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.