diff --git a/align.c b/align.c
index 10fe689..73890da 100644
--- a/align.c
+++ b/align.c
@@ -381,6 +381,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
 	if (is_splice) {
 		if (splice_flag & MM_F_SPLICE_FOR) extra_flag |= rev? KSW_EZ_SPLICE_REV : KSW_EZ_SPLICE_FOR;
 		if (splice_flag & MM_F_SPLICE_REV) extra_flag |= rev? KSW_EZ_SPLICE_FOR : KSW_EZ_SPLICE_REV;
+		if (opt->flag & MM_F_SPLICE_FLANK) extra_flag |= KSW_EZ_SPLICE_FLANK;
 	}
 
 	/* Look for the start and end of regions to perform DP. This sounds easy
diff --git a/ksw2.h b/ksw2.h
index e82dd82..dcea9f8 100644
--- a/ksw2.h
+++ b/ksw2.h
@@ -14,6 +14,7 @@
 #define KSW_EZ_REV_CIGAR   0x80 // reverse CIGAR in the output
 #define KSW_EZ_SPLICE_FOR  0x100
 #define KSW_EZ_SPLICE_REV  0x200
+#define KSW_EZ_SPLICE_FLANK 0x400
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/ksw2_exts2_sse.c b/ksw2_exts2_sse.c
index 82a0369..83a4fe5 100644
--- a/ksw2_exts2_sse.c
+++ b/ksw2_exts2_sse.c
@@ -111,19 +111,23 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
 
 	// set the donor and acceptor arrays. TODO: this assumes 0/1/2/3 encoding!
 	if (flag & (KSW_EZ_SPLICE_FOR|KSW_EZ_SPLICE_REV)) {
+		int semi_cost = flag&KSW_EZ_SPLICE_FLANK? -noncan/2 : 0; // GTr or yAG is worth 0.5 bit; see PMID:18688272
 		memset(donor, -noncan, tlen_ * 16);
-		for (t = 0; t < tlen - 2; ++t) {
-			int is_can = 0; // is a canonical site
-			if ((flag & KSW_EZ_SPLICE_FOR) && target[t+1] == 2 && target[t+2] == 3) is_can = 1;
-			if ((flag & KSW_EZ_SPLICE_REV) && target[t+1] == 1 && target[t+2] == 3) is_can = 1;
-			if (is_can) ((int8_t*)donor)[t] = 0;
+		for (t = 0; t < tlen - 4; ++t) {
+			int can_type = 0; // type of canonical site: 0=none, 1=GT/AG only, 2=GTr/yAG
+			if ((flag & KSW_EZ_SPLICE_FOR) && target[t+1] == 2 && target[t+2] == 3) can_type = 1; // GTr...
+			if ((flag & KSW_EZ_SPLICE_REV) && target[t+1] == 1 && target[t+2] == 3) can_type = 1; // CTr...
+			if (can_type && (target[t+3] == 0 || target[t+3] == 2)) can_type = 2;
+			if (can_type) ((int8_t*)donor)[t] = can_type == 2? 0 : semi_cost;
+			if (can_type) ((int8_t*)donor)[t] = 0;
 		}
 		memset(acceptor, -noncan, tlen_ * 16);
 		for (t = 2; t < tlen; ++t) {
-			int is_can = 0;
-			if ((flag & KSW_EZ_SPLICE_FOR) && target[t-1] == 0 && target[t] == 2) is_can = 1;
-			if ((flag & KSW_EZ_SPLICE_REV) && target[t-1] == 0 && target[t] == 1) is_can = 1;
-			if (is_can) ((int8_t*)acceptor)[t] = 0;
+			int can_type = 0;
+			if ((flag & KSW_EZ_SPLICE_FOR) && target[t-1] == 0 && target[t] == 2) can_type = 1; // ...yAG
+			if ((flag & KSW_EZ_SPLICE_REV) && target[t-1] == 0 && target[t] == 1) can_type = 1; // ...yAC
+			if (can_type && (target[t-2] == 1 || target[t-2] == 3)) can_type = 2;
+			if (can_type) ((int8_t*)acceptor)[t] = can_type == 2? 0 : semi_cost;
 		}
 	}
 
diff --git a/main.c b/main.c
index 63cbb2c..b9e0add 100644
--- a/main.c
+++ b/main.c
@@ -6,7 +6,7 @@
 #include "mmpriv.h"
 #include "getopt.h"
 
