Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000730.1 Kokia drynarioides strain JFW-HI SEQ_111754, 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: 14207
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:1651 original size:2 final size:2

Alignment explanation


    Indices: 1644--1687  Score: 88
    Period size: 2  Copynumber: 22.0  Consensus size: 2

       1634 AAGAAAAAGA

                                                                          
       1644 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

              
       1686 AT
          1 AT

       1688 TTGCTAGAAA


Statistics
Matches: 42,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   42  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:6633 original size:18 final size:18

Alignment explanation


    Indices: 6610--6652  Score: 77
    Period size: 18  Copynumber: 2.4  Consensus size: 18

       6600 TGATTCGAGT

                             *
       6610 GAAGATCTTGAAGAAGAG
          1 GAAGATCTTGAAGAAGAA

                              
       6628 GAAGATCTTGAAGAAGAA
          1 GAAGATCTTGAAGAAGAA

                   
       6646 GAAGATC
          1 GAAGATC

       6653 CTAAATAAAC


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  18   24  1.00

ACGTcount: A:0.47, C:0.07, G:0.30, T:0.16


Consensus pattern (18 bp):   
GAAGATCTTGAAGAAGAA

Found at i:10704 original size:37 final size:37

Alignment explanation


    Indices: 10628--10727  Score: 141
    Period size: 37  Copynumber: 2.8  Consensus size: 37

      10618 AAAGTACTGG

                                                *
      10628 TGTTGTGGCGGGATGTTAATTG-AA-AGAAGTATCAG
          1 TGTTGTGGCGGGATGTTAATTGAAAGAGAAGTATCAA

                   * *                      *    
      10663 TGTTGTGACTGGATGTTAATTGAAAGAGAAGTTTCAA
          1 TGTTGTGGCGGGATGTTAATTGAAAGAGAAGTATCAA

                                 *      
      10700 TGTTGTGGCGGGATGTTAATTAAAAGAG
          1 TGTTGTGGCGGGATGTTAATTGAAAGAG

      10728 GACTGGCGTT


Statistics
Matches: 56,  Mismatches: 7, Indels: 2
        0.86            0.11        0.03

Matches are distributed among these distances:
  35   20  0.36
  36    2  0.04
  37   34  0.61

ACGTcount: A:0.30, C:0.05, G:0.32, T:0.33


Consensus pattern (37 bp):   
TGTTGTGGCGGGATGTTAATTGAAAGAGAAGTATCAA

Found at i:12482 original size:39 final size:39

Alignment explanation


    Indices: 12439--12570  Score: 95
    Period size: 43  Copynumber: 3.2  Consensus size: 39

      12429 AAAGATATTT

                                                   
      12439 TTTAAAATAAAATAAACTCTACTCTTACATATTTAGTAA
          1 TTTAAAATAAAATAAACTCTACTCTTACATATTTAGTAA

                     *            *   * *    *    *   *    
      12478 TTT-AAATCTAAATAAAACAATATATGTGTGTATATATGTATTTAAA
          1 TTTAAAAT-AAAAT-AAAC--TCTA-CTCT-TACATATTTA-GT-AA

              *                                      
      12524 TTGAATAATTAAAATAAACTCTACTCTTACATATTTAGTAA
          1 TTTAA-AA-TAAAATAAACTCTACTCTTACATATTTAGTAA

                  
      12565 TTTAAA
          1 TTTAAA

      12571 TCTAAATAAA


Statistics
Matches: 66,  Mismatches: 16, Indels: 21
        0.64            0.16        0.20

Matches are distributed among these distances:
  38    4  0.06
  39    7  0.11
  40    5  0.08
  41    6  0.09
  42    4  0.06
  43   10  0.15
  44   10  0.15
  45    4  0.06
  46    4  0.06
  47    5  0.08
  48    6  0.09
  49    1  0.02

ACGTcount: A:0.45, C:0.09, G:0.05, T:0.40


Consensus pattern (39 bp):   
TTTAAAATAAAATAAACTCTACTCTTACATATTTAGTAA

Found at i:12543 original size:87 final size:86

Alignment explanation


    Indices: 12446--12619  Score: 339
    Period size: 87  Copynumber: 2.0  Consensus size: 86

      12436 TTTTTTAAAA

                                                                             
      12446 TAAAATAAACTCTACTCTTACATATTTAGTAATTTAAATCTAAATAAAACAATATATGTGTGTAT
          1 TAAAATAAACTCTACTCTTACATATTTAGTAATTTAAATCTAAAT-AAACAATATATGTGTGTAT

                                  
      12511 ATATGTATTTAAATTGAATAAT
         65 ATATGTATTTAAATTGAATAAT

                                                                             
      12533 TAAAATAAACTCTACTCTTACATATTTAGTAATTTAAATCTAAATAAACAATATATGTGTGTATA
          1 TAAAATAAACTCTACTCTTACATATTTAGTAATTTAAATCTAAATAAACAATATATGTGTGTATA

                                 
      12598 TATGTATTTAAATTGAATAAT
         66 TATGTATTTAAATTGAATAAT

             
      12619 T
          1 T

      12620 TTATGTATTT


Statistics
Matches: 87,  Mismatches: 0, Indels: 1
        0.99            0.00        0.01

Matches are distributed among these distances:
  86   42  0.48
  87   45  0.52

ACGTcount: A:0.44, C:0.08, G:0.07, T:0.41


Consensus pattern (86 bp):   
TAAAATAAACTCTACTCTTACATATTTAGTAATTTAAATCTAAATAAACAATATATGTGTGTATA
TATGTATTTAAATTGAATAAT
Done.