Alignment RNA Structure Consensus Annotation

The RNA structure consensus displayed below the alignment is the percentage of valid base pairs per column. It is calculated in relation to a secondary structure and just paired columns are calculated. The canonical Watson-Crick base pairings (A-T/U, G-C) and the wobble base pair (G-T/U) are regarded as valid pairings.
The amount of valid base pairs is indicated by the profile in the Alignment Annotation row.
By default this calculation includes gaps in columns. You can choose to ignore gaps in the calculation by right clicking on the label "StrConsensus" to the left of the structure consensus bar chart.

Structure logo

By clicking on the label you can also activate the structure logo. It is very similar to a sequence logo but counts the numbers of base pairs. There are two residues per column, the actual column and the interacting base. The opening bracket is always the one on the left side.
Like sequence logos the relative amount of a specific base pair can be estimated by it's size in the logo. The tool tip of a column gives the exact numbers for all occurring valid base pairs.