X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentUtils.java;fp=src%2Fjalview%2Fanalysis%2FAlignmentUtils.java;h=0d2e00233919efbceb41797269f23a5c01bad06b;hb=834b2f0f7bee2c61ab68b285d5e81ff94b425400;hp=7a082bef225c7d12398c13639ab3b284b4ece1e6;hpb=50452c1ba64e6a8eb7fb06a79b779357d6488cbf;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 7a082be..0d2e002 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -2425,7 +2425,8 @@ public class AlignmentUtils
   static int computePeptideVariants(SequenceI peptide, int peptidePos,
           List<DnaVariant>[] codonVariants)
   {
-    String residue = String.valueOf(peptide.getCharAt(peptidePos - 1));
+    String residue = String
+            .valueOf(peptide.getCharAt(peptidePos - peptide.getStart()));
     int count = 0;
     String base1 = codonVariants[0].get(0).base;
     String base2 = codonVariants[1].get(0).base;