diff --git a/uk/ac/sanger/artemis/io/IndexFastaStream.java b/uk/ac/sanger/artemis/io/IndexFastaStream.java
index b8128b275f35b491f5c6efd153da2dd3dd9b3209..e02f58d0c6aae6ef9b8e24f19f0c51d32835c108 100644
--- a/uk/ac/sanger/artemis/io/IndexFastaStream.java
+++ b/uk/ac/sanger/artemis/io/IndexFastaStream.java
@@ -47,6 +47,12 @@ public class IndexFastaStream extends StreamSequence
   private FastaSequenceIndex fastaIndex;
   private int len;
   private String contig;
+  static {
+    ReferenceSequenceFileFactory.FASTA_EXTENSIONS.add(".dna");
+    ReferenceSequenceFileFactory.FASTA_EXTENSIONS.add(".seq");
+    ReferenceSequenceFileFactory.FASTA_EXTENSIONS.add(".fas");
+    ReferenceSequenceFileFactory.FASTA_EXTENSIONS.add(".ffn");
+  }
   
   public IndexFastaStream(Entry entry)
   {