-#define MM_VERSION "2.3-r536-dirty"
+#define MM_VERSION "2.3-r537-dirty"
 
 #ifdef __linux__
 #include <sys/resource.h>
@@ -34,7 +34,7 @@ static struct option long_options[] = {
 	{ "min-dp-len",     required_argument, 0, 0 },
 	{ "print-aln-seq",  no_argument,       0, 0 },
 	{ "splice",         no_argument,       0, 0 },
-	{ "cost-non-gt-ag", required_argument, 0, 0 },
+	{ "cost-non-gt-ag", required_argument, 0, 'C' },
 	{ "no-long-join",   no_argument,       0, 0 },
 	{ "sr",             no_argument,       0, 0 },
 	{ "frag",           optional_argument, 0, 0 },
@@ -42,6 +42,7 @@ static struct option long_options[] = {
 	{ "cs",             optional_argument, 0, 0 },
 	{ "end-bonus",      required_argument, 0, 0 },
 	{ "no-pairing",     no_argument,       0, 0 },
+	{ "splice-flank",   optional_argument, 0, 0 },
 	{ "help",           no_argument,       0, 'h' },
 	{ "max-intron-len", required_argument, 0, 'G' },
 	{ "version",        no_argument,       0, 'V' },
@@ -66,7 +67,7 @@ static inline int64_t mm_parse_num(const char *str)
 
 int main(int argc, char *argv[])
 {
-	const char *opt_str = "2aSw:k:K:t:r:f:Vv:g:G:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Qu:R:hF:i:L";
+	const char *opt_str = "2aSw:k:K:t:r:f:Vv:g:G:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Qu:R:hF:i:LC:";
 	mm_mapopt_t opt;
 	mm_idxopt_t ipt;
 	int i, c, n_threads = 3, long_idx;
@@ -117,6 +118,7 @@ int main(int argc, char *argv[])
 		else if (c == 'B') opt.b = atoi(optarg);
 		else if (c == 'z') opt.zdrop = atoi(optarg);
 		else if (c == 's') opt.min_dp_max = atoi(optarg);
+		else if (c == 'C') opt.noncan = atoi(optarg);
 		else if (c == 'I') ipt.batch_size = mm_parse_num(optarg);
 		else if (c == 'K') opt.mini_batch_size = (int)mm_parse_num(optarg);
 		else if (c == 'R') rg = optarg;
@@ -132,7 +134,6 @@ int main(int argc, char *argv[])
 		else if (c == 0 && long_idx == 8) opt.min_ksw_len = atoi(optarg); // --min-dp-len
 		else if (c == 0 && long_idx == 9) mm_dbg_flag |= MM_DBG_PRINT_QNAME | MM_DBG_PRINT_ALN_SEQ; // --print-aln-seq
 		else if (c == 0 && long_idx ==10) opt.flag |= MM_F_SPLICE; // --splice
-		else if (c == 0 && long_idx ==11) opt.noncan = atoi(optarg); // --cost-non-gt-ag
 		else if (c == 0 && long_idx ==12) opt.flag |= MM_F_NO_LJOIN; // --no-long-join
 		else if (c == 0 && long_idx ==13) opt.flag |= MM_F_SR; // --sr
 		else if (c == 0 && long_idx ==17) opt.end_bonus = atoi(optarg); // --end-bonus
@@ -156,6 +157,10 @@ int main(int argc, char *argv[])
 			} else if (mm_verbose >= 2) {
 				fprintf(stderr, "[WARNING]\033[1;31m --cs only takes 'short' or 'long'. Invalid values are assumed to be 'short'.\033[0m\n");
 			}
+		} else if (c == 0 && long_idx == 19) { // --splice-flank
+			if (optarg == 0 || strcmp(optarg, "yes") == 0 || strcmp(optarg, "y") == 0)
+				opt.flag |= MM_F_SPLICE_FLANK;
+			else opt.flag &= ~MM_F_SPLICE_FLANK;
 		} else if (c == 'S') {
 			opt.flag |= MM_F_OUT_CS | MM_F_CIGAR | MM_F_OUT_CS_LONG;
 			if (mm_verbose >= 2)
diff --git a/map.c b/map.c
index a31bceb..f99626d 100644
--- a/map.c
+++ b/map.c
@@ -108,7 +108,7 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
 		mo->flag |= MM_F_SPLICE | MM_F_SPLICE_FOR | MM_F_SPLICE_REV;
 		mo->max_gap = 2000, mo->max_gap_ref = mo->bw = 200000;
 		mo->a = 1, mo->b = 2, mo->q = 2, mo->e = 1, mo->q2 = 32, mo->e2 = 0;
-		mo->noncan = 5;
+		mo->noncan = 9;
 		mo->zdrop = 200;
 	} else return -1;
 	return 0;
diff --git a/minimap.h b/minimap.h
index 058c1e3..17e411c 100644
--- a/minimap.h
+++ b/minimap.h
@@ -23,6 +23,7 @@
 #define MM_F_2_IO_THREADS  0x8000
 #define MM_F_LONG_CIGAR    0x10000
 #define MM_F_INDEPEND_SEG  0x20000
+#define MM_F_SPLICE_FLANK  0x40000
 
