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.

Constituent sequences are shown in the lower portion of the view. To see the sequence orientation, examine the arrow to the left of each sequence string. A right arrow ( ) indicates that SeqMan NGen used the input orientation for the alignment. A left 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 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 Variant view, and T’s there are not colored as variants.

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