X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=f7e8f2ebe26d9fc58f28be41f5f534103c91a311;hb=1e943acf589b7393c666204f533d2ebce28d7471;hp=3ad31884642b1e734930db7aec7088641ab97f01;hpb=03588608e1a4d290bacfad482c827356e65aef51;p=jalview.git

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 3ad3188..f7e8f2e 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.compareChars(
+                  astr1.charAt(i + (j * len)), astr2.charAt(i + (j * len)),
+                  false);
+          if (sameChar
                   && !jalview.util.Comparison.isGap(astr1.charAt(i
                           + (j * len))))
           {