Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009916.1 Kokia drynarioides strain JFW-HI SEQ_124656, 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: 37345
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:9772 original size:32 final size:32

Alignment explanation


    Indices: 9733--9799  Score: 125
    Period size: 32  Copynumber: 2.1  Consensus size: 32

       9723 TTTCTACATT

                                            
       9733 AAAAAAAGTTAAAAGTTCTGCAACTTGGAGTA
          1 AAAAAAAGTTAAAAGTTCTGCAACTTGGAGTA

                             *              
       9765 AAAAAAAGTTAAAAGTTTTGCAACTTGGAGTA
          1 AAAAAAAGTTAAAAGTTCTGCAACTTGGAGTA

               
       9797 AAA
          1 AAA

       9800 TCTTGGATCC


Statistics
Matches: 34,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  32   34  1.00

ACGTcount: A:0.49, C:0.07, G:0.18, T:0.25


Consensus pattern (32 bp):   
AAAAAAAGTTAAAAGTTCTGCAACTTGGAGTA

Found at i:21796 original size:18 final size:18

Alignment explanation


    Indices: 21774--21819  Score: 58
    Period size: 18  Copynumber: 2.6  Consensus size: 18

      21764 TATATTTGGT

                              
      21774 TGAGCTCGCATCTTT-AG
          1 TGAGCTCGCATCTTTAAG

                   *    *      
      21791 TAGAGCTTGCATGTTTAAG
          1 T-GAGCTCGCATCTTTAAG

                      
      21810 TGAGCTCGCA
          1 TGAGCTCGCA

      21820 GTTATGTAGA


Statistics
Matches: 24,  Mismatches: 3, Indels: 3
        0.80            0.10        0.10

Matches are distributed among these distances:
  17    1  0.04
  18   20  0.83
  19    3  0.12

ACGTcount: A:0.22, C:0.20, G:0.26, T:0.33


Consensus pattern (18 bp):   
TGAGCTCGCATCTTTAAG

Found at i:32741 original size:13 final size:13

Alignment explanation


    Indices: 32715--32748  Score: 52
    Period size: 13  Copynumber: 2.7  Consensus size: 13

      32705 TAAAGAGCAT

                         
      32715 AAAAT-AAAAGAG
          1 AAAATAAAAAGAG

                      *  
      32727 AAAATAAAAATAG
          1 AAAATAAAAAGAG

                     
      32740 AAAATAAAA
          1 AAAATAAAA

      32749 GAAAAATGGC


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  12    5  0.25
  13   15  0.75

ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12


Consensus pattern (13 bp):   
AAAATAAAAAGAG

Found at i:34553 original size:42 final size:42

Alignment explanation


    Indices: 34442--34620  Score: 211
    Period size: 42  Copynumber: 4.2  Consensus size: 42

      34432 TGATGTATAA

                                * *    *        *      
      34442 AAAGGAAGACTCATGTCTCGGGTTGAGCATGAGAATTTG-TAT
          1 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGAT-T

                         *  * *          *    *         
      34484 AAATGGAAGACTCGTGACGCG-GAATGAGCATGAAAATATGATT
          1 AAA-GGAAGACTCATGTCTCGAG-ATGAGAATGAGAATATGATT

                                              *       
      34527 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGATT
          1 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATT

                                                       
      34569 AAAGGAAGACTCATGTCTC-AGGATGAGAATGAGAATATGATT
          1 AAAGGAAGACTCATGTCTCGA-GATGAGAATGAGAATATGATT

                      
      34611 AAAGGAAGAC
          1 AAAGGAAGAC

      34621 CTATGACTTG


Statistics
Matches: 119,  Mismatches: 13, Indels: 10
        0.84            0.09        0.07

Matches are distributed among these distances:
  41    1  0.01
  42   84  0.71
  43   33  0.28
  44    1  0.01

ACGTcount: A:0.39, C:0.11, G:0.27, T:0.23


Consensus pattern (42 bp):   
AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATT

Found at i:36106 original size:23 final size:24

Alignment explanation


    Indices: 36075--36122  Score: 64
    Period size: 26  Copynumber: 2.0  Consensus size: 24

      36065 TAAAATCAAA

                                    
      36075 AAAATATCTC-TAGAG-ATTTTCT
          1 AAAATATCTCTTAGAGAATTTTCT

                                      
      36097 AAAATAATCTCTTTAGAGAATTTTCT
          1 AAAAT-ATCTC-TTAGAGAATTTTCT

      36123 CTATACAACT


Statistics
Matches: 22,  Mismatches: 0, Indels: 4
        0.85            0.00        0.15

Matches are distributed among these distances:
  22    5  0.23
  23    5  0.23
  25    5  0.23
  26    7  0.32

ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42


Consensus pattern (24 bp):   
AAAATATCTCTTAGAGAATTTTCT

Found at i:36335 original size:61 final size:59

Alignment explanation


    Indices: 36233--36348  Score: 178
    Period size: 61  Copynumber: 1.9  Consensus size: 59

      36223 ATCACTTTAA

                   *     *                                             
      36233 TATTAAATTAATATAATATTTATCAAGATAAATATTAAATTAAATGTAATATTAAATCT
          1 TATTAAAATAATAAAATATTTATCAAGATAAATATTAAATTAAATGTAATATTAAATCT

                                  *                        *         
      36292 TATTAAAATAATAAAATATTTTTTACAAGATAAATATTAAATTAAATTTAATATTAA
          1 TATTAAAATAATAAAATA-TTTAT-CAAGATAAATATTAAATTAAATGTAATATTAA

      36349 GATAATCACT


Statistics
Matches: 51,  Mismatches: 4, Indels: 2
        0.89            0.07        0.04

Matches are distributed among these distances:
  59   16  0.31
  60    4  0.08
  61   31  0.61

ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42


Consensus pattern (59 bp):   
TATTAAAATAATAAAATATTTATCAAGATAAATATTAAATTAAATGTAATATTAAATCT
Done.