X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;fp=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=86bf7216d14c0e2dc6705f3fd7a04084f9f76951;hb=2595e9d4ee0dbbd3406a98c4e49a61ccde806479;hp=3ad31884642b1e734930db7aec7088641ab97f01;hpb=e20075ba805d744d7cc4976e2b8d5e5840fb0a8d;p=jalview.git

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 3ad3188..86bf721 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -620,7 +620,10 @@ public class AlignSeq
       {
         if ((i + (j * len)) < astr1.length())
         {
-          if (astr1.charAt(i + (j * len)) == astr2.charAt(i + (j * len))
+          boolean sameChar = Comparison.isSameResidue(
+                  astr1.charAt(i + (j * len)), astr2.charAt(i + (j * len)),
+                  false);
+          if (sameChar
                   && !jalview.util.Comparison.isGap(astr1.charAt(i
                           + (j * len))))
           {