Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002347.1 Kokia drynarioides strain JFW-HI SEQ_114407, 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: 6157
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34


Found at i:628 original size:24 final size:24

Alignment explanation


    Indices: 599--742  Score: 99
    Period size: 24  Copynumber: 5.8  Consensus size: 24

        589 CTCGATAAAT

                              *     
        599 AAGCTGGCGAGCGTAAACATGTGC
          1 AAGCTGGCGAGCGTAAACGTGTGC

                                * ****
        623 AAGCTGGCGAGCGTAAATGCATAAAT
          1 AAGCTGGCGAGCGTAAA--CGTGTGC

                 **          *      
        649 AAGCTAACGAGCGTAAATGTGTGC
          1 AAGCTGGCGAGCGTAAACGTGTGC

                 *                   **
        673 AAGCTAGCGAGCGTAAACGTGATAAAT
          1 AAGCTGGCGAGCGTAAACGTG-T--GC

                  * *  *            
        700 AAGCTGACCAGTGTAAACGTGTGC
          1 AAGCTGGCGAGCGTAAACGTGTGC

                       *       
        724 AAGCTGGCGAGTGTAAACG
          1 AAGCTGGCGAGCGTAAACG

        743 CGTAAATAAA


Statistics
Matches: 91,  Mismatches: 24, Indels: 10
        0.73            0.19        0.08

Matches are distributed among these distances:
  24   54  0.59
  25    1  0.01
  26   19  0.21
  27   17  0.19

ACGTcount: A:0.34, C:0.17, G:0.30, T:0.19


Consensus pattern (24 bp):   
AAGCTGGCGAGCGTAAACGTGTGC

Found at i:665 original size:50 final size:50

Alignment explanation


    Indices: 552--851  Score: 305
    Period size: 50  Copynumber: 5.9  Consensus size: 50

        542 AACATAATCT

                *            *       *   *  *      *            
        552 TGACGAGCGTAAACGTGCGCAAG-TTGACTAGAGTAAACTCGATAAATAAGC
          1 TGACCAGCGTAAACGTGTGCAAGCTAG-CGAGCGTAAACGC-ATAAATAAGC

              * *         *          *           *            
        603 TGGCGAGCGTAAACATGTGCAAGCTGGCGAGCGTAAATGCATAAATAAGC
          1 TGACCAGCGTAAACGTGTGCAAGCTAGCGAGCGTAAACGCATAAATAAGC

             *  *        *                          *          
        653 TAACGAGCGTAAATGTGTGCAAGCTAGCGAGCGTAAACGTGATAAATAAGC
          1 TGACCAGCGTAAACGTGTGCAAGCTAGCGAGCGTAAACG-CATAAATAAGC

                   *                 *     *        *       * 
        704 TGACCAGTGTAAACGTGTGCAAGCTGGCGAGTGTAAACGCGTAAATAAAC
          1 TGACCAGCGTAAACGTGTGCAAGCTAGCGAGCGTAAACGCATAAATAAGC

               **                       *   *     *           
        754 TGATAAGCGTAAACGTGTGCAAGCTAGCTAGCATAAACACATAAATAAGC
          1 TGACCAGCGTAAACGTGTGCAAGCTAGCGAGCGTAAACGCATAAATAAGC

                         *                  *       *       
        804 TGACCAGCGTAAATGTGTGCAAGCTAGCGAGCATAAACGTAATAAATA
          1 TGACCAGCGTAAACGTGTGCAAGCTAGCGAGCGTAAACG-CATAAATA

        852 TCTTGATATG


Statistics
Matches: 206,  Mismatches: 40, Indels: 6
        0.82            0.16        0.02

Matches are distributed among these distances:
  50  125  0.61
  51   79  0.38
  52    2  0.01

ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20


Consensus pattern (50 bp):   
TGACCAGCGTAAACGTGTGCAAGCTAGCGAGCGTAAACGCATAAATAAGC

Found at i:729 original size:101 final size:100

Alignment explanation


    Indices: 557--851  Score: 331
    Period size: 101  Copynumber: 2.9  Consensus size: 100

        547 AATCTTGACG

                        *       *   *  *                     * *         *   
        557 AGCGTAAACGTGCGCAAG-TTGACTAGAGTAAACTCGATAAATAAGCTGGCGAGCGTAAACATGT
          1 AGCGTAAACGTGTGCAAGCTAG-CGAGCGTAAACT-GATAAATAAGCTGACCAGCGTAAACGTGT

                               *          *     *
        621 GCAAGCTGGCGAGCGTAAATGCATAAATAAGCTAACG
         64 GCAAGCTGGCGAGCGTAAACGCATAAATAAACTAACA

                    *                                            *           
        658 AGCGTAAATGTGTGCAAGCTAGCGAGCGTAAACGTGATAAATAAGCTGACCAGTGTAAACGTGTG
          1 AGCGTAAACGTGTGCAAGCTAGCGAGCGTAAAC-TGATAAATAAGCTGACCAGCGTAAACGTGTG

                        *        *          * * 
        723 CAAGCTGGCGAGTGTAAACGCGTAAATAAACTGATA
         65 CAAGCTGGCGAGCGTAAACGCATAAATAAACTAACA

                                   *   *     **                       *      
        759 AGCGTAAACGTGTGCAAGCTAGCTAGCATAAACACATAAATAAGCTGACCAGCGTAAATGTGTGC
          1 AGCGTAAACGTGTGCAAGCTAGCGAGCGTAAACTGATAAATAAGCTGACCAGCGTAAACGTGTGC

                 *      *       *       
        824 AAGCTAGCGAGCATAAACGTAATAAATA
         66 AAGCTGGCGAGCGTAAACG-CATAAATA

        852 TCTTGATATG


Statistics
Matches: 163,  Mismatches: 28, Indels: 6
        0.83            0.14        0.03

Matches are distributed among these distances:
 100   44  0.27
 101  116  0.71
 102    3  0.02

ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20


Consensus pattern (100 bp):   
AGCGTAAACGTGTGCAAGCTAGCGAGCGTAAACTGATAAATAAGCTGACCAGCGTAAACGTGTGC
AAGCTGGCGAGCGTAAACGCATAAATAAACTAACA

Found at i:4064 original size:15 final size:15

Alignment explanation


    Indices: 4044--4074  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       4034 ATTCTCAAGT

                           
       4044 ATTAATCTAAATTAA
          1 ATTAATCTAAATTAA

                      *    
       4059 ATTAATCTAAGTTAA
          1 ATTAATCTAAATTAA

             
       4074 A
          1 A

       4075 GCTAAAATAA


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39


Consensus pattern (15 bp):   
ATTAATCTAAATTAA
Done.