X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Freferenceseq.html;h=a79541b4b6808d13de4afc0e3a36d63d1ade5895;hb=dde303bc73617ab4eb3e681e67cf899e6a971318;hp=912be55fdd33d9899590f29ff1328704ec475c5a;hpb=528c0f1815bc67b54618ad5b16c2162946974caf;p=jalview.git

diff --git a/help/html/calculations/referenceseq.html b/help/html/calculations/referenceseq.html
index 912be55..a79541b 100644
--- a/help/html/calculations/referenceseq.html
+++ b/help/html/calculations/referenceseq.html
@@ -31,12 +31,11 @@
     organisms that are similar to a newly sequenced gene, or when
     searching for structurally similar sequences for use in homology
     modelling.</p>
-<p>
+  <p>
     <strong>What happens when a reference sequence is defined ?</strong>
   </p>
-  <p>
-    The reference sequence for an alignment is indicated by its ID being
-    shown in bold. In addition:</p>
+  <p>The reference sequence for an alignment is indicated by its ID
+    being shown in bold. In addition:</p>
   <ul>
     <li><strong>Reference sequence numbering</strong>. Instead of
       column numbers, the alignment ruler shows the reference sequence
@@ -61,8 +60,8 @@
       sequence when importing analysis results, such as those returned
       from <a href="../webServices/jnet.html">JPred4</a> . A reference
       sequence can also be assigned via the <a
-      href="../features/annotationsFormat.html#refsandviews">SET_REF</a> command in
-      an alignment annotation file.</li>
+      href="../features/annotationsFormat.html#refsandviews">SET_REF</a>
+      command in an alignment annotation file.</li>
   </ul>
   <p>
     <em>Reference sequence based alignment visualisation was