To export a consensus sequence of the assembly, select either the Export consensus item in the Consensus Area context menu or the Export ‣ Consensus item in the Reads Area context menu.
The Export Consensus dialog appears:
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Select a file and the file format. The consensus can be exported to a FASTA, FASTQ, GFF or GenBank file.
Modify, if required, the exported sequence name and choose the consensus algorithm.
The consensus is exported with gaps if the Keep gaps check box has been checked.
Also you can select the exporting region. It can be either a Whole sequence, a Visible region, or a Custom region.
When all the parameters are set click the Export button.
The consensus sequence is exported to the file and if the Add to project check box has been checked it is added to the current project and opened.