diff --git a/src/mapper.cpp b/src/mapper.cpp
index f60134d67dc..337837560e9 100644
--- a/src/mapper.cpp
+++ b/src/mapper.cpp
@@ -3532,9 +3532,11 @@ Mapper::find_mems_simple(string::const_iterator seq_begin,
     mems.erase(std::remove_if(mems.begin(), mems.end(),
                               [&smems_begin,
                                &min_mem_length](const MaximalExactMatch& m) {
-                                  return m.end-m.begin == 0
-                                      || m.length() < min_mem_length
-                                      || smems_begin[m.begin] != m.end;
+                                  return ( m.end-m.begin == 0
+                                           || m.length() < min_mem_length
+                                           || smems_begin[m.begin] != m.end
+                                           || m.count_Ns() > 0
+                                      );
                               }),
                mems.end());
     // return the matches in natural order
@@ -6721,6 +6723,11 @@ void MaximalExactMatch::fill_positions(Mapper* mapper) {
     }
 }
 
+// counts Ns in the MEM
+size_t MaximalExactMatch::count_Ns(void) const {
+    return std::count(begin, end, 'N');
+}
+
 ostream& operator<<(ostream& out, const MaximalExactMatch& mem) {
     size_t len = mem.begin - mem.end;
     out << mem.sequence() << ":";
diff --git a/src/mapper.hpp b/src/mapper.hpp
index 7606af6171b..65ed854ea99 100644
--- a/src/mapper.hpp
+++ b/src/mapper.hpp
@@ -54,6 +54,8 @@ class MaximalExactMatch {
     int length(void) const;
     // uses an xgindex to fill out the MEM positions
     void fill_positions(Mapper* mapper);
+    // tells if the MEM contains an N
+    size_t count_Ns(void) const;
 
     friend bool operator==(const MaximalExactMatch& m1, const MaximalExactMatch& m2);
     friend bool operator<(const MaximalExactMatch& m1, const MaximalExactMatch& m2);