Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008446.1 Kokia drynarioides strain JFW-HI SEQ_123118, 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: 25964
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:8764 original size:15 final size:15

Alignment explanation


    Indices: 8744--8776  Score: 57
    Period size: 15  Copynumber: 2.2  Consensus size: 15

       8734 TCCAATATTC

                  *        
       8744 AATAAATCCAACTTA
          1 AATAAAACCAACTTA

                           
       8759 AATAAAACCAACTTA
          1 AATAAAACCAACTTA

               
       8774 AAT
          1 AAT

       8777 GTTCCAAAAC


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.58, C:0.18, G:0.00, T:0.24


Consensus pattern (15 bp):   
AATAAAACCAACTTA

Found at i:9564 original size:29 final size:29

Alignment explanation


    Indices: 9529--9584  Score: 103
    Period size: 29  Copynumber: 1.9  Consensus size: 29

       9519 ACAATATTTA

                                         
       9529 AAAGCAAACAGTGAAGATTCTTCTTTATT
          1 AAAGCAAACAGTGAAGATTCTTCTTTATT

                                  *    
       9558 AAAGCAAACAGTGAAGATTCTTTTTTA
          1 AAAGCAAACAGTGAAGATTCTTCTTTA

       9585 GTCATAGTCT


Statistics
Matches: 26,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  29   26  1.00

ACGTcount: A:0.39, C:0.12, G:0.14, T:0.34


Consensus pattern (29 bp):   
AAAGCAAACAGTGAAGATTCTTCTTTATT

Found at i:12447 original size:9 final size:9

Alignment explanation


    Indices: 12428--12458  Score: 55
    Period size: 9  Copynumber: 3.6  Consensus size: 9

      12418 CTACATCATT

                     
      12428 TGAAT-ATC
          1 TGAATAATC

                     
      12436 TGAATAATC
          1 TGAATAATC

                     
      12445 TGAATAATC
          1 TGAATAATC

                 
      12454 TGAAT
          1 TGAAT

      12459 CTGTAAAAGA


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   8    5  0.23
   9   17  0.77

ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35


Consensus pattern (9 bp):   
TGAATAATC

Found at i:14675 original size:27 final size:27

Alignment explanation


    Indices: 14641--14704  Score: 119
    Period size: 27  Copynumber: 2.4  Consensus size: 27

      14631 AGGATCTTCT

                                *      
      14641 GGAGAAGGAGTTGATTTTGATGGTGGA
          1 GGAGAAGGAGTTGATTTTGACGGTGGA

                                       
      14668 GGAGAAGGAGTTGATTTTGACGGTGGA
          1 GGAGAAGGAGTTGATTTTGACGGTGGA

                      
      14695 GGAGAAGGAG
          1 GGAGAAGGAG

      14705 GAGGATTCTG


Statistics
Matches: 36,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  27   36  1.00

ACGTcount: A:0.28, C:0.02, G:0.47, T:0.23


Consensus pattern (27 bp):   
GGAGAAGGAGTTGATTTTGACGGTGGA

Found at i:16143 original size:41 final size:41

Alignment explanation


    Indices: 16086--16168  Score: 157
    Period size: 41  Copynumber: 2.0  Consensus size: 41

      16076 ACCATGGTTG

                                                     
      16086 AAGAATTCTTTCTGAATTAAGATCAAAACTAATTAAAACCT
          1 AAGAATTCTTTCTGAATTAAGATCAAAACTAATTAAAACCT

                                           *         
      16127 AAGAATTCTTTCTGAATTAAGATCAAAACTAGTTAAAACCT
          1 AAGAATTCTTTCTGAATTAAGATCAAAACTAATTAAAACCT

             
      16168 A
          1 A

      16169 TGGCTTTGAT


Statistics
Matches: 41,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  41   41  1.00

ACGTcount: A:0.46, C:0.14, G:0.08, T:0.31


Consensus pattern (41 bp):   
AAGAATTCTTTCTGAATTAAGATCAAAACTAATTAAAACCT

Found at i:24879 original size:32 final size:32

Alignment explanation


    Indices: 24838--25143  Score: 387
    Period size: 32  Copynumber: 9.6  Consensus size: 32

      24828 CAAAAAATTC

                      *       *          *  
      24838 TTCACAGATTGATAGCTCCTATGAGCATATTG
          1 TTCACAGATTAATAGCTCTTATGAGCATACTG

                                        *   
      24870 TTCACAGATTAATAGCTCTTATGAGCATGCTG
          1 TTCACAGATTAATAGCTCTTATGAGCATACTG

                  *   *             *    *  
      24902 TTCACAAATTGATAGCTCTTATGACCATATTG
          1 TTCACAGATTAATAGCTCTTATGAGCATACTG

                *         *                 
      24934 TTCATAGATTAATAACTCTTATGAGCATACTG
          1 TTCACAGATTAATAGCTCTTATGAGCATACTG

                      *                    *
      24966 TTCACAGATTGATAGCTCTTATGAGCATACTA
          1 TTCACAGATTAATAGCTCTTATGAGCATACTG

                                         * *
      24998 TTCACAGATTAATAGCTCTTATGAGCATATTA
          1 TTCACAGATTAATAGCTCTTATGAGCATACTG

             *    *                         
      25030 TGCACAAATTAATAGCTCTTATGAGCATACTG
          1 TTCACAGATTAATAGCTCTTATGAGCATACTG

                          *  *           *  
      25062 TTCACAGATTAATAACTATTATGAGCATAATG
          1 TTCACAGATTAATAGCTCTTATGAGCATACTG

                      *   *      *   *     *
      25094 TTCACAGATTGATATCTCTTACGAGTATACTA
          1 TTCACAGATTAATAGCTCTTATGAGCATACTG

                *             
      25126 TTCATAGATTAATAGCTC
          1 TTCACAGATTAATAGCTC

      25144 ATACAAATAT


Statistics
Matches: 234,  Mismatches: 40, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  32  234  1.00

ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36


Consensus pattern (32 bp):   
TTCACAGATTAATAGCTCTTATGAGCATACTG

Done.