diff --git a/test/x3s-aln.txt b/test/x3s-aln.txt
new file mode 100644
index 0000000..5b83ae8
--- /dev/null
+++ b/test/x3s-aln.txt
@@ -0,0 +1,5 @@
+mm2: TGTTATCCCTAGGGTAACTTGTTCCGTTGGTCAAGTTATTGGATCAATTGAGTATAGTAGTGCACTCAC......................................................................................................................................CACTTGGAGCCATTCATACAGGTCCCTATTTAAGGAACAAGTGATTATGCTACCTTTGCACGGTT
+     |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||                                                                                                                                      |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ref: TGTTATCCCTAGGGTAACTTGTTCCGTTGGTCAAGTTATTGGATCAATTGAGTATAGTAGTGCACTCACctGCTTCGCTTTGACTGGTGAAGTCTTAGCATGTACTGCTCGGAGGTTGGGTTCTGCTCCGAGGTCGCCCCAACCGAAATTTTTAATGCAGGTTTGGTAGTTTAGGACCTGTGGGTTTGTTAGGCTAACCTCacCACTTGGAGCCATTCATACAGGTCCCTATTTAAGGAACAAGTGATTATGCTACCTTTGCACGGTT
+     ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||                                                                                                                                      ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+sta: TGTTATCCCTAGGGTAACTTGTTCCGTTGGTCAAGTTATTGGATCAATTGAGTATAGTAGTGCA......................................................................................................................................CTCACCACTTGGAGCCATTCATACAGGTCCCTATTTAAGGAACAAGTGATTATGCTACCTTTGCACGGTT
diff --git a/test/x3s-qry.fa b/test/x3s-qry.fa
new file mode 100644
index 0000000..dd54e97
--- /dev/null
+++ b/test/x3s-qry.fa
@@ -0,0 +1,5 @@
+>query
+AACCGTGCAAAGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCC
+AAGTG
+GTGAGTGCA
+CTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA
diff --git a/test/x3s-ref.fa b/test/x3s-ref.fa
new file mode 100644
index 0000000..1f9c1cc
--- /dev/null
+++ b/test/x3s-ref.fa
@@ -0,0 +1,10 @@
+>ref
+TGATCCAACATCGAGGTCGTAAACCCTATTGTTGATATGGACTCTAGAATAGGATTGCGC
+TGTTATCCCTAGGGTAACTTGTTCCGTTGGTCAAGTTATTGGATCAATTGAGTATAGTAG
+TGCACTCAC
+ctGCTTCGCTTTGACTGGTGAAGTCTTAGCATGTACTGCTCGGAGGTTGGGTTCTGCTCC
+GAGGTCGCCCCAACCGAAATTTTTAATGCAGGTTTGGTAGTTTAGGACCTGTGGGTTTGT
+TAGGCTAACCTCac
+CACTTGGAGCCATTCATACAGGTCCCTATTTAAGGAACAAGTGATTATGCTACCTTTGCA
+CGGTTAGGGTACCGCGGCCGTTAAACATGTGTCACTGGGCAGGCGGTGCCTCTAATACTG
+GTGAT