diff --git a/uk/ac/sanger/artemis/io/GenbankStreamSequence.java b/uk/ac/sanger/artemis/io/GenbankStreamSequence.java
index bdbe336424787899721f3b9fff94bf701cae6c92..add840798cac02e0386b2cb2c18cb964e5de2913 100644
--- a/uk/ac/sanger/artemis/io/GenbankStreamSequence.java
+++ b/uk/ac/sanger/artemis/io/GenbankStreamSequence.java
@@ -203,7 +203,9 @@ public class GenbankStreamSequence extends StreamSequence
                                            in_stream.getLineNumber());
         }
       }
-      appendChar(this_line_sequence_buffer.toString().toLowerCase().toCharArray());
+      
+      if(this_line_sequence_buffer.length() > 0)
+        appendChar(this_line_sequence_buffer.toString().toLowerCase().toCharArray());
     }
     setCounts();
   }