diff --git a/python/obitools3/commands/ngsfilter.pyx b/python/obitools3/commands/ngsfilter.pyx
index 88c8127..7f4598f 100644
--- a/python/obitools3/commands/ngsfilter.pyx
+++ b/python/obitools3/commands/ngsfilter.pyx
@@ -479,6 +479,8 @@ cdef tuple annotate(sequences, infos, no_tags, verbose=False):
     if not directmatch[0].forward:
         sequences[0] = sequences[0].reverse_complement
         sequences[0][b'reversed'] = True   # used by the alignpairedend tool (in kmer_similarity.c)
+    else:
+        sequences[0][b'reversed'] = False   # used by the alignpairedend tool (in kmer_similarity.c)
 
     sample=None
     if not no_tags: