Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009961.1 Kokia drynarioides strain JFW-HI SEQ_124709, 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: 4898
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33

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


Found at i:4647 original size:58 final size:58

Alignment explanation


    Indices: 4555--4868  Score: 176
    Period size: 58  Copynumber: 5.3  Consensus size: 58

       4545 TCTTGGGGGC

                                     * *                   *          
       4555 AAAATGGTAATTTTTGGAAAGTTCGAAATCAAAAATGAAATTTTAGACGTTCGAGGGT
          1 AAAATGGTAATTTTTGGAAAGTTCGGAGTCAAAAATGAAATTTTAGAAGTTCGAGGGT

                 *                    *  *      *               *   *    
       4613 AAAATTGTAATTTTTGGAAAGTTCGGTGTTAAAAA-CAGAATTTCTAGATA-CTCGTGGGT
          1 AAAATGGTAATTTTTGGAAAGTTCGGAGTCAAAAATGA-AATTT-TAGA-AGTTCGAGGGT

                                ** *  *             *             *    
       4672 AAAATGGTAATTTTT-GAAAAATAGGGGTCAAAAATAGAATTTTTAGAAGTTCGGGGGT
          1 AAAATGGTAATTTTTGGAAAGTTCGGAGTCAAAAAT-GAAATTTTAGAAGTTCGAGGGT

            *     *   *          *  *     *  *    *               *      
       4730 GAAATGATAAATTTTGGAAAAATTAGG-GTTAATAATGGAATTATT-GAAAGTTTGAGGGT
          1 AAAATGGTAATTTTTGG-AAAGTTCGGAGTCAAAAATGAAATT-TTAG-AAGTTCGAGGGT

            *    *    *             *     *          *      *        *     
       4789 GAAATAGTAAATTTTGGAAAAAAAATT-GGGGTCAAAAATGGAATTTTGGAAAGTT-TAGGGT
          1 AAAATGGTAATTTTTGG----AAAGTTCGGAGTCAAAAATGAAATTTTAG-AAGTTCGAGGGT

                                
       4850 AAAAT-GTAATTTTTGGAAA
          1 AAAATGGTAATTTTTGGAAA

       4869 ATTTAGGGTT


Statistics
Matches: 205,  Mismatches: 36, Indels: 32
        0.75            0.13        0.12

Matches are distributed among these distances:
  56    3  0.01
  57    2  0.01
  58   77  0.38
  59   64  0.31
  60   19  0.09
  61   13  0.06
  62   27  0.13

ACGTcount: A:0.40, C:0.04, G:0.24, T:0.32


Consensus pattern (58 bp):   
AAAATGGTAATTTTTGGAAAGTTCGGAGTCAAAAATGAAATTTTAGAAGTTCGAGGGT

Found at i:4771 original size:29 final size:28

Alignment explanation


    Indices: 4739--4891  Score: 114
    Period size: 29  Copynumber: 5.2  Consensus size: 28

       4729 TGAAATGATA

                        *                
       4739 AATTTTGGAAAAATTAGGGTTAATAATGG
          1 AATTTTGGAAAATTTAGGGTTAA-AATGG

                        *          *       *
       4768 AATTATT-GAAAGTTTGAGGG-TGAAATAGTA
          1 AATT-TTGGAAAATTT-AGGGTTAAAAT-G-G

                           *  *     *       
       4798 AATTTTGGAAAAAAAATTGGGGTCAAAAATGG
          1 AATTTTGG---AAAATTTAGGGT-TAAAATGG

                       *               *
       4830 AATTTTGGAAAGTTTAGGG-TAAAATGT
          1 AATTTTGGAAAATTTAGGGTTAAAATGG

                                         
       4857 AATTTTTGGAAAATTTAGGGTTAAAATGG
          1 AA-TTTTGGAAAATTTAGGGTTAAAATGG

                  
       4886 AATTTT
          1 AATTTT

       4892 AAAAAGT


Statistics
Matches: 95,  Mismatches: 17, Indels: 25
        0.69            0.12        0.18

Matches are distributed among these distances:
  27    8  0.08
  28   23  0.24
  29   32  0.34
  30   11  0.12
  32   11  0.12
  33    6  0.06
  34    4  0.04

ACGTcount: A:0.41, C:0.01, G:0.24, T:0.35


Consensus pattern (28 bp):   
AATTTTGGAAAATTTAGGGTTAAAATGG

Found at i:4771 original size:59 final size:58

Alignment explanation


    Indices: 4680--4891  Score: 200
    Period size: 59  Copynumber: 3.6  Consensus size: 58

       4670 GTAAAATGGT

                  *                     *                  *             
       4680 AATTTTTGAAAAA-TAGGGGTCAAAAATAGAATTTTT-AGAAGTTCGGGGGTGAAATGATA
          1 AATTTTGGAAAAATTA-GGGTCAAAAATGGAATTTTTGA-AAGTT-GAGGGTGAAATGATA

                                *  *         *                          
       4739 AATTTTGGAAAAATTAGGGTTAATAATGGAATTATTGAAAGTTTGAGGGTGAAAT-AGTA
          1 AATTTTGGAAAAATTAGGGTCAAAAATGGAATTTTTGAAAG-TTGAGGGTGAAATGA-TA

                              *                   *       *     *        
       4798 AATTTTGGAAAAAAAATTGGGGTCAAAAATGGAATTTTGGAAAGTTTAGGGTAAAATG-TA
          1 AATTTTGG---AAAAATTAGGGTCAAAAATGGAATTTTTGAAAGTTGAGGGTGAAATGATA

             *          *        *             
       4858 ATTTTTGGAAAATTTAGGGT-TAAAATGGAATTTT
          1 AATTTTGGAAAAATTAGGGTCAAAAATGGAATTTT

       4892 AAAAAGT


Statistics
Matches: 128,  Mismatches: 17, Indels: 19
        0.78            0.10        0.12

Matches are distributed among these distances:
  56   13  0.10
  57   10  0.08
  58    1  0.01
  59   51  0.40
  60   14  0.11
  61   11  0.09
  62   28  0.22

ACGTcount: A:0.41, C:0.01, G:0.25, T:0.33


Consensus pattern (58 bp):   
AATTTTGGAAAAATTAGGGTCAAAAATGGAATTTTTGAAAGTTGAGGGTGAAATGATA

Done.