The Alignment view displays the consensus sequence and the alignment of all sequences making up a contig at the nucleotide level. The Alignment view also allows you to edit contigs and contig scaffolds.

To access the Alignment view, choose a contig from the Explorer panel and either use the Show Alignment view of selected contigs tool ( ) or choose View > Alignment > Show Alignment View.

For .sqd projects, the default view displays letters only if the base differs from the consensus.

For .assembly projects, the default view shows all letters in gray, with variants shown in other colors.

See Default colors in the Alignment view for details. The color schemes and bases shown can be changed using the Alignment section of the Style panel.

The sequence orientation is shown by the arrow to the left of each sequence string. A right-facing arrow ( ) indicates that SeqMan NGen used the input orientation for the alignment. A left-facing arrow ( ) shows that SeqMan NGen used the complementary strand.

To learn the length/range of a sequence, look at the sequence name in the left margin of the view. The sequence range is shown in parentheses.

To put a sequence in a different order, select its name on the left, then use your mouse to drag and drop it to a new position in the sequence list.

To zoom in or out on the Alignment view, use the green vertical and horizontal zoom in/out sliders. Grab either green slider with your mouse and drag left/right or up/down to zoom in or out in the view.

To learn more about using this view, see the following topics:

U’s vs. T’s in the Alignment view:

If you are viewing a SeqMan NGen assembly in which DNA sequencing reads were assembled against an RNA reference sequence, the reference row in the Alignment view will contain U’s where the read rows have T’s. Though not actually mismatches, the T’s will appear in the mismatch color scheme in the Alignment view. By contrast, the T/U equivalency is recognized in the Variants view, and T’s there are not colored as variants.

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