- href="overview.html">alignment overview</a> panel is opened by
- default for a new alignment window.</p>
-<p><em>Show Annotations</em> - If this is selected the new window will display an annotation
- panel below the sequences. This annotation panel may have several rows describing
- the whole alignment. The 3 standard annotations <em>Conservation</em>, <em>Quality</em> and <em>Consensus</em>
- may be shown or hidden by default.</p>
-<p><em>Full Sequence ID</em> - If selected the ID panel will display the name of a sequence
- plus the start and end residues in the format name/start-end. If not selected,
- the displayed ID will be the name of the sequence.</p>
-<p><em>Right Align IDs</em> - select to align all sequence IDs to the
-left-hand edge of the sequence alignment, rather than the left-hand
+ href="overview.html">alignment overview</a> panel is opened by default
+for a new alignment window.</p>
+<p><em>Show Annotations</em> - If this is selected the new window
+will display an annotation panel below the sequences. This annotation
+panel may have several rows describing the whole alignment. The 3
+standard annotations <em>Conservation</em>, <em>Quality</em> and <em>Consensus</em>
+for the alignment may be shown or hidden by default using the checkboxes
+below.</p>
+<p><em>Show group: Conservation and Consensus</em> controls the
+display of per-group automatic annotation.</p>
+<p><em>Consensus: Histogram and Logo</em> checkboxes control the
+display of the consensus histogram and sequence logo for consensus
+annotation rows.</p>
+<p><em>Full Sequence ID</em> - If selected the ID panel will display
+the name of a sequence plus the start and end residues in the format
+name/start-end. If not selected, the displayed ID will be the name of
+the sequence.</p>
+<p><em>Right Align IDs</em> - select to align all sequence IDs to
+the left-hand edge of the sequence alignment, rather than the left-hand