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23 <title>Alignment RNA Structure Consensus Annotation</title>
27 <strong>Alignment RNA Structure Consensus Annotation</strong>
30 <p>The RNA structure consensus displayed below the alignment gives
31 the percentage of valid base pairs per column for the first
32 secondary structure annotation shown on the annotation panel. The
33 symbol below each histogram indicates whether the majority of base
36 <li>'(' - Watson-Crick (A:C, G:T)</li>
37 <li>'[' - Canonical Pairs (A:C, G:U, A:U)</li>
38 <li>'{' - Invalid Pairs (the rest)</li>
40 <p>Mousing over the column gives the fraction of pairs classified as Watson-Crick, Canonical or Invalid.</p>
43 this calculation includes gaps in columns. You can choose to ignore
44 gaps in the calculation by right clicking on the label
45 "StrConsensus" to the left of the structure consensus bar
48 <strong>Structure logo</strong>
50 Right-clicking on the label allows you to enable the structure logo.
51 It is very similar to a sequence logo but instead shows the
52 distribution of base pairs. There are two residues per column, the
53 actual column and the interacting base. The opening bracket is always
54 the one on the left side.
55 <br> Like sequence logos the relative amount of a specific base pair
56 can be estimated by its size in the logo. When the logo is displayed,
57 the tool tip of a column gives the exact numbers for all occurring