Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012036.1 Kokia drynarioides strain JFW-HI SEQ_127034, 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, 628

Length: 1047
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34


Found at i:608 original size:24 final size:26

Alignment explanation


    Indices: 581--628  Score: 66
    Period size: 24  Copynumber: 1.9  Consensus size: 26

        571 AGAGAAATGT

                                       
        581 AAATG-TGATATATGA-A-ATTATGAG
          1 AAATGATGA-ATATGAGAGATTATGAG

                                    
        605 AAATGATGAATATGAGAGATTATG
          1 AAATGATGAATATGAGAGATTATG

        629 CCCATGTAGA


Statistics
Matches: 21,  Mismatches: 0, Indels: 4
        0.84            0.00        0.16

Matches are distributed among these distances:
  24   11  0.52
  25    4  0.19
  26    6  0.29

ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31


Consensus pattern (26 bp):   
AAATGATGAATATGAGAGATTATGAG

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

Alignment explanation


    Indices: 691--783  Score: 150
    Period size: 23  Copynumber: 4.0  Consensus size: 23

        681 ACACTAGCGC

                                   
        691 GCTCTCTGATTAGCACTTTGTGT
          1 GCTCTCTGATTAGCACTTTGTGT

                     *   *         
        714 GCTCTCTGACTAGTACTTTGTGT
          1 GCTCTCTGATTAGCACTTTGTGT

            *                *     
        737 ACTCTCTGATTAGCACTGTGTGT
          1 GCTCTCTGATTAGCACTTTGTGT

                                   
        760 GCTCTCTGATTAGCACTTTGTGT
          1 GCTCTCTGATTAGCACTTTGTGT

             
        783 G
          1 G

        784 TTCAGCACTT


Statistics
Matches: 62,  Mismatches: 8, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  23   62  1.00

ACGTcount: A:0.14, C:0.22, G:0.23, T:0.42


Consensus pattern (23 bp):   
GCTCTCTGATTAGCACTTTGTGT

Found at i:792 original size:16 final size:16

Alignment explanation


    Indices: 771--814  Score: 70
    Period size: 16  Copynumber: 2.8  Consensus size: 16

        761 CTCTCTGATT

                         *  
        771 AGCACTTTGTGTGTTC
          1 AGCACTTTGTGTGCTC

                            
        787 AGCACTTTGTGTGCTC
          1 AGCACTTTGTGTGCTC

              *         
        803 AGTACTTTGTGT
          1 AGCACTTTGTGT

        815 ACTCTCTGTT


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   26  1.00

ACGTcount: A:0.14, C:0.18, G:0.25, T:0.43


Consensus pattern (16 bp):   
AGCACTTTGTGTGCTC

Found at i:830 original size:39 final size:39

Alignment explanation


    Indices: 725--841  Score: 116
    Period size: 39  Copynumber: 3.0  Consensus size: 39

        715 CTCTCTGACT

                                *        *         
        725 AGTACTTTGTGTACTCTCTGATTAGCACTGTGTGTGCTC
          1 AGTACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC

                       * *   * *                       
        764 --T-CTGATT-AGCACTTTGTGTGTTCAGCACTTTGTGTGCTC
          1 AGTACT--TTGTGTACTCTCTGT-TT-AGCACTTTGTGTGCTC

                                                   
        803 AGTACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
          1 AGTACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC

        842 TCTGTTGCCC


Statistics
Matches: 60,  Mismatches: 10, Indels: 16
        0.70            0.12        0.19

Matches are distributed among these distances:
  36    2  0.03
  37    8  0.13
  38    4  0.07
  39   31  0.52
  40    4  0.07
  41    9  0.15
  42    2  0.03

ACGTcount: A:0.14, C:0.21, G:0.22, T:0.44


Consensus pattern (39 bp):   
AGTACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC

Found at i:836 original size:23 final size:23

Alignment explanation


    Indices: 806--895  Score: 78
    Period size: 23  Copynumber: 3.9  Consensus size: 23

        796 TGTGCTCAGT

                                   
        806 ACTTTGTGTACTCTCTGTTTAGC
          1 ACTTTGTGTACTCTCTGTTTAGC

                     *            *   
        829 ACTTTGTGTGCTCTCTGTTGCCCAGC
          1 ACTTTGTGTACTCTCTGTT---TAGC

                  *                *
        855 ACTTATATG--CTCTCTGTTTAGT
          1 ACTT-TGTGTACTCTCTGTTTAGC

                *               
        877 ACTTCG-GTACTCTCTGTTT
          1 ACTTTGTGTACTCTCTGTTT

        896 GTTCCGTTTA


Statistics
Matches: 54,  Mismatches: 7, Indels: 13
        0.73            0.09        0.18

Matches are distributed among these distances:
  20    1  0.02
  22   16  0.30
  23   18  0.33
  25    9  0.17
  26    7  0.13
  27    3  0.06

ACGTcount: A:0.12, C:0.24, G:0.18, T:0.46


Consensus pattern (23 bp):   
ACTTTGTGTACTCTCTGTTTAGC
Done.