Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013379.1 Kokia drynarioides strain JFW-HI SEQ_128402, 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: 24687
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33


Found at i:4661 original size:13 final size:14

Alignment explanation


    Indices: 4643--4672  Score: 53
    Period size: 14  Copynumber: 2.2  Consensus size: 14

       4633 GTCAACGCAA

                          
       4643 TCAGA-GTTAAATG
          1 TCAGAGGTTAAATG

                          
       4656 TCAGAGGTTAAATG
          1 TCAGAGGTTAAATG

               
       4670 TCA
          1 TCA

       4673 ATGTATTGAA


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

Matches are distributed among these distances:
  13    5  0.31
  14   11  0.69

ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30


Consensus pattern (14 bp):   
TCAGAGGTTAAATG

Found at i:5893 original size:11 final size:11

Alignment explanation


    Indices: 5877--5909  Score: 57
    Period size: 11  Copynumber: 3.0  Consensus size: 11

       5867 TGATACATGC

                     * 
       5877 TAAATGAGATA
          1 TAAATGAGACA

                       
       5888 TAAATGAGACA
          1 TAAATGAGACA

                       
       5899 TAAATGAGACA
          1 TAAATGAGACA

       5910 CTTAAAACAC


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  11   21  1.00

ACGTcount: A:0.55, C:0.06, G:0.18, T:0.21


Consensus pattern (11 bp):   
TAAATGAGACA

Found at i:6952 original size:24 final size:24

Alignment explanation


    Indices: 6925--6977  Score: 63
    Period size: 24  Copynumber: 2.2  Consensus size: 24

       6915 GCTCACCCTC

                   *              *  
       6925 ATCCTGGTG-CTTTTTCTTCTTTTT
          1 ATCCTGGCGCCTTTTTC-TCTTCTT

                 *                  
       6949 ATCCTTGCGCCTTTTTCTCTTCTT
          1 ATCCTGGCGCCTTTTTCTCTTCTT

                 
       6973 ATCCT
          1 ATCCT

       6978 CCGTACAAAC


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  24   18  0.72
  25    7  0.28

ACGTcount: A:0.06, C:0.28, G:0.09, T:0.57


Consensus pattern (24 bp):   
ATCCTGGCGCCTTTTTCTCTTCTT

Found at i:7282 original size:21 final size:21

Alignment explanation


    Indices: 7258--7305  Score: 71
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       7248 CTTGGCAGGG

                              *   
       7258 TCCTTCTCTTCATTC-TCTTTT
          1 TCCTTCTCTTC-TTCTTCCTTT

                                 
       7279 TCCTTCTCTTCTTCTTCCTTT
          1 TCCTTCTCTTCTTCTTCCTTT

                  
       7300 TCCTTC
          1 TCCTTC

       7306 AAATGGTCAT


Statistics
Matches: 25,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  20    3  0.12
  21   22  0.88

ACGTcount: A:0.02, C:0.38, G:0.00, T:0.60


Consensus pattern (21 bp):   
TCCTTCTCTTCTTCTTCCTTT

Found at i:16363 original size:27 final size:27

Alignment explanation


    Indices: 16333--16387  Score: 101
    Period size: 27  Copynumber: 2.0  Consensus size: 27

      16323 TACACATAGT

                 *                     
      16333 AGCTTTACTTGGAATACATTATCGTGC
          1 AGCTTCACTTGGAATACATTATCGTGC

                                       
      16360 AGCTTCACTTGGAATACATTATCGTGC
          1 AGCTTCACTTGGAATACATTATCGTGC

             
      16387 A
          1 A

      16388 TACTTATTGA


Statistics
Matches: 27,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  27   27  1.00

ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35


Consensus pattern (27 bp):   
AGCTTCACTTGGAATACATTATCGTGC

Found at i:17443 original size:21 final size:22

Alignment explanation


    Indices: 17417--17476  Score: 70
    Period size: 21  Copynumber: 2.8  Consensus size: 22

      17407 AAGAGCTACA

                          *       
      17417 GAGTTCTACCGATATAAC-TGG
          1 GAGTTCTACCGATACAACTTGG

                    **          * 
      17438 GAGTTCTATTGATACAACTTTG
          1 GAGTTCTACCGATACAACTTGG

                              
      17460 GA-TTCTACCGATACAAC
          1 GAGTTCTACCGATACAAC

      17477 CTAGACTTCT


Statistics
Matches: 32,  Mismatches: 6, Indels: 2
        0.80            0.15        0.05

Matches are distributed among these distances:
  21   28  0.88
  22    4  0.12

ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32


Consensus pattern (22 bp):   
GAGTTCTACCGATACAACTTGG
Done.