diff --git a/bwamem.c b/bwamem.c
index fd164be..1880512 100644
--- a/bwamem.c
+++ b/bwamem.c
@@ -331,6 +331,8 @@ void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int
 				}
 			}
 		}
+		//printf("[Q] "); for (i = qe; i < l_query; ++i) putchar("ACGTN"[(int)query[i]]); putchar('\n');
+		//printf("[R] "); for (i = re; i < rmax[1] - rmax[0]; ++i) putchar("ACGTN"[(int)rseq[i]]); putchar('\n');
 		a->score = ksw_extend(l_query - qe, query + qe, rmax[1] - rmax[0] - re, rseq + re, 5, opt->mat, opt->q, opt->r, opt->w, a->score, qw, &qle, &tle);
 		a->qe = qe + qle; a->re = rmax[0] + re + tle;
 		free(qw);
@@ -347,8 +349,8 @@ void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int
 	w += abs((a->re - a->rb) - (a->qe - a->qb));
 	nw_score = ksw_global(a->qe - a->qb, query + a->qb, a->re - a->rb, rseq + (a->rb - rmax[0]), 5, opt->mat, opt->q, opt->r, w, &a->n_cigar, &a->cigar);
 
-	printf("[%d] ", c->n); for (i = a->qb; i < a->qe; ++i) putchar("ACGTN"[(int)query[i]]); putchar('\n');
-	printf("[%d] ", c->n); for (i = a->rb; i < a->re; ++i) putchar("ACGTN"[(int)rseq[i - rmax[0]]]); putchar('\n');
+	//printf("[Q] "); for (i = a->qb; i < a->qe; ++i) putchar("ACGTN"[(int)query[i]]); putchar('\n');
+	//printf("[R] "); for (i = a->rb; i < a->re; ++i) putchar("ACGTN"[(int)rseq[i - rmax[0]]]); putchar('\n');
 	printf("[%d] score=%d,%d\t[%d,%d) <=> [%lld,%lld)\tis_all=%d\t", c->n, a->score, nw_score, a->qb, a->qe, a->rb, a->re, a->is_all);
 	for (i = 0; i < a->n_cigar; ++i) printf("%d%c", a->cigar[i]>>4, "MIDS"[a->cigar[i]&0xf]);
 	putchar('\n');
diff --git a/ksw.c b/ksw.c
index 6708e40..405bd86 100644
--- a/ksw.c
+++ b/ksw.c
@@ -392,8 +392,8 @@ int ksw_extend(int qlen, const uint8_t *query, int tlen, const uint8_t *target,
 		//beg = 0; end = qlen; // uncomment this line for debugging
 	}
 	free(eh); free(qp);
-	if (_qle) *_qle = max_i + 1;
-	if (_tle) *_tle = max_j + 1;
+	if (_qle) *_qle = max_j + 1;
+	if (_tle) *_tle = max_i + 1;
 	return max;
 }