diff --git a/align.c b/align.c
index 9586dd8..5981e13 100644
--- a/align.c
+++ b/align.c
@@ -343,7 +343,7 @@ static void mm_align_pair(void *km, const mm_mapopt_t *opt, int qlen, const uint
 	} else if (opt->flag & MM_F_SPLICE) {
 		int flag_tmp = flag;
 		if (!(opt->flag & MM_F_SPLICE_OLD)) flag_tmp |= KSW_EZ_SPLICE_CMPLX;
-		ksw_exts2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, opt->q2, opt->noncan, zdrop, opt->junc_bonus, flag_tmp, junc, ez);
+		ksw_exts2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, opt->q2, opt->noncan, zdrop, opt->junc_bonus, opt->junc_pen, flag_tmp, junc, ez);
 	} else if (opt->q == opt->q2 && opt->e == opt->e2)
 		ksw_extz2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, w, zdrop, end_bonus, flag, ez);
 	else
diff --git a/ksw2.h b/ksw2.h
index 296030b..71c6aad 100644
--- a/ksw2.h
+++ b/ksw2.h
@@ -71,7 +71,7 @@ void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
 				   int8_t gapo, int8_t gape, int8_t gapo2, int8_t gape2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez);
 
 void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
-				   int8_t gapo, int8_t gape, int8_t gapo2, int8_t noncan, int zdrop, int8_t junc_bonus, int flag, const uint8_t *junc, ksw_extz_t *ez);
+				   int8_t gapo, int8_t gape, int8_t gapo2, int8_t noncan, int zdrop, int8_t junc_bonus, int8_t junc_pen, int flag, const uint8_t *junc, ksw_extz_t *ez);
 
 void ksw_extf2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t mch, int8_t mis, int8_t e, int w, int xdrop, ksw_extz_t *ez);
 
diff --git a/ksw2_dispatch.c b/ksw2_dispatch.c
index 792b267..6083214 100644
--- a/ksw2_dispatch.c
+++ b/ksw2_dispatch.c
@@ -80,17 +80,17 @@ void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
 }
 
