Must follow alignmentPosition

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index e95ca02..460c6d1 100755 (executable)
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -91,6 +91,8 @@ public class SequenceRenderer
 \r
       allGroups = av.alignment.findAllGroups(seq);\r
 \r
+      i = seq.findIndex(i);\r
+\r
       drawBoxes(seq, i,i, 0, 0, 1,1);\r
 \r
       return new Color(bi.getRGB(0, 0));\r