Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013873.1 Kokia drynarioides strain JFW-HI SEQ_128901, 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: 20551
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34


Found at i:6830 original size:38 final size:38

Alignment explanation


    Indices: 6747--6834  Score: 95
    Period size: 38  Copynumber: 2.3  Consensus size: 38

       6737 TTCATGTAAA

                        *               *   *   * 
       6747 AACAGTAGACATGCATAACATGTATTCAGTTCGACAGT
          1 AACAGTAGACATACATAACATGTATTCAATTCAACAAT

             **           *  *             *      
       6785 AGTAGTAGACATACTTATCATGTATTCAATTTAACAAT
          1 AACAGTAGACATACATAACATGTATTCAATTCAACAAT

                        
       6823 AACAGTAGACAT
          1 AACAGTAGACAT

       6835 GCTAAATATG


Statistics
Matches: 39,  Mismatches: 11, Indels: 0
        0.78            0.22        0.00

Matches are distributed among these distances:
  38   39  1.00

ACGTcount: A:0.40, C:0.16, G:0.15, T:0.30


Consensus pattern (38 bp):   
AACAGTAGACATACATAACATGTATTCAATTCAACAAT

Found at i:7513 original size:12 final size:13

Alignment explanation


    Indices: 7498--7526  Score: 51
    Period size: 12  Copynumber: 2.3  Consensus size: 13

       7488 TTAGGGTTTC

                         
       7498 TTTTCTTTTC-TT
          1 TTTTCTTTTCATT

                         
       7510 TTTTCTTTTCATT
          1 TTTTCTTTTCATT

                
       7523 TTTT
          1 TTTT

       7527 GTTTATGTTT


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  12   10  0.62
  13    6  0.38

ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83


Consensus pattern (13 bp):   
TTTTCTTTTCATT

Found at i:7514 original size:17 final size:17

Alignment explanation


    Indices: 7494--7543  Score: 57
    Period size: 18  Copynumber: 2.8  Consensus size: 17

       7484 ACTTTTAGGG

                              
       7494 TTTCTTTTCTTTTCTT-T
          1 TTTCTTTTCTTTT-TTGT

                              
       7511 TTTCTTTTCATTTTTTGT
          1 TTTCTTTTC-TTTTTTGT

                *          
       7529 TTATGTTTTCTTTTT
          1 TT-TCTTTTCTTTTT

       7544 AAAGTATATT


Statistics
Matches: 29,  Mismatches: 1, Indels: 5
        0.83            0.03        0.14

Matches are distributed among these distances:
  17   11  0.38
  18   12  0.41
  19    6  0.21

ACGTcount: A:0.04, C:0.12, G:0.04, T:0.80


Consensus pattern (17 bp):   
TTTCTTTTCTTTTTTGT

Found at i:7793 original size:18 final size:18

Alignment explanation


    Indices: 7770--7806  Score: 56
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       7760 TTTGTGATCA

                              
       7770 AAATTGAAAGTGAAAGTG
          1 AAATTGAAAGTGAAAGTG

                  *  *        
       7788 AAATTGGAATTGAAAGTG
          1 AAATTGAAAGTGAAAGTG

             
       7806 A
          1 A

       7807 TATGAATTGT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24


Consensus pattern (18 bp):   
AAATTGAAAGTGAAAGTG

Found at i:11830 original size:29 final size:29

Alignment explanation


    Indices: 11798--11882  Score: 143
    Period size: 29  Copynumber: 2.9  Consensus size: 29

      11788 CCACACCTTG

                                         
      11798 TGTGATATTATTCTGTGTTGTGTTATCTA
          1 TGTGATATTATTCTGTGTTGTGTTATCTA

                                     *   
      11827 TGTGATATTATTCTGTGTTGTGTTAACTA
          1 TGTGATATTATTCTGTGTTGTGTTATCTA

                  *       *            
      11856 TGTGATTTTATTCTATGTTGTGTTATC
          1 TGTGATATTATTCTGTGTTGTGTTATC

      11883 GCATGATGAT


Statistics
Matches: 52,  Mismatches: 4, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  29   52  1.00

ACGTcount: A:0.18, C:0.07, G:0.20, T:0.55


Consensus pattern (29 bp):   
TGTGATATTATTCTGTGTTGTGTTATCTA

Found at i:13597 original size:3 final size:3

Alignment explanation


    Indices: 13589--13621  Score: 66
    Period size: 3  Copynumber: 11.0  Consensus size: 3

      13579 AAATATAATA

                                                       
      13589 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT

      13622 ACAAATAAAA


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   30  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (3 bp):   
TAT

Found at i:17082 original size:51 final size:51

Alignment explanation


    Indices: 17023--17124  Score: 204
    Period size: 51  Copynumber: 2.0  Consensus size: 51

      17013 TTCAAATGGT

                                                               
      17023 GAAGAGATGGAAGTGAAAGGTATGAAACCAGTTGGTTTTGCCCGAATTATC
          1 GAAGAGATGGAAGTGAAAGGTATGAAACCAGTTGGTTTTGCCCGAATTATC

                                                               
      17074 GAAGAGATGGAAGTGAAAGGTATGAAACCAGTTGGTTTTGCCCGAATTATC
          1 GAAGAGATGGAAGTGAAAGGTATGAAACCAGTTGGTTTTGCCCGAATTATC

      17125 TTAGCAATAA


Statistics
Matches: 51,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  51   51  1.00

ACGTcount: A:0.33, C:0.12, G:0.29, T:0.25


Consensus pattern (51 bp):   
GAAGAGATGGAAGTGAAAGGTATGAAACCAGTTGGTTTTGCCCGAATTATC
Done.