Create the alignment
Select all the sequences you want to align in your Expanded View. In the "More" dropdown, select Analyze, and then Create alignment.
You'll then be prompted to select the folder you wish to save your new consensus sequence to.
View different regions of the alignment
Once the alignment is complete, click and drag the bottom summary (grey bars) to view different regions. Zoom in by decreasing the width of the viewing window.
Add a comment
Misalignments are shown in red in the summary. You can also add a comment by selecting bases and clicking Add Comment at the top of the tab.
View reading frames
Turn on the "reading frames" view to see for each frame which amino acid is encoded. If an amino acid differs from the consensus, it is highlighted red. If it's not clear what base is present, those amino acids are highlighted yellow:
You can select which reading frame(s) you want to keep in the viewer:
View previous consensus alignments
View the consensus alignment again by going to the inventory file that was created, and clicking on the Alignment icon. Then click on the Saved Alignment.
After having reviewed this tutorial, you might want to learn about how to align to a template next.