JAL-2629 fix issue where HMM sequences would be too long

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 57fe83e..4f3d026 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -403,7 +403,8 @@ public class FileLoader implements Runnable
               if (sg != null)
               {
                 seq.insertCharAt(0, sg.getStartRes(), '-');
-                seq.insertCharAt(sg.getEndRes(), alignment.getWidth(), '-');
+                seq.insertCharAt(sg.getEndRes(),
+                        alignment.getWidth() - sg.getEndRes(), '-');
                 SequenceI topSeq = sg.getSequencesInOrder(alignment)[0];
                 int topIndex = alignment.findIndex(topSeq);
                 alignment.getSequences().add(topIndex, seq);