Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011390.1 Kokia drynarioides strain JFW-HI SEQ_126372, 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: 26228
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.32

Warning! 64 characters in sequence are not A, C, G, or T


Found at i:2122 original size:17 final size:18

Alignment explanation


    Indices: 2084--2137  Score: 56
    Period size: 17  Copynumber: 2.9  Consensus size: 18

       2074 CAAATTAAAA

                           *    
       2084 ATTAATATAAAGATAATAAT
          1 ATTAATA-AAA-ATATTAAT

                  *           
       2104 ATTAATTAAAAT-TTAAT
          1 ATTAATAAAAATATTAAT

               *             
       2121 ATTCATAAAAATATTAA
          1 ATTAATAAAAATATTAA

       2138 ACATTACCTA


Statistics
Matches: 29,  Mismatches: 4, Indels: 4
        0.78            0.11        0.11

Matches are distributed among these distances:
  17   14  0.48
  18    6  0.21
  19    3  0.10
  20    6  0.21

ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39


Consensus pattern (18 bp):   
ATTAATAAAAATATTAAT

Found at i:25014 original size:26 final size:27

Alignment explanation


    Indices: 24977--25033  Score: 98
    Period size: 26  Copynumber: 2.1  Consensus size: 27

      24967 ATTATAATTT

                                       
      24977 TTATGATAGTAAAATGTAAATTTTAAA
          1 TTATGATAGTAAAATGTAAATTTTAAA

                               *       
      25004 TTAT-ATAGTAAAATGTAATTTTTAAA
          1 TTATGATAGTAAAATGTAAATTTTAAA

                
      25030 TTAT
          1 TTAT

      25034 TAAATTAAAA


Statistics
Matches: 29,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  26   25  0.86
  27    4  0.14

ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46


Consensus pattern (27 bp):   
TTATGATAGTAAAATGTAAATTTTAAA

Found at i:25543 original size:58 final size:60

Alignment explanation


    Indices: 25469--25641  Score: 201
    Period size: 58  Copynumber: 2.9  Consensus size: 60

      25459 TTAACATAAG

                               *                                    *     
      25469 ATTTGATACTTGAACTTGATACTTTTTAC-TAATTTTG-TACCT-AA-TTTTTTTTTACCCA
          1 ATTTGATACTTGAACTTGACACTTTTT-CTTAA-TTTGATACCTAAACTTTTTTTTAACCCA

                       *                                                
      25527 ATTTGATACTTAAACTTGACACTTTTTCTTAATTTGATACCTAAACTTTTTTTTAACCCA
          1 ATTTGATACTTGAACTTGACACTTTTTCTTAATTTGATACCTAAACTTTTTTTTAACCCA

                 *            *     *      *               *       
      25587 ATTTGGTACTTGAACTTGCCATTTTTTTTTCCTAATTTGATACCTAAGCTTTTTT
          1 ATTTGATACTTGAACTTGACA---CTTTTTCTTAATTTGATACCTAAACTTTTTT

      25642 AGATTCAATT


Statistics
Matches: 99,  Mismatches: 9, Indels: 9
        0.85            0.08        0.08

Matches are distributed among these distances:
  57    5  0.05
  58   33  0.33
  59    2  0.02
  60   31  0.31
  63   28  0.28

ACGTcount: A:0.25, C:0.17, G:0.08, T:0.50


Consensus pattern (60 bp):   
ATTTGATACTTGAACTTGACACTTTTTCTTAATTTGATACCTAAACTTTTTTTTAACCCA

Found at i:25917 original size:31 final size:29

Alignment explanation


    Indices: 25815--25986  Score: 97
    Period size: 31  Copynumber: 5.8  Consensus size: 29

      25805 AATCAGGTAT

                                *  *      
      25815 CAAATTAAGAAAAAAATCAAGTTCAAGTAC
          1 CAAATTAAG-AAAAAATCAAATTTAAGTAC

                        **       *         
      25845 CAAATT-AGACCTCAAA--AAGTTTAAGTAC
          1 CAAATTAAGA--AAAAATCAAATTTAAGTAC

               *    *                      
      25873 CAACTTAAAAAAAAGAGTCAAATTTAAGTAC
          1 CAAATTAAGAAAAA-A-TCAAATTTAAGTAC

                   *             *   * *   
      25904 CAAATTATGAAAAAGTATCAAGTTTGATTAC
          1 CAAATTAAGAAAAA--ATCAAATTTAAGTAC

                                      *   
      25935 C-AATT-AGACAAAAA--AAATTTAAATAC
          1 CAAATTAAGA-AAAAATCAAATTTAAGTAC

                                      
      25961 CAAATTAAGAAAAAATGTCAAATTTA
          1 CAAATTAAGAAAAAA--TCAAATTTA

      25987 GGTAGAGCCA


Statistics
Matches: 108,  Mismatches: 19, Indels: 29
        0.69            0.12        0.19

Matches are distributed among these distances:
  26   10  0.09
  27   11  0.10
  28   22  0.20
  29    6  0.06
  30   17  0.16
  31   41  0.38
  32    1  0.01

ACGTcount: A:0.53, C:0.12, G:0.09, T:0.25


Consensus pattern (29 bp):   
CAAATTAAGAAAAAATCAAATTTAAGTAC

Found at i:25940 original size:89 final size:88

Alignment explanation


    Indices: 25815--25986  Score: 204
    Period size: 88  Copynumber: 1.9  Consensus size: 88

      25805 AATCAGGTAT

                                                     **     *     *      *   
      25815 CAAATTAAGAAAAAAATCAAGTTCAAGTACCAAATTAGACCTCAAAAAGTTTAAGTACCAACTTA
          1 CAAATTAAGAAAAAAATCAAGTTCAAGTACCAAATTAGA-CAAAAAAAATTTAAATACCAAATTA

                                     
      25880 A-AAAAAAGAGTCAAATTTAAGTAC
         65 AGAAAAAA-AGTCAAATTTAAGTAC

                   *       *        ** *                                     
      25904 CAAATTATGAAAAAGTATCAAGTTTGATTACC-AATTAGACAAAAAAAATTTAAATACCAAATTA
          1 CAAATTAAGAAAAA-AATCAAGTTCAAGTACCAAATTAGACAAAAAAAATTTAAATACCAAATTA

                    *          
      25968 AGAAAAAATGTCAAATTTA
         65 AGAAAAAAAGTCAAATTTA

      25987 GGTAGAGCCA


Statistics
Matches: 70,  Mismatches: 11, Indels: 5
        0.81            0.13        0.06

Matches are distributed among these distances:
  88   31  0.44
  89   26  0.37
  90   13  0.19

ACGTcount: A:0.53, C:0.12, G:0.09, T:0.25


Consensus pattern (88 bp):   
CAAATTAAGAAAAAAATCAAGTTCAAGTACCAAATTAGACAAAAAAAATTTAAATACCAAATTAA
GAAAAAAAGTCAAATTTAAGTAC
Done.