Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010185.1 Kokia drynarioides strain JFW-HI SEQ_124994, 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, 832

Length: 1387
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27


Found at i:600 original size:29 final size:29

Alignment explanation


    Indices: 540--724  Score: 142
    Period size: 29  Copynumber: 6.3  Consensus size: 29

        530 CGAACATCTA

                *         *               
        540 GGGGCAAAAATGGTAATTTTTGGAAGTTTC
          1 GGGGTAAAAATGG-GATTTTTGGAAGTTTC

                                   *      
        570 GGGGTCAAAAATGGGATTTTTGGGAG-TTC
          1 GGGGT-AAAAATGGGATTTTTGGAAGTTTC

                        * *      **      *
        599 GGGGGT-AAAATAGTATTTTTAAAAGTTTT
          1 -GGGGTAAAAATGGGATTTTTGGAAGTTTC

            *           *       *       *
        628 AGGGTAAAAATGAGATTTTTAGAAGTTTA
          1 GGGGTAAAAATGGGATTTTTGGAAGTTTC

                         *               *
        657 GGGGT-AAAATGGTATTTTTTGGAAGTTTT
          1 GGGGTAAAAATGGGA-TTTTTGGAAGTTTC

                                 *   *   *
        686 GGGGTCAAAAATGGGATTTTTAGAAATTTA
          1 GGGGT-AAAAATGGGATTTTTGGAAGTTTC

            *        
        716 AGGGTAAAA
          1 GGGGTAAAA

        725 TGATAATTTT


Statistics
Matches: 123,  Mismatches: 25, Indels: 15
        0.75            0.15        0.09

Matches are distributed among these distances:
  28   25  0.20
  29   48  0.39
  30   34  0.28
  31   16  0.13

ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35


Consensus pattern (29 bp):   
GGGGTAAAAATGGGATTTTTGGAAGTTTC

Found at i:625 original size:28 final size:28

Alignment explanation


    Indices: 600--748  Score: 99
    Period size: 29  Copynumber: 5.1  Consensus size: 28

        590 TGGGAGTTCG

                                         
        600 GGGGTAAAATAGTATTTTTAAAAGTTTTA
          1 GGGGTAAAATAGTATTTTTAAAAG-TTTA

                                  *       
        629 -GGGTAAAAATGAG-ATTTTTAGAAGTTTA
          1 GGGGT-AAAAT-AGTATTTTTAAAAGTTTA

                      *         **      *
        657 GGGGTAAAATGGTATTTTTTGGAAGTTTT
          1 GGGGTAAAATAGTA-TTTTTAAAAGTTTA

                        * *                
        686 GGGGTCAAAAATGGGATTTTTAGAAA-TTTA
          1 GGGGT--AAAATAGTATTTTTA-AAAGTTTA

            *                       *      
        716 AGGGTAAAAT-GATAATTTTTGAACAGTTTA
          1 GGGGTAAAATAG-T-ATTTTT-AAAAGTTTA

               
        746 GGG
          1 GGG

        749 ACCTTCAGGA


Statistics
Matches: 96,  Mismatches: 12, Indels: 23
        0.73            0.09        0.18

Matches are distributed among these distances:
  27    2  0.02
  28   19  0.20
  29   44  0.46
  30   21  0.22
  31   10  0.10

ACGTcount: A:0.35, C:0.01, G:0.26, T:0.38


Consensus pattern (28 bp):   
GGGGTAAAATAGTATTTTTAAAAGTTTA

Found at i:710 original size:59 final size:59

Alignment explanation


    Indices: 546--736  Score: 242
    Period size: 59  Copynumber: 3.3  Consensus size: 59

        536 TCTAGGGGCA

                                   *                     * *    **     
        546 AAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGGAGTTCGGGGGT
          1 AAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTAGAAGTTTAGGGGT

                 *         **       *            *                     
        605 AAAATAGT-ATTTTTAAAAGTTTTAGGGT-AAAAATGAGATTTTTAGAAGTTTAGGGGT
          1 AAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTAGAAGTTTAGGGGT

                     *                                       *    *    
        662 AAAATGGTATTTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTAGAAATTTAAGGGT
          1 AAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTAGAAGTTTAGGGGT

                  *         
        721 AAAATGATAATTTTTG
          1 AAAATGGTAATTTTTG

        737 AACAGTTTAG


Statistics
Matches: 110,  Mismatches: 20, Indels: 4
        0.82            0.15        0.03

Matches are distributed among these distances:
  57   31  0.28
  58   32  0.29
  59   47  0.43

ACGTcount: A:0.33, C:0.02, G:0.27, T:0.38


Consensus pattern (59 bp):   
AAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTAGAAGTTTAGGGGT

Done.