diff --git a/python/obitools3/commands/alignpairedend.pyx b/python/obitools3/commands/alignpairedend.pyx
index fd5d826..dab3483 100755
--- a/python/obitools3/commands/alignpairedend.pyx
+++ b/python/obitools3/commands/alignpairedend.pyx
@@ -2,7 +2,6 @@
 
 from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
 from obitools3.dms import DMS
-from obitools3.dms.view import RollbackException
 from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
 from obitools3.dms.column.column cimport Column
 from obitools3.dms.capi.obiview cimport QUALITY_COLUMN
@@ -201,26 +200,23 @@ def run(config):
         pb(i)
         
         consensus = view[i]
-        
+               
         if not two_views:
             seqF = entries[i]
         else:
             seqF = forward[i]
-                
-        if smin > 0:
-            if (ali.score > smin) :
-                buildConsensus(ali, consensus, seqF)
-            else:
-                if not two_views:
-                    seqR = Nuc_Seq(seqF.id, seqF[REVERSE_SEQ_COLUMN_NAME], quality = seqF[REVERSE_QUALITY_COLUMN_NAME])
-                else:
-                    seqR = reverse[i]
-                buildJoinedSequence(ali, seqR, consensus, forward=seqF)
-                
-            consensus[b"smin"] = smin
-        else:
+                        
+        if ali.score > smin and ali.consensus_len > 0 :
             buildConsensus(ali, consensus, seqF)
-                
+        else:
+            if not two_views:
+                seqR = Nuc_Seq(seqF.id, seqF[REVERSE_SEQ_COLUMN_NAME], quality = seqF[REVERSE_QUALITY_COLUMN_NAME])
+            else:
+                seqR = reverse[i]
+            buildJoinedSequence(ali, seqR, consensus, forward=seqF)
+        
+        consensus[b"smin"] = smin
+           
         if kmer_ali :
             ali.free()
     
diff --git a/python/obitools3/dms/capi/kmer_similarity.pxd b/python/obitools3/dms/capi/kmer_similarity.pxd
index 232ecb4..f3fb77f 100755
--- a/python/obitools3/dms/capi/kmer_similarity.pxd
+++ b/python/obitools3/dms/capi/kmer_similarity.pxd
@@ -35,10 +35,10 @@ cdef extern from "kmer_similarity.h" nogil:
                               OBIDMS_column_p qual_col1,
                               OBIDMS_column_p qual_col2,
                               uint8_t kmer_size,
-                              int32_t* kmer_pos_array,
+                              int32_t** kmer_pos_array,
                               int32_t* kmer_pos_array_height_p,
-                              int32_t* shift_array,
+                              int32_t** shift_array,
                               int32_t* shift_array_height_p,
-                              int32_t* shift_count_array, 
+                              int32_t** shift_count_array, 
                               int32_t* shift_count_array_height_p,
                               bint build_consensus)
diff --git a/python/obitools3/libalign/shifted_ali.pyx b/python/obitools3/libalign/shifted_ali.pyx
index 8edd2c4..7a247ad 100755
--- a/python/obitools3/libalign/shifted_ali.pyx
+++ b/python/obitools3/libalign/shifted_ali.pyx
@@ -112,9 +112,9 @@ cdef class Kmer_similarity:
                                self.view2_p, self.column2_p, seq2.index, 0, \
                                self.qual_col1_p, self.qual_col2_p, \
                                self.kmer_size, \
-                               self.kmer_pos_array_p, self.kmer_pos_array_height_a, \
-                               self.shift_array_p, self.shift_array_height_a, \
-                               self.shift_count_array_p, self.shift_count_array_height_a,
+                               &(self.kmer_pos_array_p), self.kmer_pos_array_height_a, \
+                               &(self.shift_array_p), self.shift_array_height_a, \
+                               &(self.shift_count_array_p), self.shift_count_array_height_a,
                                self.build_consensus)
         
         ali = Ali_shifted.new_ali(ali_p)
diff --git a/src/kmer_similarity.c b/src/kmer_similarity.c
index 4aab869..74f8e8d 100755
--- a/src/kmer_similarity.c
+++ b/src/kmer_similarity.c
@@ -67,11 +67,14 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
 						  Obiview_p view2, OBIDMS_column_p column2, index_t idx2, index_t elt_idx2,
 						  OBIDMS_column_p qual_col1, OBIDMS_column_p qual_col2,
 						  uint8_t kmer_size,
-						  int32_t* kmer_pos_array, int32_t* kmer_pos_array_height_p,
-						  int32_t* shift_array, int32_t* shift_array_height_p,
-						  int32_t* shift_count_array, int32_t* shift_count_array_length_p,
+						  int32_t** kmer_pos_array_p, int32_t* kmer_pos_array_height_p,
+						  int32_t** shift_array_p, int32_t* shift_array_height_p,
+						  int32_t** shift_count_array_p, int32_t* shift_count_array_length_p,
 						  bool build_consensus)
 {
+	int32_t*        kmer_pos_array;
+	int32_t*        shift_array;
+	int32_t*        shift_count_array;
 	Obi_ali_p       ali = NULL;
 	int 			i, j;
 	bool 			switched_seqs;
@@ -191,11 +194,11 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
 	total_len = len1 + len2 + 1;   // +1 for shift 0
 
