Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001469.1 Kokia drynarioides strain JFW-HI SEQ_112993, 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: 16666
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33

Warning! 40 characters in sequence are not A, C, G, or T


Found at i:7740 original size:29 final size:30

Alignment explanation


    Indices: 7706--7851  Score: 110
    Period size: 29  Copynumber: 4.9  Consensus size: 30

       7696 GCTCAATAAG

                                          
       7706 CCCCTATTCTATTTTAAAATTATATTTTAA
          1 CCCCTATTCTATTTTAAAATTATATTTTAA

                            *               
       7736 -CCCTAAATT-T-TTTCAAAATTATATTTTAA
          1 CCCCT--ATTCTATTTTAAAATTATATTTTAA

                          *            *    
       7765 CCCCT-TTAC-ATTCTAAAATTTATATATTAA
          1 CCCCTATT-CTATTTTAAAA-TTATATTTTAA

                   *      **               
       7795 CCCCCTAAT-T-TTCCAAAATTATATTTTAA
          1 -CCCCTATTCTATTTTAAAATTATATTTTAA

                  **                     
       7824 CCCCTAAACT-TTTTAAAAATTATATTTT
          1 CCCCTATTCTATTTT-AAAATTATATTTT

       7852 GACTCTCGAA


Statistics
Matches: 94,  Mismatches: 10, Indels: 24
        0.73            0.08        0.19

Matches are distributed among these distances:
  27    2  0.02
  28    7  0.07
  29   41  0.44
  30   35  0.37
  31    8  0.09
  32    1  0.01

ACGTcount: A:0.36, C:0.18, G:0.00, T:0.46


Consensus pattern (30 bp):   
CCCCTATTCTATTTTAAAATTATATTTTAA

Found at i:7789 original size:59 final size:57

Alignment explanation


    Indices: 7720--7851  Score: 158
    Period size: 59  Copynumber: 2.2  Consensus size: 57

       7710 TATTCTATTT

                                         *                     **      
       7720 TAAAATTATATTTTAA-CCCTAAATTTTTTCAAAATTATATTTTAACCCCTTTACATTC
          1 TAAAATTATATTTTAACCCCT-AA-TTTTCCAAAATTATATTTTAACCCCTAAACATTC

                        *                                          *  *
       7778 TAAAATTTATATATTAACCCCCTAATTTTCCAAAATTATATTTTAACCCCTAAACTTTT
          1 TAAAA-TTATATTTTAA-CCCCTAATTTTCCAAAATTATATTTTAACCCCTAAACATTC

                           
       7837 TAAAAATTATATTTT
          1 T-AAAATTATATTTT

       7852 GACTCTCGAA


Statistics
Matches: 63,  Mismatches: 7, Indels: 7
        0.82            0.09        0.09

Matches are distributed among these distances:
  58    5  0.08
  59   48  0.76
  60    6  0.10
  61    4  0.06

ACGTcount: A:0.38, C:0.17, G:0.00, T:0.45


Consensus pattern (57 bp):   
TAAAATTATATTTTAACCCCTAATTTTCCAAAATTATATTTTAACCCCTAAACATTC

Found at i:7813 original size:30 final size:29

Alignment explanation


    Indices: 7721--7851  Score: 115
    Period size: 30  Copynumber: 4.4  Consensus size: 29

       7711 ATTCTATTTT

                                         * 
       7721 AAAATTATATTTTAA--CCCTAAATTTTTTC
          1 AAAATTATATTTTAACCCCCT-AA-TTTTCC

                               * * **   *
       7750 AAAATTATATTTTAACCCCTTTACATTCT
          1 AAAATTATATTTTAACCCCCTAATTTTCC

                       *                  
       7779 AAAATTTATATATTAACCCCCTAATTTTCC
          1 AAAA-TTATATTTTAACCCCCTAATTTTCC

                                         **
       7809 AAAATTATATTTTAA-CCCCTAAACTTTTTA
          1 AAAATTATATTTTAACCCCCT-AA-TTTTCC

                         
       7839 AAAATTATATTTT
          1 AAAATTATATTTT

       7852 GACTCTCGAA


Statistics
Matches: 82,  Mismatches: 15, Indels: 9
        0.77            0.14        0.08

Matches are distributed among these distances:
  28    5  0.06
  29   33  0.40
  30   41  0.50
  31    3  0.04

ACGTcount: A:0.38, C:0.17, G:0.00, T:0.45


Consensus pattern (29 bp):   
AAAATTATATTTTAACCCCCTAATTTTCC

Found at i:7959 original size:29 final size:30

Alignment explanation


    Indices: 7876--7976  Score: 125
    Period size: 30  Copynumber: 3.4  Consensus size: 30

       7866 CTAAAAATTG

                    *  *                  
       7876 CATTTTGACCCCCAAACCTTTTGAAAATCA
          1 CATTTTGAACCTCAAACCTTTTGAAAATCA

                    *                     
       7906 CATTTTGACCCTCAAACCTTTTGAAAATCA
          1 CATTTTGAACCTCAAACCTTTTGAAAATCA

                *                          *
       7936 CATTCT-AACCTCAAA-CTTTCTGAAGAATCG
          1 CATTTTGAACCTCAAACCTTT-TGAA-AATCA

                       
       7966 CATTTTGAACC
          1 CATTTTGAACC

       7977 ATAAAACTTT


Statistics
Matches: 63,  Mismatches: 5, Indels: 5
        0.86            0.07        0.07

Matches are distributed among these distances:
  28    4  0.06
  29   12  0.19
  30   43  0.68
  31    4  0.06

ACGTcount: A:0.33, C:0.28, G:0.08, T:0.32


Consensus pattern (30 bp):   
CATTTTGAACCTCAAACCTTTTGAAAATCA
Done.