviated version of the guideline will remain visible in the header and footer.

To show/hide the header, sequences area, or footer in the Sequences view The display of the header, sequences area or footer can be toggled on/off by clicking on the small dark gray arrows near the upper right corners of each section.

Need more help with this?

Thanks for your feedback.