 #define MM_IDX_MAGIC   "MMI\2"
 
diff --git a/minimap2.1 b/minimap2.1
index 0064d77..b7d7177 100644
--- a/minimap2.1
+++ b/minimap2.1
@@ -1,4 +1,4 @@
-.TH minimap2 1 "22 October 2017" "minimap2-2.2-dirty (r531)" "Bioinformatics tools"
+.TH minimap2 1 "27 October 2017" "minimap2-2.3-dirty (r537)" "Bioinformatics tools"
 .SH NAME
 .PP
 minimap2 - mapping and alignment between collections of DNA sequences
@@ -219,6 +219,9 @@ costs
 .RI min{ O1 + k * E1 , O2 + k * E2 }.
 In the splice mode, the second gap penalties are not used.
 .TP
+.BI -C \ INT
+Cost for a non-canonical GT-AG splicing [0]
+.TP
 .BI -z \ INT
 Break an alignment if the running score drops too quickly along the diagonal of
 the DP matrix (diagonal X-drop, or Z-drop) [400]. Increasing the value improves
@@ -239,9 +242,6 @@ both strands;
 .BR n :
 no attempt to match GT-AG [n]
 .TP
-.BI --cost-non-gt-ag \ INT
-Cost of non-canonical splicing sites [0].
-.TP
 .BI --end-bonus \ INT
 Score bonus when alignment extends to the end of the query sequence [10].
 .SS Input/output options
@@ -371,8 +371,8 @@ is that this preset is not using HPC minimizers.
 .B splice
 Long-read spliced alignment
 .RB ( -k15
-.B -w5 --splice -g2000 -G200k -A1 -B2 -O2,32 -E1,0 -z200 -ub --cost-non-gt-ag
-.BR 5 ).
+.B -w5 --splice -g2000 -G200k -A1 -B2 -O2,32 -E1,0 -C9 -z200
+.BR -ub ).
 In the splice mode, 1) long deletions are taken as introns and represented as
 the
 .RB ` N '