diff --git a/src/ecoPrimer b/src/ecoPrimer
index c3e5c3e..96477a6 100755
Binary files a/src/ecoPrimer and b/src/ecoPrimer differ
diff --git a/src/global.mk b/src/global.mk
index 7135690..94cf61d 100644
--- a/src/global.mk
+++ b/src/global.mk
@@ -3,7 +3,7 @@ LIBPATH= -Llibapat -LlibecoPCR -Llibecoprimer
 MAKEDEPEND = gcc -D$(MACHINE) -M $(CPPFLAGS) -o $*.d $<
 
 CC=gcc
-CFLAGS= -W -Wall -O3 -m64 -fast -g
+CFLAGS= -W -Wall -O5 -m64 -fast -g
 #CFLAGS= -W -Wall -O0 -m64  -g
 #CFLAGS= -W -Wall -O5 -fast -g
 
diff --git a/src/libecoprimer/aproxpattern.c b/src/libecoprimer/aproxpattern.c
index d924281..2dc13bf 100644
--- a/src/libecoprimer/aproxpattern.c
+++ b/src/libecoprimer/aproxpattern.c
@@ -61,7 +61,7 @@ void encodeSequence(ecoseq_t *seq)
 
      for (i=0;i<seq->SQ_length;i++,data++,cseq++)
      {
-         *data = encoder[(IS_UPPER(*cseq) ? *cseq - 'A' : 'Z')];
+         *data = encoder[(IS_UPPER(*cseq) ? *cseq : 'Z') - 'A'];
      }
 }
 
@@ -82,7 +82,7 @@ pprimercount_t lookforAproxPrimer(pecodnadb_t database, uint32_t seqdbsize,uint3
 	uint32_t  inSequenceQuorum;
 	uint32_t  outSequenceQuorum;
 	bool_t    conserved = TRUE;
-	
+
 	//poslist_t ttt;
 
 
diff --git a/src/libecoprimer/pairs.c b/src/libecoprimer/pairs.c
index f01da82..0af6825 100644
--- a/src/libecoprimer/pairs.c
+++ b/src/libecoprimer/pairs.c
@@ -275,6 +275,7 @@ static void buildPrimerPairsForOneSeq(uint32_t seqid,
 	pprimer_t		   wswp;
 	bool_t			   bswp;
 	size_t			   distance;
+	bool_t             strand;
 
 	for (i=0;i < primers->size; i++)
 	{
@@ -362,7 +363,8 @@ static void buildPrimerPairsForOneSeq(uint32_t seqid,
 
 		    	   // Standardize the pair
 
-		    	   if (current.p2->word < current.p1->word)
+	    		   strand = current.p2->word > current.p1->word;
+		    	   if (!strand)
 		    	   {
 		    		   wswp = current.p1;
 		    		   current.p1=current.p2;
@@ -384,7 +386,7 @@ static void buildPrimerPairsForOneSeq(uint32_t seqid,
 		    		   pcurrent->inexample++;
 		    		   pcurrent->sumd+=distance;
 
-		    		   if (pcurrent->maxd=DMAX || distance > pcurrent->maxd)
+		    		   if ((pcurrent->maxd==DMAX) || (distance > pcurrent->maxd))
 			    		   pcurrent->maxd = distance;
 
 			    	   if (distance < pcurrent->mind)
@@ -412,10 +414,14 @@ static void buildPrimerPairsForOneSeq(uint32_t seqid,
 		    		   }
 		    	   }
 
-		    	   pcurrent->pcr.amplifias[pcr.ampcount].length=distance;
-		    	   pcurrent->pcr.amplifias[pcr.ampcount].sequence=*(seqdb[seqid]);
-		 //   	   pcurrent->pcr.amplifias[pcr.ampcount].strand=  ;
-		 //   	   pcurrent->pcr.amplifias[pcr.ampcount].amplifia=  ;
+		    	   pcurrent->pcr.amplifias[pcurrent->pcr.ampcount].length=distance;
+		    	   pcurrent->pcr.amplifias[pcurrent->pcr.ampcount].sequence=seqdb[seqid];
+		    	   pcurrent->pcr.amplifias[pcurrent->pcr.ampcount].strand=strand;
+
+		    	   if (strand)
+		    	   	   pcurrent->pcr.amplifias[pcurrent->pcr.ampcount].amplifia=  seqdb[seqid]->SQ + matches[i].position + options->primer_length;
+		    	   else
+		    	   	   pcurrent->pcr.amplifias[pcurrent->pcr.ampcount].amplifia=  seqdb[seqid]->SQ + matches[j].position - 1 ;
 
 		    	   pcurrent->pcr.ampcount++;
 
diff --git a/src/libecoprimer/pairtree.c b/src/libecoprimer/pairtree.c
index 53a38c3..d1c0895 100644
--- a/src/libecoprimer/pairtree.c
+++ b/src/libecoprimer/pairtree.c
@@ -39,6 +39,7 @@ static ppairlist_t newpairlist(ppairlist_t parent, size_t size)
 	if (parent)
 		parent->next=(void*)tmp;
 
+
 	return tmp;
 }
 
@@ -103,7 +104,7 @@ ppair_t insertpair(pair_t key,
 
 	if (list->last->paircount==list->last->pairslots)
 	{
-		list->last->next=newpairlist(list,100);
+		list->last->next=newpairlist(list->last,100);
 		list->last=list->last->next;
 	}
 
@@ -121,13 +122,13 @@ ppair_t insertpair(pair_t key,
 
 ppairtree_t initpairtree(ppairtree_t tree)
 {
-	fprintf(stderr,"coucou from initpairtree\n");
 
 	if (!tree)
 		tree = ECOMALLOC(sizeof(pairtree_t),"Cannot allocate pair tree");
 
-	tree->first=newpairlist(NULL,500);
+	tree->first=newpairlist(NULL,300);
 	tree->last=tree->first;
 
 	tree->tree=NULL;
+	return tree;
 }