testdata/ref

   1 >chr1
   2 GGAGAACTGTGCTCCGCCTTCAGA
   3 acgtgcactgtgagcgcatctgca
   4 ACACATGCTAGCGCGTCGGGGTGG
   5 actgcgatctgagctatcatacgt
   6 GACTCTAGCAGAGTGGCCAGCCAC
   7 atctgcatgactgcatgctagtgc
   8 CCTCCCGAGCCGAGCCACCCGTCA
   9 atattacgctatagcgcatatgcc
  10 GTTATTAATAATAACTTATCATCA
  11 atatatgcgcgctgatggcctgct
  12 GCTCTCAAACCTTGTATTTTTCTT
  13 atccatacttgcnnnnnnnnnnnn
  14 AAAACTGATCCAAAAAAAATACAA
  15 nnnnnncatctatccggggggggg
  16 CCTATGAGTCAATCCTATTTTCAA
  17 actgtctgactgcgctgatggttg
  18 ATGTTTAGCTCCCCCTTGTTAGGT