diff --git a/uk/ac/sanger/artemis/components/SequenceViewer.java b/uk/ac/sanger/artemis/components/SequenceViewer.java
index cc901fd5ff48e927f072837bd69c23e633eb6092..e6fb5b1c4b74e782e238ac59389cdae7800f01d6 100644
--- a/uk/ac/sanger/artemis/components/SequenceViewer.java
+++ b/uk/ac/sanger/artemis/components/SequenceViewer.java
@@ -290,7 +290,7 @@ public class SequenceViewer extends FileViewer {
       StyleConstants.setBackground(style, colourHash.get(aa));
     }
     
-    final String seq = getText();
+    final String seq = getText().toUpperCase();
     int seqStart = 0;
     if(seq.startsWith(">"))
     {