 	// Allocate or reallocate memory for the array of shift counts if necessary
-	if (shift_count_array == NULL)
+	if (*shift_count_array_p == NULL)
 	{
 		shift_count_array_length = total_len;
-		shift_count_array = (int32_t*) malloc(shift_count_array_length * sizeof(int32_t));
-		if (shift_count_array == NULL)
+		*shift_count_array_p = (int32_t*) malloc(shift_count_array_length * sizeof(int32_t));
+		if (*shift_count_array_p == NULL)
 		{
 		 	obi_set_errno(OBI_MALLOC_ERROR);
 		 	obidebug(1, "\nError computing the kmer similarity between two sequences: error allocating memory");
@@ -205,8 +208,8 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
 	else if (total_len >= shift_count_array_length)
 	{
 		shift_count_array_length = total_len;
-		shift_count_array = (int32_t*) realloc(shift_count_array, shift_count_array_length * sizeof(int32_t));
-		if (shift_count_array == NULL)
+		*shift_count_array_p = (int32_t*) realloc(*shift_count_array_p, shift_count_array_length * sizeof(int32_t));
+		if (*shift_count_array_p == NULL)
 		{
 		 	obi_set_errno(OBI_MALLOC_ERROR);
 		 	obidebug(1, "\nError computing the kmer similarity between two sequences: error allocating memory");
@@ -215,11 +218,11 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
 	}
 
 	// Allocate or reallocate memory for the array of shifts if necessary
-	if (shift_array == NULL)
+	if (*shift_array_p == NULL)
 	{
 		shift_array_height = total_len;
-		shift_array = (int32_t*) malloc(ARRAY_LENGTH * shift_array_height * sizeof(int32_t));
-		if (shift_array == NULL)
+		*shift_array_p = (int32_t*) malloc(ARRAY_LENGTH * shift_array_height * sizeof(int32_t));
+		if (*shift_array_p == NULL)
 		{
 		 	obi_set_errno(OBI_MALLOC_ERROR);
 		 	obidebug(1, "\nError computing the kmer similarity between two sequences: error allocating memory");
@@ -229,8 +232,8 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
 	else if (len1 >= shift_array_height)
 	{
 		shift_array_height = total_len;
-		shift_array = (int32_t*) realloc(shift_array, ARRAY_LENGTH * shift_array_height * sizeof(int32_t));
-		if (shift_array == NULL)
+		*shift_array_p = (int32_t*) realloc(*shift_array_p, ARRAY_LENGTH * shift_array_height * sizeof(int32_t));
+		if (*shift_array_p == NULL)
 		{
 		 	obi_set_errno(OBI_MALLOC_ERROR);
 		 	obidebug(1, "\nError computing the kmer similarity between two sequences: error allocating memory");
@@ -239,11 +242,11 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
 	}
 
 	// Allocate or reallocate memory for the array of positions if necessary
-	if (kmer_pos_array == NULL)
+	if (*kmer_pos_array_p == NULL)
 	{
 		kmer_pos_array_height = len1;
-		kmer_pos_array = (int32_t*) malloc(ARRAY_LENGTH * kmer_pos_array_height * sizeof(int32_t));
-		if (kmer_pos_array == NULL)
+		*kmer_pos_array_p = (int32_t*) malloc(ARRAY_LENGTH * kmer_pos_array_height * sizeof(int32_t));
+		if (*kmer_pos_array_p == NULL)
 		{
 		 	obi_set_errno(OBI_MALLOC_ERROR);
 		 	obidebug(1, "\nError computing the kmer similarity between two sequences: error allocating memory");
@@ -253,8 +256,8 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
 	else if (len1 >= kmer_pos_array_height)
 	{
 		kmer_pos_array_height = len1;
-		kmer_pos_array = (int32_t*) realloc(kmer_pos_array, ARRAY_LENGTH * kmer_pos_array_height * sizeof(int32_t));
-		if (kmer_pos_array == NULL)
+		*kmer_pos_array_p = (int32_t*) realloc(*kmer_pos_array_p, ARRAY_LENGTH * kmer_pos_array_height * sizeof(int32_t));
+		if (*kmer_pos_array_p == NULL)
 		{
 		 	obi_set_errno(OBI_MALLOC_ERROR);
 		 	obidebug(1, "\nError computing the kmer similarity between two sequences: error allocating memory");
@@ -262,6 +265,10 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
 		}
 	}
 
+	shift_count_array = *shift_count_array_p;
+	shift_array = *shift_array_p;
+	kmer_pos_array = *kmer_pos_array_p;
+
 	// Initialize all positions to -1
 	for (i=0; i<(ARRAY_LENGTH * kmer_pos_array_height); i++)
 		kmer_pos_array[i] = -1;
diff --git a/src/kmer_similarity.h b/src/kmer_similarity.h
index 8d4cb5f..2d2b920 100755
--- a/src/kmer_similarity.h
+++ b/src/kmer_similarity.h
@@ -110,11 +110,11 @@ Obi_ali_p kmer_similarity(Obiview_p view1,
 						  OBIDMS_column_p qual_col1,
 						  OBIDMS_column_p qual_col2,
 						  uint8_t kmer_size,
-						  int32_t* kmer_pos_array,
+						  int32_t** kmer_pos_array_p,
 						  int32_t* kmer_pos_array_height_p,
-						  int32_t* shift_array,
+						  int32_t** shift_array_p,
 						  int32_t* shift_array_height_p,
-						  int32_t* shift_count_array,
+						  int32_t** shift_count_array_p,
 						  int32_t* shift_count_array_height_p,
 						  bool build_consensus);