diff --git a/ksw2_ll_sse.c b/ksw2_ll_sse.c
index 14b9b50..4acd0f0 100644
--- a/ksw2_ll_sse.c
+++ b/ksw2_ll_sse.c
@@ -67,7 +67,7 @@ void *ksw_ll_qinit(void *km, int size, int qlen, const uint8_t *query, int m, co
 			const int8_t *ma = mat + a * m;
 			for (i = 0; i < slen; ++i)
 				for (k = i; k < nlen; k += slen) // p iterations
-					*t++ = (k >= qlen? 0 : ma[query[k]]) + q->shift;
+					*t++ = (k >= qlen? -1 : ma[query[k]]) + q->shift;
 		}
 	} else {
 		int16_t *t = (int16_t*)q->qp;
@@ -76,7 +76,7 @@ void *ksw_ll_qinit(void *km, int size, int qlen, const uint8_t *query, int m, co
 			const int8_t *ma = mat + a * m;
 			for (i = 0; i < slen; ++i)
 				for (k = i; k < nlen; k += slen) // p iterations
-					*t++ = (k >= qlen? 0 : ma[query[k]]);
+					*t++ = (k >= qlen? -1 : ma[query[k]]);
 		}
 	}
 	return q;
diff --git a/minimap.h b/minimap.h
index 92f5673..ee92aec 100644
--- a/minimap.h
+++ b/minimap.h
@@ -5,7 +5,7 @@
 #include <stdio.h>
 #include <sys/types.h>
 
-#define MM_VERSION "2.30-r1290-dirty"
+#define MM_VERSION "2.30-r1298-dirty"
 
 #define MM_F_NO_DIAG       (0x001LL) // no exact diagonal hit
 #define MM_F_NO_DUAL       (0x002LL) // skip pairs where query name is lexicographically larger than target name