To export consensus sequence use the Exprot consensus tab of the Options Panel:
The following parameters are available:
Save path - here you need to select path and format for the output file. Also you can add the document to the project with a help of the Add to project checkbox.
Settings - here you can select the Non-alphabet symbols polisy. There are four modes: Skip, Replace with gaps, Replace with default symbol and Keep all symbols.
When you click on the Export button the consensus sequence will be exported into selected output file.