diff --git a/ksw2.h b/ksw2.h
index 48f3596..89bc9bb 100644
--- a/ksw2.h
+++ b/ksw2.h
@@ -142,7 +142,7 @@ static inline void ksw_backtrack(void *km, int is_rot, int is_rev, int min_intro
 		else if (state == 3 && min_intron_len > 0) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, 3, 1), --i; // intron
 		else cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, 1, 1), --j; // insertion
 	}
-	if (i >= 0) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, i >= min_intron_len? 3 : 2, i + 1); // first deletion
+	if (i >= 0) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, min_intron_len > 0 && i >= min_intron_len? 3 : 2, i + 1); // first deletion
 	if (j >= 0) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, 1, j + 1); // first insertion
 	if (!is_rev)
 		for (i = 0; i < n_cigar>>1; ++i) // reverse CIGAR
diff --git a/main.c b/main.c
index c51f747..ed488e9 100644
--- a/main.c
+++ b/main.c
@@ -6,7 +6,7 @@
 #include "mmpriv.h"
 #include "getopt.h"
 
-#define MM_VERSION "2.6-r651-dirty"
+#define MM_VERSION "2.6-r653-dirty"
 
 #ifdef __linux__
 #include <sys/resource.h>