Due to the integrated nature of CLC Genomics Workbench it is easy to use the consensus sequences as input for additional analyses. If you wish to extract the consensus sequence for further use, use the Extract Consensus Sequence tool (see Extract consensus sequence).
You can also right-click the consensus sequence and select Open Sequence. This 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 for Primer design () for example.
If you wish to BLAST the consensus sequence, simply select the whole contig for your BLAST search. It will automatically extract the consensus sequence and perform the BLAST search.
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.