diff --git a/modules/seq/base/doc/seq.rst b/modules/seq/base/doc/seq.rst
index dec35ea21c04484d3637559652cc3d4f3013f5e3..e210687d102b159c1196596f9ac759846f807115 100644
--- a/modules/seq/base/doc/seq.rst
+++ b/modules/seq/base/doc/seq.rst
@@ -755,7 +755,8 @@ probabilities between Match, Insertion or Deletion states or neff values
     :type to:  :class:`int`
 
     :returns: sub-profile as defined by given indices
-              (:attr:`null_model` is copied)
+              (:attr:`null_model` and :attr:`neff` are copied,
+              you might want to manually reset neff)
     :rtype: :class:`ProfileHandle`
 
     :raises: :exc:`~exceptions.Error` if *to* <= *from* or
diff --git a/modules/seq/base/src/profile_handle.cc b/modules/seq/base/src/profile_handle.cc
index 8a4582620d95644a4ec842e2c56c3e9682685ff9..80b4565838f3ac0c888a766c0fa2be36635bb8a1 100644
--- a/modules/seq/base/src/profile_handle.cc
+++ b/modules/seq/base/src/profile_handle.cc
@@ -149,6 +149,7 @@ ProfileHandlePtr ProfileHandle::Extract(uint from, uint to) const {
   // get subset to return
   ProfileHandlePtr return_prof(new ProfileHandle);
   return_prof->SetNullModel(null_model_);
+  return_prof->SetNeff(neff_);
   for (uint i = from; i < to; ++i) {
     return_prof->AddColumn(columns_[i], seq_[i]);
   }