diff --git a/bwamem_pair.c b/bwamem_pair.c
index 27973ca..a3aeb80 100644
--- a/bwamem_pair.c
+++ b/bwamem_pair.c
@@ -123,7 +123,7 @@ int mem_matesw(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
 	if (skip[0] + skip[1] + skip[2] + skip[3] == 4) return 0; // consistent pair exist; no need to perform SW
 	for (r = 0; r < 4; ++r) {
 		int is_rev, is_larger;
-		uint8_t *seq, *rev = 0, *ref;
+		uint8_t *seq, *rev = 0, *ref = 0;
 		int64_t rb, re;
 		if (skip[r]) continue;
 		is_rev = (r>>1 != (r&1)); // whether to reverse complement the mate
@@ -142,8 +142,8 @@ int mem_matesw(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
 		}
 		if (rb < 0) rb = 0;
 		if (re > l_pac<<1) re = l_pac<<1;
-		ref = bns_fetch_seq(bns, pac, &rb, (rb+re)>>1, &re, &rid);
-		if (a->rid == rid) { // no funny things happening
+		if (rb < re) ref = bns_fetch_seq(bns, pac, &rb, (rb+re)>>1, &re, &rid);
+		if (a->rid == rid && re - rb >= opt->min_seed_len) { // no funny things happening
 			kswr_t aln;
 			mem_alnreg_t b;
 			int tmp, xtra = KSW_XSUBO | KSW_XSTART | (l_ms * opt->a < 250? KSW_XBYTE : 0) | (opt->min_seed_len * opt->a);
diff --git a/main.c b/main.c
index da7cd19..b3ce197 100644
--- a/main.c
+++ b/main.c
@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.9-r783"
+#define PACKAGE_VERSION "0.7.9a-r786"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);