ilen and jlen no longer +1

diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index d8e599b..e6aae96 100755 (executable)
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -13,8 +13,8 @@ public class Comparison {
      String si   = ii.getSequence();\r
      String sj   = jj.getSequence();\r
 \r
-     int ilen = end-start+1;\r
-     int jlen = end-start+1;\r
+     int ilen = end-start;\r
+     int jlen = end-start;\r
 \r
      if ( jalview.util.Comparison.isGap( si.charAt(start+ilen)) )\r
       {\r