Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013916.1 Kokia drynarioides strain JFW-HI SEQ_128946, 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: 4222
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34

Warning! 50 characters in sequence are not A, C, G, or T


Found at i:3742 original size:30 final size:30

Alignment explanation


    Indices: 3697--3981  Score: 238
    Period size: 30  Copynumber: 9.7  Consensus size: 30

       3687 TTAGGGTTAA

                           *           *  
       3697 AAAAT-GGAATTTTTAGAAGTTTCGGGCTT
          1 AAAATGGGAATTTTTGGAAGTTTCGGGGTT

                     *     *            **
       3726 AAAATGGGATTTTTTAGAAGTTT-GGGGGA
          1 AAAATGGGAATTTTTGGAAGTTTCGGGGTT

                                   * *    
       3755 AAAAT-GGAATTTTTGGAAGTTTTGAGGTT
          1 AAAATGGGAATTTTTGGAAGTTTCGGGGTT

                                 *          
       3784 AAAAATGGG-ATTTTTGGAA-ATTCGAGGG-T
          1 -AAAATGGGAATTTTTGGAAGTTTCG-GGGTT

                 *         *         * *  
       3813 AAAATTGGAATTTTTAGAAGTTTCGAGATT
          1 AAAATGGGAATTTTTGGAAGTTTCGGGGTT

                                            
       3843 AAAAATGGG-ATTTTTGGAAG-TTCAGGGGTT
          1 -AAAATGGGAATTTTTGGAAGTTTC-GGGGTT

                             *             *
       3873 AAAAATGGG-ATTTTTGAAAG-TTCAGGGGTA
          1 -AAAATGGGAATTTTTGGAAGTTTC-GGGGTT

                  *             *         
       3903 AAAAT-AGAATTTTTGGAAGCTTCGGGGTT
          1 AAAATGGGAATTTTTGGAAGTTTCGGGGTT

               *                        * 
       3932 AAATTGGG-ATTTTTGGAAG-TTCGGGGGT
          1 AAAATGGGAATTTTTGGAAGTTTCGGGGTT

                                   
       3960 AAAATTGGG-ATTTTTGGAAGTT
          1 AAAA-TGGGAATTTTTGGAAGTT

       3982 CGGTTAATTG


Statistics
Matches: 211,  Mismatches: 30, Indels: 29
        0.78            0.11        0.11

Matches are distributed among these distances:
  28   34  0.16
  29   83  0.39
  30   85  0.40
  31    9  0.04

ACGTcount: A:0.32, C:0.03, G:0.29, T:0.36


Consensus pattern (30 bp):   
AAAATGGGAATTTTTGGAAGTTTCGGGGTT

Found at i:3798 original size:59 final size:58

Alignment explanation


    Indices: 3687--3981  Score: 269
    Period size: 59  Copynumber: 5.0  Consensus size: 58

       3677 TTGGGAAAAT

                  *                                                 *    
       3687 TTAGGGTTAAAAAATGGAATTTTTAGAAGTTTCG-GGCTT-AAAATGGGATTTTTTAGAAG
          1 TTAGGGGT-AAAAATGGAATTTTTAGAAGTTTCGAGG-TTAAAAATGGGA-TTTTTGGAAG

              *    *               *       *                         *
       3746 TTTGGGGGAAAAATGGAATTTTTGGAAGTTTTGAGGTTAAAAATGGGATTTTTGGAAA
          1 TTAGGGGTAAAAATGGAATTTTTAGAAGTTTCGAGGTTAAAAATGGGATTTTTGGAAG

              *          *                      *                      
       3804 TTCGAGGGTAAAATTGGAATTTTTAGAAGTTTCGAGATTAAAAATGGGATTTTTGGAAG
          1 TTAG-GGGTAAAAATGGAATTTTTAGAAGTTTCGAGGTTAAAAATGGGATTTTTGGAAG

                              *                     *       * *           
       3863 TTCAGGGGTTAAAAATGGGATTTTT-GAAAG-TTC-AGGGGTAAAAATAGAATTTTTGGAAG
          1 TT-AGGGG-TAAAAATGGAATTTTTAG-AAGTTTCGA-GGTTAAAAATGGGATTTTTGGAAG

               *     *   *   *      *         *  *     *               
       3922 CTTCGGGGTTAAATTGGGATTTTTGGAAG-TTCGGGGGTAAAATTGGGATTTTTGGAAG
          1 -TTAGGGGTAAAAATGGAATTTTTAGAAGTTTCGAGGTTAAAAATGGGATTTTTGGAAG

              
       3980 TT
          1 TT

       3982 CGGTTAATTG


Statistics
Matches: 198,  Mismatches: 28, Indels: 22
        0.80            0.11        0.09

Matches are distributed among these distances:
  57    2  0.01
  58   78  0.39
  59   98  0.49
  60   20  0.10

ACGTcount: A:0.32, C:0.03, G:0.29, T:0.36


Consensus pattern (58 bp):   
TTAGGGGTAAAAATGGAATTTTTAGAAGTTTCGAGGTTAAAAATGGGATTTTTGGAAG

Found at i:3982 original size:29 final size:29

Alignment explanation


    Indices: 3696--3984  Score: 269
    Period size: 29  Copynumber: 9.9  Consensus size: 29

       3686 TTTAGGGTTA

                    *      *            * 
       3696 AAAAATGGAATTTTTAGAAGTTTC-GGGCT
          1 AAAAATGGGATTTTTGGAAG-TTCGGGGGT

            *               *      *      
       3725 TAAAATGGGATTTTTTAGAAGTTTGGGGG-
          1 AAAAATGGGA-TTTTTGGAAGTTCGGGGGT

                    *              * *  * 
       3754 AAAAATGGAATTTTTGGAAGTTTTGAGGTT
          1 AAAAATGGGATTTTTGGAAG-TTCGGGGGT

                               *    *    
       3784 AAAAATGGGATTTTTGGAAATTCGAGGGT
          1 AAAAATGGGATTTTTGGAAGTTCGGGGGT

                *   *      *         * ** 
       3813 AAAATTGGAATTTTTAGAAGTTTCGAGATT
          1 AAAAATGGGATTTTTGGAAG-TTCGGGGGT

                                        * 
       3843 AAAAATGGGATTTTTGGAAGTTCAGGGGTT
          1 AAAAATGGGATTTTTGGAAGTTC-GGGGGT

                            *      *     
       3873 AAAAATGGGATTTTTGAAAGTTCAGGGGT
          1 AAAAATGGGATTTTTGGAAGTTCGGGGGT

                  * *                     
       3902 AAAAATAGAATTTTTGGAAGCTTC-GGGGT
          1 AAAAATGGGATTTTTGGAAG-TTCGGGGGT

            *   *                        
       3931 TAAATTGGGATTTTTGGAAGTTCGGGGGT
          1 AAAAATGGGATTTTTGGAAGTTCGGGGGT

                *                    
       3960 AAAATTGGGATTTTTGGAAGTTCGG
          1 AAAAATGGGATTTTTGGAAGTTCGG

       3985 TTAATTGGTT


Statistics
Matches: 217,  Mismatches: 35, Indels: 16
        0.81            0.13        0.06

Matches are distributed among these distances:
  28   12  0.06
  29  121  0.56
  30   84  0.39

ACGTcount: A:0.31, C:0.03, G:0.30, T:0.35


Consensus pattern (29 bp):   
AAAAATGGGATTTTTGGAAGTTCGGGGGT
Done.