diff --git a/ksw2_exts2_sse.c b/ksw2_exts2_sse.c
index cfb32a1..c16866d 100644
--- a/ksw2_exts2_sse.c
+++ b/ksw2_exts2_sse.c
@@ -191,7 +191,13 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
 		}
 	}
 
-	if (junc && !(flag & KSW_EZ_SPLICE_SCORE)) {
+	if (junc && (flag & KSW_EZ_SPLICE_SCORE)) { // junc[] keeps the donor score
+		uint8_t donor_val = !(flag & KSW_EZ_REV_CIGAR)? 0 : 1;
+		for (t = 0; t < tlen - 1; ++t)
+			((int8_t*)donor)[t]    += junc[t+1] == 0xff? -junc_pen : (junc[t+1]&1) == donor_val?  (int8_t)(junc[t+1]>>1) - (int8_t)KSW_SPSC_OFFSET : 0;
+		for (t = 0; t < tlen - 1; ++t)
+			((int8_t*)acceptor)[t] += junc[t+1] == 0xff? -junc_pen : (junc[t+1]&1) == !donor_val? (int8_t)(junc[t+1]>>1) - (int8_t)KSW_SPSC_OFFSET : 0;
+	} else if (junc) { // junc[] keeps the splice sites
 		if (!(flag & KSW_EZ_REV_CIGAR)) {
 			for (t = 0; t < tlen - 1; ++t)
 				if (((flag & KSW_EZ_SPLICE_FOR) && (junc[t+1]&1)) || ((flag & KSW_EZ_SPLICE_REV) && (junc[t+1]&8)))
@@ -207,10 +213,6 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
 				if (((flag & KSW_EZ_SPLICE_FOR) && (junc[t]&1)) || ((flag & KSW_EZ_SPLICE_REV) && (junc[t]&8)))
 					((int8_t*)acceptor)[t] += junc_bonus;
 		}
-	} else if (junc) {
-		if (!(flag & KSW_EZ_REV_CIGAR)) {
-		} else {
-		}
 	}
 
 	for (r = 0, last_st = last_en = -1; r < qlen + tlen - 1; ++r) {