diff --git a/bwamem.c b/bwamem.c
index b44e54e..68078d0 100644
--- a/bwamem.c
+++ b/bwamem.c
@@ -345,14 +345,18 @@ int mem_sort_and_dedup(int n, mem_alnreg_t *a)
 	return m;
 }
 
-int mem_choose_alnreg_se(const mem_opt_t *opt, int n, mem_alnreg_t *a) // IMPORTANT: must run mem_sort_and_dedup() before calling this function
+void mem_mark_primary_se(const mem_opt_t *opt, int n, mem_alnreg_t *a) // IMPORTANT: must run mem_sort_and_dedup() before calling this function
 { // similar to the loop in mem_chain_flt()
-	int i, j, m, tmp;
-	if (n <= 1) return n;
-	for (i = 0; i < n; ++i) a[i].sub = 0;
+	int i, k, tmp;
+	kvec_t(int) z;
+	if (n == 0) return;
+	kv_init(z);
+	for (i = 0; i < n; ++i) a[i].sub = a[i].is_primary = 0;
 	tmp = opt->a + opt->b > opt->q + opt->r? opt->a + opt->b : opt->q + opt->r;
-	for (i = 1, m = 1; i < n; ++i) {
-		for (j = 0; j < m; ++j) {
+	kv_push(int, z, 0);
+	for (i = 1; i < n; ++i) {
+		for (k = 0; k < z.n; ++k) {
+			int j = z.a[k];
 			int b_max = a[j].qb > a[i].qb? a[j].qb : a[i].qb;
 			int e_min = a[j].qe < a[i].qe? a[j].qe : a[i].qe;
 			if (e_min > b_max) { // have overlap
@@ -364,9 +368,10 @@ int mem_choose_alnreg_se(const mem_opt_t *opt, int n, mem_alnreg_t *a) // IMPORT
 				}
 			}
 		}
-		if (j == m) a[m++] = a[i];
+		if (k == z.n) kv_push(int, z, i);
 	}
-	return m;
+	for (k = 0; k < z.n; ++k) a[z.a[k]].is_primary = 1;
+	free(z.a);
 }
 
 /************************
@@ -601,10 +606,11 @@ void mem_sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, b
 	int k;
 	kstring_t str;
 	str.l = str.m = 0; str.s = 0;
-	a->n = mem_choose_alnreg_se(opt, a->n, a->a); // NOTE: mem_sort_and_dedup() called in worker1()
 	if (a->n > 0) {
+		mem_mark_primary_se(opt, a->n, a->a); // NOTE: mem_sort_and_dedup() called in worker1()
 		for (k = 0; k < a->n; ++k) {
 			bwahit_t h;
+			if (!a->a[k].is_primary) continue;
 			mem_alnreg2hit(&a->a[k], &h);
 			h.qual = approx_mapq_se(opt, &a->a[k]);
 			bwa_hit2sam(&str, opt->mat, opt->q, opt->r, opt->w, bns, pac, s, &h, opt->is_hard);
diff --git a/bwamem.h b/bwamem.h
index 4e2e5ce..d511254 100644
--- a/bwamem.h
+++ b/bwamem.h
@@ -34,7 +34,7 @@ typedef struct {
 typedef struct {
 	int64_t rb, re;
 	int score, qb, qe, seedcov, sub, csub; // sub: suboptimal score; csub: suboptimal inside the chain
-	int sub_n;
+	int sub_n, is_primary;
 } mem_alnreg_t;
 
 typedef struct {