diff --git a/bwamem_pair.c b/bwamem_pair.c
index cab7c2f..d926857 100644
--- a/bwamem_pair.c
+++ b/bwamem_pair.c
@@ -136,7 +136,8 @@ int mem_matesw(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, const me
 			aln = ksw_align(l_ms, seq, len, ref, 5, opt->mat, opt->q, opt->r, xtra, 0);
 			memset(&b, 0, sizeof(mem_alnreg_t));
 			if (aln.score >= opt->min_seed_len) {
-				b.qb = aln.qb; b.qe = aln.qe + 1;
+				b.qb = is_rev? l_ms - (aln.qe + 1) : aln.qb;                                                                                                                                                                              
+				b.qe = is_rev? l_ms - aln.qb : aln.qe + 1; 
 				b.rb = is_rev? (l_pac<<1) - (rb + aln.te + 1) : rb + aln.tb;
 				b.re = is_rev? (l_pac<<1) - (rb + aln.tb) : rb + aln.te + 1;
 				b.score = aln.score;