In the Alignment view, you may edit constituent or consensus sequences in an .sqd project contig by removing or adding nucleotides or gaps. Only the editing of gaps is supported.

Task How To
Remove or add gaps Insert the cursor into an individual sequence and type one or more dashes (-) or delete the same. As you do this, the Consensus sequence will be recalculated per your changes.
Remove or add nucleotides If you attempt to type in or delete sequence other than gaps, you will receive the following warning:

If you still wish to proceed, click OK. You may then insert the cursor into an individual sequence and type in an IUPAC nucleic acid code or delete the same. As with gaps, the Consensus sequence will be recalculated. When you add new nucleotides, they will appear in lower case to signify a manual addition.
Cut or copy a selected portion of the sequence Select some or all of the sequence, then right-click and choose Cut or Copy.
Slide a Sanger sequence relative to other sequences Use the Banana tool (). in the Alignment view header. When this tool is activated, the cursor is shaped like a banana. Use your mouse and the banana-shaped cursor to drag any sequence in the Alignment view to the left or right, as desired. When you are done, click the Banana tool again to return the cursor to its normal state. Note that this tool is only active when the alignment contains Sanger trace files.
Remove a selected sequence from the contig Select a sequence name at the left of the Alignment view, then choose Sequence > Remove Sequence.

Note that changes made to a constituent sequence only directly affect that sequence, but changes made to the consensus sequence affect the consensus and every constituent sequence in the contig. Note that the original sequence files stored on your computer will not be affected by these procedures.

To reassemble one or more contigs after editing them, see Reassemble contigs.

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