Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007584.1 Kokia drynarioides strain JFW-HI SEQ_122214, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 20845
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:7822 original size:17 final size:17

Alignment explanation


    Indices: 7799--7848  Score: 75
    Period size: 17  Copynumber: 2.9  Consensus size: 17

       7789 TCAAGATACA

                              
       7799 CCAGTGATCCTGCGACAT
          1 CCAGTGATCCTGCGAC-T

                             
       7817 -CAGTGATCCTGCGACT
          1 CCAGTGATCCTGCGACT

                  *         
       7833 CCAGTGGTCCTGCGAC
          1 CCAGTGATCCTGCGAC

       7849 GCTGTTAAGC


Statistics
Matches: 30,  Mismatches: 1, Indels: 3
        0.88            0.03        0.09

Matches are distributed among these distances:
  16    1  0.03
  17   29  0.97

ACGTcount: A:0.18, C:0.34, G:0.26, T:0.22


Consensus pattern (17 bp):   
CCAGTGATCCTGCGACT

Found at i:9788 original size:6 final size:6

Alignment explanation


    Indices: 9752--9786  Score: 61
    Period size: 6  Copynumber: 5.8  Consensus size: 6

       9742 AGTTACTCTG

                                             *      
       9752 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAG AAGAA
          1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAA

       9787 GATAAGAGAG


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
   6   28  1.00

ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00


Consensus pattern (6 bp):   
AAGAAA

Found at i:13818 original size:32 final size:31

Alignment explanation


    Indices: 13751--13819  Score: 77
    Period size: 32  Copynumber: 2.2  Consensus size: 31

      13741 AGTTTATTTC

                       *          *       * 
      13751 TAAAATAATTAGTAAATTTAAATTTGATTAGT
          1 TAAAATAATTAATAAATTTAAACTTGA-TAAT

                                             
      13783 TAAAATAATTAATATAATTTTAAACTTGA-AAT
          1 TAAAATAATTAATA-AA-TTTAAACTTGATAAT

                 
      13815 TAAAA
          1 TAAAA

      13820 AAATGAGTAA


Statistics
Matches: 32,  Mismatches: 3, Indels: 4
        0.82            0.08        0.10

Matches are distributed among these distances:
  32   20  0.62
  33    2  0.06
  34   10  0.31

ACGTcount: A:0.52, C:0.01, G:0.06, T:0.41


Consensus pattern (31 bp):   
TAAAATAATTAATAAATTTAAACTTGATAAT

Found at i:17483 original size:39 final size:40

Alignment explanation


    Indices: 17429--17508  Score: 117
    Period size: 39  Copynumber: 2.0  Consensus size: 40

      17419 TATGCACTTA

                      *                             
      17429 ATGGACACATTTTGAAGAGTCACAA-CCCTTTCAAATTGG
          1 ATGGACACATATTGAAGAGTCACAATCCCTTTCAAATTGG

                    *                   *     *     
      17468 ATGGACACCTATTGAAGAGTCACAATCCTTTTCATATTGG
          1 ATGGACACATATTGAAGAGTCACAATCCCTTTCAAATTGG

             
      17508 A
          1 A

      17509 CATACCTCTT


Statistics
Matches: 36,  Mismatches: 4, Indels: 1
        0.88            0.10        0.02

Matches are distributed among these distances:
  39   23  0.64
  40   13  0.36

ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30


Consensus pattern (40 bp):   
ATGGACACATATTGAAGAGTCACAATCCCTTTCAAATTGG

Found at i:17524 original size:39 final size:38

Alignment explanation


    Indices: 17440--17525  Score: 93
    Period size: 39  Copynumber: 2.2  Consensus size: 38

      17430 TGGACACATT

                                           *       
      17440 TTGAAGAGTCACAACCCTTTCAAATTGGATGGACACCTA
          1 TTGAAGAGTCACAACCCTTTCAAATTGGA-GCACACCTA

                             *     *         *    *
      17479 TTGAAGAGTCACAATCCTTTTCATATTGGA-CATACCTC
          1 TTGAAGAGTCACAA-CCCTTTCAAATTGGAGCACACCTA

                     
      17517 TTGGAAGAG
          1 TT-GAAGAG

      17526 ACTTGTTCCA


Statistics
Matches: 40,  Mismatches: 5, Indels: 4
        0.82            0.10        0.08

Matches are distributed among these distances:
  38    7  0.17
  39   20  0.50
  40   13  0.32

ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29


Consensus pattern (38 bp):   
TTGAAGAGTCACAACCCTTTCAAATTGGAGCACACCTA
Done.