diff --git a/align.c b/align.c
index 8f062bb..496829a 100644
--- a/align.c
+++ b/align.c
@@ -2,31 +2,60 @@
 #include "minimap.h"
 #include "ksw2.h"
 
-static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, uint8_t *qseq0[2], mm_reg1_t *r, mm_reg1_t *r_split, mm128_t *a)
+static inline void mm_seq_rev(uint32_t len, uint8_t *seq)
+{
+	uint32_t i;
+	uint8_t t;
+	for (i = 0; i < len>>1; ++i)
+		t = seq[i], seq[i] = seq[len - 1 - i], seq[len - 1 - i] = t;
+}
+
+static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, uint8_t *qseq0[2], mm_reg1_t *r, mm_reg1_t *r2, mm128_t *a)
 {
 	int32_t rid = a[r->as].x<<1>>33, rev = a[r->as].x>>63;
-	uint8_t *tseq0, *tseq, *qseq;
-	int32_t i, l, rs0, re0;
+	uint8_t *tseq, *qseq;
+	int32_t i, k, l, rs0, re0, qs0, qe0;
 	int32_t rs, re, qs, qe, ret;
+	mm_reg1_t r1;
 
-	l = r->qs < opt->max_gap? r->qs : opt->max_gap;
-	l = (l * opt->a - opt->q) / opt->e;
-	l = l < opt->max_gap? l : opt->max_gap;
-	l = l < r->rs? l : r->rs;
-	rs0 = r->rs - l;
+	rs = (int32_t)a[r->as].x + 1; // NB: this is the same as r->{rs,re}
+	re = (int32_t)a[r->as + r->cnt - 1].x + 1;
+	qs = (int32_t)a[r->as].y + 1; // NB: this is the coordinate on the reverse strand; r->{qs,qe} are on the reverse strand
+	qe = (int32_t)a[r->as + r->cnt - 1].y + 1;
 
-	l = qlen - r->re < opt->max_gap? qlen - r->re : opt->max_gap;
-	l = (l * opt->a - opt->q) / opt->e;
-	l = l < opt->max_gap? l : opt->max_gap;
-	l = l < mi->seq[rid].len - r->re? l : mi->seq[rid].len - r->re;
-	re0 = r->re + l;
+	if (qs > 0 && rs > 0) {
+		l = qs < opt->max_gap? qs : opt->max_gap;
+		qs0 = qs - l;
+		l = (l * opt->a - opt->q) / opt->e;
+		l = l < opt->max_gap? l : opt->max_gap;
+		l = l < rs? l : rs;
+		rs0 = rs - l;
+	} else rs0 = rs, qs0 = qs;
 
-	tseq0 = (uint8_t*)kmalloc(km, re0 - rs0);
-	ret = mm_idx_getseq(mi, rid, rs0, re0, tseq0);
-	assert(ret > 0);
+	if (qe < qlen && re < mi->seq[rid].len) {
+		l = qlen - re < opt->max_gap? qlen - re : opt->max_gap;
+		qe0 = qe + l;
+		l = (l * opt->a - opt->q) / opt->e;
+		l = l < opt->max_gap? l : opt->max_gap;
+		l = l < mi->seq[rid].len - re? l : mi->seq[rid].len - re;
+		re0 = re + l;
+	} else re0 = re, qe0 = qe;
 
-	rs = (int32_t)a[r->as].x + 1;
-	qs = (int32_t)a[r->as].y + 1;
+	tseq = (uint8_t*)kmalloc(km, re0 - rs0);
+
+	if (qs > 0 && rs > 0) { // left extension
+		uint32_t ql = qs - qs0, tl = rs - rs0;
+		qseq = &qseq0[rev][qs0];
+		ret = mm_idx_getseq(mi, rid, rs0, rs, tseq);
+		assert(ret > 0);
+		mm_seq_rev(ql, qseq);
+		mm_seq_rev(tl, tseq);
+		fprintf(stderr, "===> [-1] %d-%d %c (%s:%d-%d) <===\n", qs0, qs, "+-"[rev], mi->seq[rid].name, rs0, rs);
+		for (k = 0; k < tl; ++k) fputc("ACGTN"[tseq[k]], stderr); fputc('\n', stderr);
+		for (k = 0; k < ql; ++k) fputc("ACGTN"[qseq[k]], stderr); fputc('\n', stderr);
+		mm_seq_rev(ql, qseq);
+	}
+/*
 	for (i = 1; i < r->cnt; ++i) {
 		re = (int32_t)a[r->as + i].x + 1;
 		qe = (int32_t)a[r->as + i].y + 1;
@@ -41,7 +70,8 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
 			rs = re, qs = qe;
 		}
 	}
-	kfree(km, tseq0);
+*/
+	kfree(km, tseq);
 }
 
 void mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, const char *qstr, int n_regs, mm_reg1_t *regs, mm128_t *a)
@@ -58,8 +88,8 @@ void mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
 	}
 
 	for (reg = 0; reg < n_regs; ++reg) {
-		mm_reg1_t r_split;
-		mm_align1(km, opt, mi, qlen, qseq0, &regs[reg], &r_split, a);
+		mm_reg1_t r2;
+		mm_align1(km, opt, mi, qlen, qseq0, &regs[reg], &r2, a);
 	}
 
 	kfree(km, qseq0[0]); kfree(km, qseq0[1]);
diff --git a/minimap.h b/minimap.h
index 79ef7c5..807ce9e 100644
--- a/minimap.h
+++ b/minimap.h
@@ -41,6 +41,11 @@ typedef struct {
 	mm_idx_bucket_t *B; // index
 } mm_idx_t;
 
+typedef struct {
+	uint32_t n_cigar, m_cigar;
+	uint32_t cigar[];
+} mm_cigar_t;
+
 typedef struct {
 	uint32_t cnt:31, rev:1;
 	uint32_t rid:31, rep:1;
@@ -48,6 +53,7 @@ typedef struct {
 	int32_t qs, qe, rs, re;
 	int32_t parent, subsc;
 	int32_t as;
+	mm_cigar_t *cigar;
 } mm_reg1_t;
 
 typedef struct {