From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 20 Oct 2020 16:13:33 +0000 (+0100)
Subject: fix for JAL-3765
X-Git-Tag: Develop-2_11_2_0-d20201215~22^2~1
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=bf1fd68e2aea9ef1f5c0cbbae814b78d69f29e3a;p=jalview.git

fix for JAL-3765
---

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