Open to the Alignment panel on your right nav bar, and click Create New Alignment.
In the alignment window, click Choose File(s) and select either sequence and trace files (.ab1 or .ftv) from your computer or existing Benchling sequences. Be sure the sequence you want to be your template has the *Template* icon next to the sequence name. Select "Create Alignment" when ready.
Trim your trace file
Benchling automatically trims your trace file to the point where the peaks start to look clean. You can also manually select the trimming bar and move it with your mouse.
Inspect part of the alignment
Use the bottom summary view to scroll to the region of interest. Zoom in by decreasing the width of the viewing window.
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 template, it is highlighted red. If it's not clear what base is present, it is highlighted yellow:
You can select which reading frame(s) you want to keep in the viewer:
Add a comment
You can also add a comment by selecting bases and clicking Add Comment at the top of the tab.