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. The symbol below each histogram 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
"StrConsensus" to the left of the structure consensus bar
chart.
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.