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-<head><title>Alignment RNA Structure Consensus Annotation</title></head>
-<body><p><strong>Alignment RNA Structure Consensus Annotation</strong></p>
+<head>
+<title>Alignment RNA Structure Consensus Annotation</title>
+</head>
+<body>
+ <p>
+ <strong>Alignment RNA Structure Consensus Annotation</strong>
+ </p>
-<p>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.<br>
-The amount of valid base pairs is indicated by the profile in the
-Alignment Annotation row.<br>
-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.<br>
-
-<p><strong>Structure logo</strong></p>
-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.<br>
-Like sequence logos the relative amount of a specific base pair can be
-estimated by its size in the logo. The tool tip of a column gives the
-exact numbers for all occurring valid base pairs.
-</p>
+ <p>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:
+ <ul>
+ <li>'(' - Watson-Crick (A:C, G:T)</li>
+ <li>'[' - Canonical Pairs (A:C, G:U, A:U)</li>
+ <li>'{' - Invalid Pairs (the rest)</li>
+ </ul>
+ <p>Mousing over the column gives the fraction of pairs classified as Watson-Crick, Canonical or Invalid.</p>
+
+<p>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.<br>
+ <p>
+ <strong>Structure logo</strong>
+ </p>
+ 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.
+ <br> Like sequence logos the relative amount of a specific base pair
+ can be estimated by its size in the logo. When the logo is displayed,
+ the tool tip of a column gives the exact numbers for all occurring
+ valid base pairs.
+ </p>
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