diff --git a/align.c b/align.c
index 70c69a3..8f062bb 100644
--- a/align.c
+++ b/align.c
@@ -2,10 +2,52 @@
 #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)
+{
+	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;
+	int32_t rs, re, qs, qe, ret;
+
+	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;
+
+	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;
+
+	tseq0 = (uint8_t*)kmalloc(km, re0 - rs0);
+	ret = mm_idx_getseq(mi, rid, rs0, re0, tseq0);
+	assert(ret > 0);
+
+	rs = (int32_t)a[r->as].x + 1;
+	qs = (int32_t)a[r->as].y + 1;
+	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;
+		if (i == r->cnt - 1 || qe - qs >= opt->min_ksw_len || re - rs >= opt->min_ksw_len) {
+			qseq = &qseq0[rev][qs];
+			tseq = &tseq0[rs - rs0];
+			#if 0
+			fprintf(stderr, "===> [%d] %d-%d %c (%s:%d-%d) <===\n", i, qs, qe, "+-"[rev], mi->seq[rid].name, rs, re);
+			for (k = 0; k < re - rs; ++k) fputc("ACGTN"[tseq[k]], stderr); fputc('\n', stderr);
+			for (k = 0; k < qe - qs; ++k) fputc("ACGTN"[qseq[k]], stderr); fputc('\n', stderr);
+			#endif
+			rs = re, qs = qe;
+		}
+	}
+	kfree(km, tseq0);
+}
+
 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)
 {
 	extern unsigned char seq_nt4_table[256];
-	int i, k, reg;
+	int i, reg;
 	uint8_t *qseq0[2];
 
 	qseq0[0] = (uint8_t*)kmalloc(km, qlen);
@@ -16,28 +58,8 @@ 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 = &regs[reg];
-		int32_t rid = a[r->as].x<<1>>33, rev = a[r->as].x>>63;
-		uint8_t *tseq0, *tseq, *qseq;
-		int32_t rs, re, qs, qe, ret;
-		tseq0 = (uint8_t*)kmalloc(km, r->re - r->rs);
-		ret = mm_idx_getseq(mi, rid, r->rs, r->re, tseq0);
-		assert(ret > 0);
-		rs = (int32_t)a[r->as].x + 1;
-		qs = (int32_t)a[r->as].y + 1;
-		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;
-			if (qe - qs >= opt->min_ksw_len || re - rs >= opt->min_ksw_len) {
-				qseq = &qseq0[rev][qs];
-				tseq = &tseq0[rs - r->rs];
-				fprintf(stderr, "===> [%d,%d] %d-%d %c (%s:%d-%d) <===\n", reg, i, qs, qe, "+-"[rev], mi->seq[rid].name, rs, re);
-				for (k = 0; k < re - rs; ++k) fputc("ACGTN"[tseq[k]], stderr); fputc('\n', stderr);
-				for (k = 0; k < qe - qs; ++k) fputc("ACGTN"[qseq[k]], stderr); fputc('\n', stderr);
-				rs = re, qs = qe;
-			}
-		}
-		kfree(km, tseq0);
+		mm_reg1_t r_split;
+		mm_align1(km, opt, mi, qlen, qseq0, &regs[reg], &r_split, a);
 	}
 
 	kfree(km, qseq0[0]); kfree(km, qseq0[1]);
diff --git a/map.c b/map.c
index 795e175..e86143c 100644
--- a/map.c
+++ b/map.c
@@ -24,6 +24,7 @@ void mm_mapopt_init(mm_mapopt_t *opt)
 	opt->mask_level = 0.5f;
 
 	opt->a = 1, opt->b = 1, opt->q = 1, opt->e = 1;
+	opt->zdrop = 100;
 	opt->min_ksw_len = 100;
 }
 
diff --git a/minimap.h b/minimap.h
index 33c6128..79ef7c5 100644
--- a/minimap.h
+++ b/minimap.h
@@ -62,6 +62,7 @@ typedef struct {
 	float pri_ratio;
 	float mask_level;
 	int a, b, q, e; // matching score, mismatch, gap-open and gap-ext penalties
+	int zdrop;
 
 	int max_occ;
 	int mid_occ;