Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009367.1 Kokia drynarioides strain JFW-HI SEQ_124074, 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: 7926
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34


Found at i:1569 original size:13 final size:13

Alignment explanation


    Indices: 1545--1569  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       1535 TATTTTATAA

                         
       1545 TTATTTTTTATTT
          1 TTATTTTTTATTT

                        
       1558 TTATTTTTTATT
          1 TTATTTTTTATT

       1570 AAAATAATTT


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84


Consensus pattern (13 bp):   
TTATTTTTTATTT

Found at i:1759 original size:21 final size:21

Alignment explanation


    Indices: 1733--1812  Score: 97
    Period size: 21  Copynumber: 3.8  Consensus size: 21

       1723 AGTGTAGACC

                                 
       1733 TCTACCGATACAAGTAATAGT
          1 TCTACCGATACAAGTAATAGT

                  *        * *   
       1754 TCTACCAATACAAGTGACAGT
          1 TCTACCGATACAAGTAATAGT

                 *         **  * 
       1775 TCTACTGATACAAGTCTTACT
          1 TCTACCGATACAAGTAATAGT

                             
       1796 TCTACCGATACAAGTAA
          1 TCTACCGATACAAGTAA

       1813 ACAAACTACC


Statistics
Matches: 47,  Mismatches: 12, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
  21   47  1.00

ACGTcount: A:0.36, C:0.23, G:0.12, T:0.29


Consensus pattern (21 bp):   
TCTACCGATACAAGTAATAGT

Found at i:1827 original size:42 final size:42

Alignment explanation


    Indices: 1734--1827  Score: 100
    Period size: 42  Copynumber: 2.2  Consensus size: 42

       1724 GTGTAGACCT

                              *                *    **
       1734 CTACCGATACAAGTAATAGTTCTACCAATACAAGTGACAGTT
          1 CTACCGATACAAGTAATACTTCTACCAATACAAGTAACAGAA

                *         **          *                
       1776 CTACTGATACAAGTCTTACTTCTACCGATACAAGTAAACA-AA
          1 CTACCGATACAAGTAATACTTCTACCAATACAAGT-AACAGAA

                      
       1818 CTACCGATAC
          1 CTACCGATAC

       1828 TTCTAAACAC


Statistics
Matches: 42,  Mismatches: 9, Indels: 2
        0.79            0.17        0.04

Matches are distributed among these distances:
  42   39  0.93
  43    3  0.07

ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26


Consensus pattern (42 bp):   
CTACCGATACAAGTAATACTTCTACCAATACAAGTAACAGAA

Found at i:2598 original size:52 final size:52

Alignment explanation


    Indices: 2482--2719  Score: 325
    Period size: 52  Copynumber: 4.6  Consensus size: 52

       2472 ATTTCATTTA

                    *                 *    **      *  *      * *
       2482 ATACTCACTATGACACATAGTCATCGGACCTTTTAATCCAT-TAGGATTTAT
          1 ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCAG

                                      *        * **            *
       2533 ATACTCACGATGACACATAGTCATCGGACCTCATATTTTGTAAAGGATTCAT
          1 ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCAG

                                                  *             
       2585 ATACTCACGATGACACATAGTCATCGAACCTCATAATCTGTAAAGGATTCAG
          1 ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCAG

                                     *                          
       2637 ATACTCACGATGACACATAGTCATCAAACCTCATAATCCGTAAAGGATTCAG
          1 ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCAG

                         *                 
       2689 ATACTCACGATGATACATAGTCATCGAACCT
          1 ATACTCACGATGACACATAGTCATCGAACCT

       2720 TTTACCATTT


Statistics
Matches: 169,  Mismatches: 17, Indels: 1
        0.90            0.09        0.01

Matches are distributed among these distances:
  51   34  0.20
  52  135  0.80

ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28


Consensus pattern (52 bp):   
ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCAG

Found at i:4719 original size:41 final size:41

Alignment explanation


    Indices: 4664--4962  Score: 393
    Period size: 41  Copynumber: 7.2  Consensus size: 41

       4654 GAGTCATAAA

                                                *      
       4664 TCTTCCTTTAAATATAATCTCATGCTCATC-CTGAGTCACGAG
          1 TCTTCCTTT-AATATAATCTCATGCTCATCTC-GAGACACGAG

                                     * * * *     *   
       4706 TCTTCCTTTAATATAATCTCATGCTTACCCCAAGACATGAG
          1 TCTTCCTTTAATATAATCTCATGCTCATCTCGAGACACGAG

             *                       * * *           
       4747 TATTCCTTTAATATAATCTCATGCTTACCCCGAGACACGAG
          1 TCTTCCTTTAATATAATCTCATGCTCATCTCGAGACACGAG

                *                       *     *      
       4788 TCTTTCTTTAATATAATCTCATGCTCATTTCGAGTCACGAG
          1 TCTTCCTTTAATATAATCTCATGCTCATCTCGAGACACGAG

              *              *          *     *      
       4829 TCCTCCTTTAATATAATTTCATGCTCATTTCGAGTCACGAG
          1 TCTTCCTTTAATATAATCTCATGCTCATCTCGAGACACGAG

                             *                    *  
       4870 TCTTCCTTTAATATAATATCATGCTCATCTCGAGACACAAG
          1 TCTTCCTTTAATATAATCTCATGCTCATCTCGAGACACGAG

                                                     
       4911 TCTTCCTTTAATATAATCTCATGCTCATCTCGAGACACGAG
          1 TCTTCCTTTAATATAATCTCATGCTCATCTCGAGACACGAG

                       
       4952 TCTTCCATTTA
          1 TCTTCC-TTTA

       4963 TACGTCAAGT


Statistics
Matches: 230,  Mismatches: 25, Indels: 4
        0.89            0.10        0.02

Matches are distributed among these distances:
  41  216  0.94
  42   14  0.06

ACGTcount: A:0.27, C:0.25, G:0.11, T:0.36


Consensus pattern (41 bp):   
TCTTCCTTTAATATAATCTCATGCTCATCTCGAGACACGAG

Found at i:7561 original size:20 final size:21

Alignment explanation


    Indices: 7515--7562  Score: 53
    Period size: 20  Copynumber: 2.3  Consensus size: 21

       7505 ATTTTATGGT

                                 
       7515 TTTAAATAATTTATGGGTAAA
          1 TTTAAATAATTTATGGGTAAA

            **      *       *    
       7536 AATAAATATTTTA-GGTTAAA
          1 TTTAAATAATTTATGGGTAAA

                   
       7556 TTTAAAT
          1 TTTAAAT

       7563 TTAAAAATAA


Statistics
Matches: 21,  Mismatches: 6, Indels: 1
        0.75            0.21        0.04

Matches are distributed among these distances:
  20   11  0.52
  21   10  0.48

ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44


Consensus pattern (21 bp):   
TTTAAATAATTTATGGGTAAA
Done.