diff --git a/uk/ac/sanger/artemis/chado/ArtemisUtils.java b/uk/ac/sanger/artemis/chado/ArtemisUtils.java
index 2c357a12a88cf99ffebf079674e9fce2027e6d89..82e76f48647d6d58dff890c731eb10b9681c309a 100644
--- a/uk/ac/sanger/artemis/chado/ArtemisUtils.java
+++ b/uk/ac/sanger/artemis/chado/ArtemisUtils.java
@@ -494,12 +494,12 @@ public class ArtemisUtils
 
     // query location
     String queryLoc = getString(qualifier_strings, "query");
-    final FeatureLoc featureLoc = getFeatureLoc(queryLoc, queryFeature, strand, 1);
+    final FeatureLoc featureLoc = getFeatureLoc(queryLoc, queryFeature, strand, 0);
     matchFeature.addFeatureLocsForFeatureId(featureLoc);
 
     // subject location
     String subjectLoc = getString(qualifier_strings, "subject");
-    final FeatureLoc subjectFeatureLoc = getFeatureLoc(subjectLoc, subjectFeature, strand, 0);
+    final FeatureLoc subjectFeatureLoc = getFeatureLoc(subjectLoc, subjectFeature, strand, 1);
     matchFeature.addFeatureLocsForFeatureId(subjectFeatureLoc);
 
     return analysisFeature;