X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FFinder.java;h=d52e42a768a0e65db9a543e05031e5a5a164de6f;hb=bf1fd68e2aea9ef1f5c0cbbae814b78d69f29e3a;hp=c545c7f1ae05fa21883641b7a03a708190f1f9e5;hpb=6b13a606027284408286d1cd2833470d1f9b9bfe;p=jalview.git

diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index c545c7f..d52e42a 100644
--- a/src/jalview/analysis/Finder.java
+++ b/src/jalview/analysis/Finder.java
@@ -417,7 +417,7 @@ public class Finder implements FinderI
      * update residueIndex to next position after the start of the match
      * (findIndex returns a value base 1, columnIndex is held base 0)
      */
-    residueIndex += offset + 1;
+    residueIndex = searchPattern.matchedFrom()+1;
 
     /*
      * return false if the match is entirely in a hidden region