diff --git a/align.c b/align.c
index fb2ebaf..d8bd519 100644
--- a/align.c
+++ b/align.c
@@ -253,16 +253,20 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
 	for (i = 1; i < cnt1; ++i) { // gap filling
 		int gap, to_patch = 0;
 		mm_adjust_minier(mi, qseq0, &a[as1 + i], &re, &qe);
-		gap = (qe - qs) - (re - rs);
-		if (gap < -40 || gap > 40) {
-			int g, j, i_next = -1;
-			for (j = i + 1; j < cnt1; ++j) {
-				if ((int32_t)a[as1 + j].y - qs > opt->max_gap || (int32_t)a[as1 + j].x - rs > opt->max_gap) break;
-				g = ((int32_t)a[as1 + j].y - (int32_t)a[as1 + j - 1].y) - (a[as1 + j].x - a[as1 + j - 1].x);
-				if (abs(gap + g) < 0.5f * abs(gap - g)) {
-					i_next = j;
-					break;
-				}
+		gap = ((int32_t)a[as1 + i].y - (int32_t)a[as1 + i - 1].y) - (a[as1 + i].x - a[as1 + i - 1].x);
+		if (gap < -20 || gap > 20) {
+			int i_next = -1, j, n_ins = 0, n_del = 0, diff, max_diff = 0;
+			if (gap < 0) n_del += -gap;
+			else n_ins += gap;
+			for (j = i + 1; j < cnt1 && j - i < 20; ++j) {
+				if ((int32_t)a[as1 + j].y - qs > opt->max_gap>>1 || (int32_t)a[as1 + j].x - rs > opt->max_gap>>1) break;
+				gap = ((int32_t)a[as1 + j].y - (int32_t)a[as1 + j - 1].y) - (a[as1 + j].x - a[as1 + j - 1].x);
+				if (gap < 0) n_del += -gap;
+				else n_ins += gap;
+				diff = n_ins + n_del - abs(n_ins - n_del);
+				if (diff >= 40) {
+					if (diff >= max_diff) max_diff = diff, i_next = j;
+				} else if (i_next > i) break;
 			}
 			if (i_next > i) {
 				i = i_next, to_patch = 1;
diff --git a/main.c b/main.c
index 3f88322..f1fce53 100644
--- a/main.c
+++ b/main.c
@@ -8,7 +8,7 @@
 #include "minimap.h"
 #include "mmpriv.h"
 
-#define MM_VERSION "2.0-r211-dirty"
+#define MM_VERSION "2.0-r212-dirty"
 
 void liftrlimit()
 {
diff --git a/map.c b/map.c
index 94320ab..6a7d373 100644
--- a/map.c
+++ b/map.c
@@ -237,11 +237,19 @@ mm_reg1_t *mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b,
 
 	if (mm_dbg_flag & MM_DBG_PRINT_SEED)
 		for (i = 0; i < n_a; ++i)
-			fprintf(stderr, "SD\t%s\t%d\t%c\t%d\t%d\n", mi->seq[a[i].x<<1>>33].name, (int32_t)a[i].x, "+-"[a[i].x>>63], (int32_t)a[i].y, (int32_t)(a[i].y>>32&0xff));
+			fprintf(stderr, "SD\t%s\t%d\t%c\t%d\t%d\t%d\n", mi->seq[a[i].x<<1>>33].name, (int32_t)a[i].x, "+-"[a[i].x>>63], (int32_t)a[i].y, (int32_t)(a[i].y>>32&0xff),
+					i == 0? 0 : ((int32_t)a[i].y - (int32_t)a[i-1].y) - ((int32_t)a[i].x - (int32_t)a[i-1].x));
 
 	n_u = mm_chain_dp(opt->max_gap, opt->bw, opt->max_chain_skip, opt->min_cnt, opt->min_chain_score, n_a, a, &u, b->km);
 	regs = mm_gen_regs(b->km, qlen, n_u, u, a);
 	*n_regs = n_u;
+
+	if (mm_dbg_flag & MM_DBG_PRINT_SEED)
+		for (j = 0; j < n_u; ++j)
+			for (i = regs[j].as; i < regs[j].as + regs[j].cnt; ++i)
+				fprintf(stderr, "CN\t%d\t%s\t%d\t%c\t%d\t%d\t%d\n", j, mi->seq[a[i].x<<1>>33].name, (int32_t)a[i].x, "+-"[a[i].x>>63], (int32_t)a[i].y, (int32_t)(a[i].y>>32&0xff),
+						i == regs[j].as? 0 : ((int32_t)a[i].y - (int32_t)a[i-1].y) - ((int32_t)a[i].x - (int32_t)a[i-1].x));
+
 	if (!(opt->flag & MM_F_AVA)) { // don't choose primary mapping(s) for read overlap
 		mm_set_parent(b->km, opt->mask_level, *n_regs, regs);
 		mm_select_sub(b->km, opt->mask_level, opt->pri_ratio, mi->k*2, opt->best_n, n_regs, regs);