X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fpairwise.html;h=10902530eb1b9cf12545f462b7906c34087c1080;hb=a6db1aeb58e79d976b1e176103a3722ae7f28240;hp=bb80b84f6dd02ab73498ecb5ee6f5b2d0184e465;hpb=c17661b22323a66090ea91e04751aa17461b17c5;p=jalview.git

diff --git a/help/html/calculations/pairwise.html b/help/html/calculations/pairwise.html
index bb80b84..1090253 100755
--- a/help/html/calculations/pairwise.html
+++ b/help/html/calculations/pairwise.html
@@ -38,11 +38,21 @@
   <p>
     Gap open : 12 <br> Gap extend : 2
   </p>
-  <p>When you select the pairwise alignment option a new window will
-    come up which will display the alignments in a text format as they
-    are calculated. Also displayed is information about the alignment
-    such as alignment score, length and percentage identity between the
+  <p>When you select the pairwise alignment option, a new window
+    will come up which displays the alignments in a text format, for
+    example:</p>
+  <p>
+  <pre>
+    FER1_SPIOL/5-13 TTMMGMAT<br />
+                    |. .. ||<br />
+    FER1_MESCR/5-15 TAALSGAT
+    </pre>
+  shows the aligned sequences, where '|' links identical residues, and
+  (for peptide) '.' links residues that have a positive PAM250 score.
+  <p>The window also shows information about the alignment such as
+    alignment score, length and percentage identity between the
     sequences.</p>
-  <p>&nbsp;</p>
+  <p>A button is also provided to allow you to view the sequences as
+    an alignment.</p>
 </body>
 </html>