-<p><em>Smooth Font</em> - Toggles anti-aliasing on / off for faster rendering
- of the alignment.</p>
-<p><em>Wrap Alignment</em> - Select whether to open new alignment windows in wrapped
- mode or not.</p>
-<p><em>Gap Symbol</em> - The default gap symbol may be set to either "-" or "."</p>
-<p><em>Colour</em> - The default colour scheme for a new alignment window. If
- the chosen option is "User Defined" then the last User Defined Colour
- loaded or saved via the User Defined Colours panel will be loaded. </p>
-<p><em>Sort by</em> - When the alignment is loaded in, it will can be sorted by
- Id or pairwise identity.</p>
-<p><em>Open file</em> - If this is selected then the default alignment file will
- be opened when Jalview is started. You can change the default file by clicking
- on file name and either typing in the file path or selecting it from the file
- chooser window. </p>
-<p><a name="connections"><strong>"Connections" Preferences tab</strong></a></p>
+<p><em>Smooth Font</em> - Toggles anti-aliasing on / off for faster
+rendering of the alignment.</p>
+<p><em>Wrap Alignment</em> - Select whether to open new alignment
+windows in wrapped mode or not.</p>
+<p><em>Gap Symbol</em> - The default gap symbol may be set to either
+"-" or "."</p>
+<p><em>Sort by</em> - When the alignment is loaded in, it will can
+be sorted by Id or pairwise identity.</p>
+<p><em>Open file</em> - If this is selected then the default
+alignment file will be opened when Jalview is started. You can change
+the default file by clicking on file name and either typing in the file
+path or selecting it from the file chooser window.</p>
+<p><a name="colours"><strong>"Colours" Preferences tab</strong></p>
+<p><em>Alignment Colour</em> - The default colour scheme for a new alignment
+window. If the chosen option is "User Defined" then the last
+User Defined Colour loaded or saved via the User Defined Colours panel
+will be loaded.</p>
+ <p>
+ <em>Annotation Shading Default</em> - set the default minimum
+ and maximum colours used when <a
+ href="../colourSchemes/annotationColouring.html">Colour by
+ Annotation ..</a> is selected from the alignment window's colours menu.
+ </p>
+ <br>
+ </p>
+<p><a name="connections"><strong>"Connections"
+Preferences tab</strong></a></p>