diff --git a/modules/seq/base/src/alignment_handle.cc b/modules/seq/base/src/alignment_handle.cc
index 62514274c110d8d6389122f848e76feef3042be8..39db09fa5c699ae792c432ef4c917133c44ff163 100644
--- a/modules/seq/base/src/alignment_handle.cc
+++ b/modules/seq/base/src/alignment_handle.cc
@@ -174,7 +174,7 @@ void AlignmentHandle::Replace(const AlignedRegion& aln_r, int start, int end){
                          "to share the same number of sequences");
   }
   int aln_rStart=aln_r.GetStart();
-  int aln_rEnd=aln_r.GetEnd();
+  int aln_rEnd=aln_r.GetEnd()-1;
   AlignmentHandle aln=aln_r.GetAlignmentHandle();
   //iterate over sequences and replace part of sequences with the substrings
   //from aligned region