right-click the name of the consensus sequence (to the left) | Open Copy of Sequence | Save () the new sequence
right-click the name of the consensus sequence (to the left) | Open Copy of Sequence Including Gaps | Save () the new sequence
right-click the name of the consensus sequence (to the left) | Open This Sequence
Open Copy of Sequence creates a copy of the sequence, omitting all gap regions, which can be saved and used independently.
Open Copy of Sequence Including Gaps replaces all gaps with Ns. Any regions that appear to be deletions will be removed if this option is chosen. For example:
reference CCCGGAAAGGTTT consensus CCC--AAA--TTT match1 CCC--AAA match2 TTT
Here, if you chose to open a copy of the consensus with gaps, you would get this output
Open This Sequence will not create a new sequence but simply let you see the sequence in a sequence view. This means that the sequence still "belong" to the mapping and will be saved together with the mapping. It also means that if you add annotations to the sequence, they will be shown in the mapping view as well. This can be very convenient e.g. for Primer design ().
In order to preserve the history of the changes you have made to the contig, the contig itself should be saved from the contig view, using either the save button () or by dragging it to the Navigation Area.