Alignment Consensus Annotation

The consensus displayed below the alignment is the percentage of the modal residue per column. By default this calculation includes gaps in columns. You can choose to ignore gaps in the calculation by right clicking on the label "Consensus" to the left of the consensus bar chart.

If the modal value is shared by more than 1 residue, a "+" symbol is used in the display for the simple reason that it is not possible to display multiple characters in a single character space.

Copying the consensus sequence

Select the "Copy Consensus Sequence" entry from the consensus annotation label to copy the alignment's consensus sequence to the clipboard.

Sequence logo

By clicking on the label you can also activate the sequence logo. It indicates the relative amount of residues per column which can be estimated by its size in the logo. The tooltip of a column gives the exact numbers for all occurring residues.
If columns of the alignment are very diverse, then it can sometimes be difficult to see the sequence logo - in this case, right click on the annotation row label and select Normalise Consensus Logo to scale all columns of the logo to the same height.

Group Consensus
If sequence groups have been defined, then selecting option 'Group Consensus' in the Annotations menu will result in Consensus being calculated for each group, as well as the alignment as a whole.

cDNA Consensus

A Split Frame View of cDNA and Protein alignments will show the consensus for cDNA below the protein alignment.
This may provide additional information on mutations in DNA that is not visible in the peptide alignment.