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<head><title>Alignment Consensus Annotation</title></head>
<body>
<p><strong>Alignment Consensus Annotation</strong></p>
<p>The consensus displayed below the alignment is the percentage of the modal
- residue per column. By default this calculation takes includes gaps in column.
+ residue per column. By default this calculation includes gaps in columns.
You can choose to ignore gaps in the calculation by right clicking on the label
"Consensus" to the left of the consensus bar chart.
<p>If the modal value is shared by more than 1 residue, a "+" symbol
the consensus annotation label to copy the alignment's consensus sequence to the
clipboard.
-<p><strong>Sequence logo</strong></p>
-By clicking on the label you can also activate the sequence logo. It
-indicates the relative amount of residues per column which can be
-estimated by it's size in the logo. The tooltip of a column gives the
-exact numbers for all occuring residues.
-</p>
+<p><strong>Sequence logo</strong></p>
+ By clicking on the label you can also activate the sequence logo. It
+ indicates the relative amount of residues per column which can be
+ estimated by its size in the logo. The tooltip of a column gives the
+ exact numbers for all occurring residues.
+ <br />If columns of the alignment are very diverse, then it can
+ sometimes be difficult to see the sequence logo - in this case, right
+ click on the annotation row label and select
+ <strong>Normalise Consensus Logo</strong> to scale all columns of the
+ logo to the same height.
+
+<p><strong>cDNA Consensus</strong></p>
+A <a href="../features/splitView.html">Split Frame View</a> of cDNA and Protein alignments will show the consensus for cDNA below the protein alignment.<br/>
+This may provide additional information on mutations in DNA that is not visible in the peptide alignment.
</body>
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