Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010377.1 Kokia drynarioides strain JFW-HI SEQ_125250, 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: 4892
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32


Found at i:639 original size:48 final size:45

Alignment explanation


    Indices: 569--744  Score: 183
    Period size: 48  Copynumber: 3.7  Consensus size: 45

        559 ACACTAGCGC

                                   *                 *  *  
        569 GCTCTCTGATTAGCACTATGTGTGCTCTCTGTTTAGCACGTCT-CGT
          1 GCTCTCTGATTAGCACT-TGTGTACTCTCTGTTTAGCAC-TATGTGT

                                             *        *     
        615 GCTCTCTGTTATTAGCACTGTGTGTACTCTCTGATTAGCACTTTGTGT
          1 GCTCTCTG--ATTAGCACT-TGTGTACTCTCTGTTTAGCACTATGTGT

                         *                                
        663 GCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCACTATGTGT
          1 GCTCTCTGATTAGCAC-TTGTGTACTCTCTGTTTAGCACTATGTGT

                    *            *   *          
        709 GCTCTCTGTTTCCCAGCACTTATGTGCTCTCTGTTT
          1 GCTCTCTGATT---AGCACTTGTGTACTCTCTGTTT

        745 GTTCCGTATA


Statistics
Matches: 111,  Mismatches: 12, Indels: 12
        0.82            0.09        0.09

Matches are distributed among these distances:
  46   51  0.46
  47    3  0.03
  48   53  0.48
  49    4  0.04

ACGTcount: A:0.13, C:0.24, G:0.20, T:0.43


Consensus pattern (45 bp):   
GCTCTCTGATTAGCACTTGTGTACTCTCTGTTTAGCACTATGTGT

Found at i:691 original size:71 final size:69

Alignment explanation


    Indices: 570--716  Score: 190
    Period size: 71  Copynumber: 2.1  Consensus size: 69

        560 CACTAGCGCG

                                          *                                 *
        570 CTCTCTGATTAGCACTATGTGTGCTCTCTGTTTAGCACGTCTCGTGCTCTCTGTTATTAGCACTG
          1 CTCTCTGATTAGCACTATGTGTGCTCTCTGATTAGCACGTCTCGTGCTCTCTG-T-TTAGCACTA

                  
        635 TGTGTA
         64 TGTGTA

                            *                  *      *                      
        641 CTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGTAC-T-TTGTGTACTCTCTGTTTAGCACTA
          1 CTCTCTGATTAGCACTATGTGTGCTCTCTGATTAGCACGTCTCGTG--CTCTCTGTTTAGCACTA

                 *
        704 TGTGTG
         64 TGTGTA

                   
        710 CTCTCTG
          1 CTCTCTG

        717 TTTCCCAGCA


Statistics
Matches: 68,  Mismatches: 6, Indels: 6
        0.85            0.08        0.08

Matches are distributed among these distances:
  69   24  0.35
  70    2  0.03
  71   42  0.62

ACGTcount: A:0.14, C:0.23, G:0.20, T:0.43


Consensus pattern (69 bp):   
CTCTCTGATTAGCACTATGTGTGCTCTCTGATTAGCACGTCTCGTGCTCTCTGTTTAGCACTATG
TGTA

Found at i:717 original size:23 final size:23

Alignment explanation


    Indices: 569--744  Score: 176
    Period size: 23  Copynumber: 7.5  Consensus size: 23

        559 ACACTAGCGC

                    *              
        569 GCTCTCTGATTAGCACTATGTGT
          1 GCTCTCTGTTTAGCACTATGTGT

                              *  *  
        592 GCTCTCTGTTTAGCACGTCT-CGT
          1 GCTCTCTGTTTAGCAC-TATGTGT

                               *     
        615 GCTCTCTGTTATTAGCACTGTGTGT
          1 GCTCTCTG-T-TTAGCACTATGTGT

            *       *        *     
        640 ACTCTCTGATTAGCACTTTGTGT
          1 GCTCTCTGTTTAGCACTATGTGT

                    *    *   *     
        663 GCTCTCTGATTAGTACTTTGTGT
          1 GCTCTCTGTTTAGCACTATGTGT

            *                      
        686 ACTCTCTGTTTAGCACTATGTGT
          1 GCTCTCTGTTTAGCACTATGTGT

                                  *   
        709 GCTCTCTGTTTCCCAGCACT-TATGT
          1 GCTCTCTGTTT---AGCACTATGTGT

                       
        734 GCTCTCTGTTT
          1 GCTCTCTGTTT

        745 GTTCCGTATA


Statistics
Matches: 130,  Mismatches: 16, Indels: 12
        0.82            0.10        0.08

Matches are distributed among these distances:
  23   88  0.68
  24    5  0.04
  25   31  0.24
  26    6  0.05

ACGTcount: A:0.13, C:0.24, G:0.20, T:0.43


Consensus pattern (23 bp):   
GCTCTCTGTTTAGCACTATGTGT

Found at i:2759 original size:39 final size:40

Alignment explanation


    Indices: 2702--2781  Score: 110
    Period size: 39  Copynumber: 2.0  Consensus size: 40

       2692 TATGCACTCA

                  *                                 
       2702 ATGGACCCCTTTTGAAGAGTCACAA-CCCTTTCAAATTGG
          1 ATGGACACCTTTTGAAGAGTCACAATCCCTTTCAAATTGG

                                         *     *     
       2741 ATGGACACCTATTT-AAGAGTCACAATCCTTTTCATATTGG
          1 ATGGACACCT-TTTGAAGAGTCACAATCCCTTTCAAATTGG

             
       2781 A
          1 A

       2782 CATACCTCTT


Statistics
Matches: 36,  Mismatches: 3, Indels: 3
        0.86            0.07        0.07

Matches are distributed among these distances:
  39   20  0.56
  40   16  0.44

ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31


Consensus pattern (40 bp):   
ATGGACACCTTTTGAAGAGTCACAATCCCTTTCAAATTGG
Done.