Alignment RNA Structure Consensus Annotation

The RNA structure consensus displayed below the alignment gives the percentage of valid base pairs per column for the first secondary structure annotation shown on the annotation panel. These values are shown as a histogram labeled "StrucConsensus", where a symbol below each bar indicates whether the majority of base pairs are:

Mousing over the column gives the fraction of pairs classified as Watson-Crick, Canonical or Invalid.

By default this calculation includes gaps in columns. You can choose to ignore gaps in the calculation by right clicking on the label "StrucConsensus" to the left of the structure consensus bar chart.

RNA Structure logo
Right-clicking on the label allows you to enable the structure logo. It is very similar to a sequence logo but instead shows the distribution 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 its size in the logo, and this can be made more obvious by normalising the logo (enabled via the popup menu). When the logo is displayed, the tool tip for a column gives the exact percentages for all base pairs at that position.