 void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
-				   int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int8_t junc_bonus, int flag, const uint8_t *junc, ksw_extz_t *ez)
+				   int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int8_t junc_bonus, int8_t junc_pen, int flag, const uint8_t *junc, ksw_extz_t *ez)
 {
 	extern void ksw_exts2_sse2(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
-				   int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int8_t junc_bonus, int flag, const uint8_t *junc, ksw_extz_t *ez);
+				   int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int8_t junc_bonus, int8_t junc_pen, int flag, const uint8_t *junc, ksw_extz_t *ez);
 	extern void ksw_exts2_sse41(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
-				   int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int8_t junc_bonus, int flag, const uint8_t *junc, ksw_extz_t *ez);
+				   int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int8_t junc_bonus, int8_t junc_pen, int flag, const uint8_t *junc, ksw_extz_t *ez);
 	if (ksw_simd < 0) ksw_simd = x86_simd();
 	if (ksw_simd & SIMD_SSE4_1)
-		ksw_exts2_sse41(km, qlen, query, tlen, target, m, mat, q, e, q2, noncan, zdrop, junc_bonus, flag, junc, ez);
+		ksw_exts2_sse41(km, qlen, query, tlen, target, m, mat, q, e, q2, noncan, zdrop, junc_bonus, junc_pen, flag, junc, ez);
 	else if (ksw_simd & SIMD_SSE2)
-		ksw_exts2_sse2(km, qlen, query, tlen, target, m, mat, q, e, q2, noncan, zdrop, junc_bonus, flag, junc, ez);
+		ksw_exts2_sse2(km, qlen, query, tlen, target, m, mat, q, e, q2, noncan, zdrop, junc_bonus, junc_pen, flag, junc, ez);
 	else abort();
 }
 #endif
diff --git a/ksw2_exts2_sse.c b/ksw2_exts2_sse.c
index 746778e..590742e 100644
--- a/ksw2_exts2_sse.c
+++ b/ksw2_exts2_sse.c
@@ -24,14 +24,14 @@
 #ifdef KSW_CPU_DISPATCH
 #ifdef __SSE4_1__
 void ksw_exts2_sse41(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
-				   int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int8_t junc_bonus, int flag, const uint8_t *junc, ksw_extz_t *ez)
+				   int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int8_t junc_bonus, int8_t junc_pen, int flag, const uint8_t *junc, ksw_extz_t *ez)
 #else
 void ksw_exts2_sse2(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
-				   int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int8_t junc_bonus, int flag, const uint8_t *junc, ksw_extz_t *ez)
+				   int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int8_t junc_bonus, int8_t junc_pen, int flag, const uint8_t *junc, ksw_extz_t *ez)
 #endif
 #else
 void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
-				   int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int8_t junc_bonus, int flag, const uint8_t *junc, ksw_extz_t *ez)
+				   int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int8_t junc_bonus, int8_t junc_pen, int flag, const uint8_t *junc, ksw_extz_t *ez)
 #endif // ~KSW_CPU_DISPATCH
 {
 #define __dp_code_block1 \
diff --git a/main.c b/main.c
index 004d0ba..beee9ff 100644
--- a/main.c
+++ b/main.c
@@ -80,6 +80,8 @@ static ko_longopt_t long_options[] = {
 	{ "ds",             ko_no_argument,       355 },
 	{ "rmq-inner",      ko_required_argument, 356 },
 	{ "spsc",           ko_required_argument, 357 },
+	{ "spsc0",          ko_required_argument, 358 },
+	{ "junc-pen",       ko_required_argument, 358 }, // an alias to --spsc0; this is not a typo
 	{ "dbg-seed-occ",   ko_no_argument,       501 },
 	{ "help",           ko_no_argument,       'h' },
 	{ "max-intron-len", ko_required_argument, 'G' },
@@ -235,6 +237,7 @@ int main(int argc, char *argv[])
 		else if (c == 338) opt.max_qlen = mm_parse_num(o.arg); // --max-qlen
 		else if (c == 340) junc_bed = o.arg; // --junc-bed
 		else if (c == 341) opt.junc_bonus = atoi(o.arg); // --junc-bonus
+		else if (c == 358) opt.junc_pen = atoi(o.arg); // --junc-pen
 		else if (c == 342) opt.flag |= MM_F_SAM_HIT_ONLY; // --sam-hit-only
 		else if (c == 343) opt.chain_gap_scale = atof(o.arg); // --chain-gap-scale
 		else if (c == 351) opt.chain_skip_scale = atof(o.arg); // --chain-skip-scale
diff --git a/minimap.h b/minimap.h
index aec09e6..8b4a7a7 100644
--- a/minimap.h
+++ b/minimap.h
@@ -159,7 +159,7 @@ typedef struct {
 	int transition; // transition mismatch score (A:G, C:T)
 	int sc_ambi; // score when one or both bases are "N"
 	int noncan;      // cost of non-canonical splicing sites
-	int junc_bonus;
+	int junc_bonus, junc_pen;
 	int zdrop, zdrop_inv;   // break alignment if alignment score drops too fast along the diagonal
 	int end_bonus;
 	int min_dp_max;  // drop an alignment if the score of the max scoring segment is below this threshold
diff --git a/options.c b/options.c
index 1689471..3d5f9a0 100644
--- a/options.c
+++ b/options.c
@@ -172,6 +172,7 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
 		mo->a = 1, mo->b = 2, mo->q = 2, mo->e = 1, mo->q2 = 32, mo->e2 = 0;
 		mo->noncan = 9;
 		mo->junc_bonus = 9;
+		mo->junc_pen = 5;
 		mo->zdrop = 200, mo->zdrop_inv = 100; // because mo->a is halved
 		if (strcmp(preset, "splice:hq") == 0)
 			mo->noncan = 5, mo->b = 4, mo->q = 6, mo->q2 = 24;