Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010049.1 Kokia drynarioides strain JFW-HI SEQ_124818, 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, 849

Length: 1415
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.28


Found at i:653 original size:30 final size:29

Alignment explanation


    Indices: 555--872  Score: 217
    Period size: 29  Copynumber: 10.9  Consensus size: 29

        545 CGGATGCACG

                *           *             
        555 GGGGGCAAAATGGT-AGTTTTGGAAGGTTC
          1 GGGGTCAAAATGGTAATTTTTGGAA-GTTC

              **           *              
        584 GGAATCAAAAATGG-GATTTTTGGAAGTTC
          1 GGGGTC-AAAATGGTAATTTTTGGAAGTTC

                                 * *       
        613 GAGGGT-AAAATGGTAATTTTCGAAAGGTTC
          1 G-GGGTCAAAATGGTAATTTTTGGAA-GTTC

                           *      *       
        643 GGGGTCAAAATTGG-GATTTTTTGAAGTTC
          1 GGGGTCAAAA-TGGTAATTTTTGGAAGTTC

                          *       *        
        672 GGGGGT-AAAATGGCAATTTTTAGAAGGTTC
          1 -GGGGTCAAAATGGTAATTTTTGGAA-GTTC

             *             *              
        702 GAGGTCAAAAATGG-GATTTTTGGAAGTTC
          1 GGGGTC-AAAATGGTAATTTTTGGAAGTTC

                                  *      *
        731 GGAGGT-AAAATGGTAATTTTTAGAAGTTT
          1 GG-GGTCAAAATGGTAATTTTTGGAAGTTC

            **             *          *   
        760 AAGGTCAAAAATGG-GATTTTTGGAAATTC
          1 GGGGTC-AAAATGGTAATTTTTGGAAGTTC

                                        *  
        789 GAGGGT-AAAATGGTAATTTTTGGAAAGATC
          1 G-GGGTCAAAATGGTAATTTTTGG-AAGTTC

            **             *              
        819 TAGGTCAAAAATGG-GATTTTTGGAAGTTC
          1 GGGGTC-AAAATGGTAATTTTTGGAAGTTC

                      *               
        848 GGGGGT-AAAGTGGTAATTTTTGGAA
          1 -GGGGTCAAAATGGTAATTTTTGGAA

        873 AGTTTAAGGA


Statistics
Matches: 225,  Mismatches: 41, Indels: 46
        0.72            0.13        0.15

Matches are distributed among these distances:
  28   33  0.15
  29   95  0.42
  30   80  0.36
  31   17  0.08

ACGTcount: A:0.31, C:0.05, G:0.31, T:0.32


Consensus pattern (29 bp):   
GGGGTCAAAATGGTAATTTTTGGAAGTTC

Found at i:831 original size:117 final size:118

Alignment explanation


    Indices: 588--881  Score: 405
    Period size: 117  Copynumber: 2.5  Consensus size: 118

        578 AGGTTCGGAA

                                                           *        ***      
        588 TCAAAAATGGGATTTTTGGAAGTTC-GAGGGTAAAATGGTAA-TTTTCGAAAGGTTCGGGGTCAA
          1 TCAAAAATGGGATTTTTGGAAGTTCGGA-GGTAAAATGGTAATTTTTAGAAA-GTTTAAGGTCAA

              *          *   *    *                       * *      
        651 AATTGGGATTTTTTGAAGTTCGGGGGTAAAATGGCAATTTTTAGAAGGTTCGAGG
         64 AAATGGGATTTTTGGAAATTCGAGGGTAAAATGGCAATTTTTAGAAAGATCGAGG

                                                                             
        706 TCAAAAATGGGATTTTTGGAAGTTCGGAGGTAAAATGGTAATTTTTAG-AAGTTTAAGGTCAAAA
          1 TCAAAAATGGGATTTTTGGAAGTTCGGAGGTAAAATGGTAATTTTTAGAAAGTTTAAGGTCAAAA

                                            *       *        *   
        770 ATGGGATTTTTGGAAATTCGAGGGTAAAATGGTAATTTTTGGAAAGATCTAGG
         66 ATGGGATTTTTGGAAATTCGAGGGTAAAATGGCAATTTTTAGAAAGATCGAGG

                                       *      *           *            
        823 TCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAGTGGTAATTTTTGGAAAGTTTAAGG
          1 TCAAAAATGGGATTTTTGGAAGTTCGGAGGTAAAATGGTAATTTTTAGAAAGTTTAAGG

        882 ACCTCCGGAG


Statistics
Matches: 157,  Mismatches: 16, Indels: 6
        0.88            0.09        0.03

Matches are distributed among these distances:
 117  100  0.64
 118   50  0.32
 119    7  0.04

ACGTcount: A:0.32, C:0.05, G:0.30, T:0.33


Consensus pattern (118 bp):   
TCAAAAATGGGATTTTTGGAAGTTCGGAGGTAAAATGGTAATTTTTAGAAAGTTTAAGGTCAAAA
ATGGGATTTTTGGAAATTCGAGGGTAAAATGGCAATTTTTAGAAAGATCGAGG

Found at i:868 original size:59 final size:59

Alignment explanation


    Indices: 588--876  Score: 402
    Period size: 59  Copynumber: 4.9  Consensus size: 59

        578 AGGTTCGGAA

                                      *                   *          *  
        588 TCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAA-TTTTCGAAAGGTTCGGGG
          1 TCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAA-GTTCGAGG

                  *          *                    *           *        
        647 TCAAAATTGGGATTTTTTGAAGTTCGGGGGTAAAATGGCAATTTTTAGAAGGTTCGAGG
          1 TCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAAGTTCGAGG

                                       *                          **   
        706 TCAAAAATGGGATTTTTGGAAGTTCGGAGGTAAAATGGTAATTTTTAG-AAGTTTAAGG
          1 TCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAAGTTCGAGG

                                 *    *                   *     *  *   
        764 TCAAAAATGGGATTTTTGGAAATTCGAGGGTAAAATGGTAATTTTTGGAAAGATCTAGG
          1 TCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAAGTTCGAGG

                                              *           *       
        823 TCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAGTGGTAATTTTTGGAAAGTT
          1 TCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAAGTT

        877 TAAGGACCTC


Statistics
Matches: 203,  Mismatches: 25, Indels: 4
        0.88            0.11        0.02

Matches are distributed among these distances:
  58   51  0.25
  59  145  0.71
  60    7  0.03

ACGTcount: A:0.32, C:0.05, G:0.30, T:0.33


Consensus pattern (59 bp):   
TCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAAGTTCGAGG
Done.