Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005528.1 Kokia drynarioides strain JFW-HI SEQ_119615, 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, 697

Length: 1162
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37


Found at i:523 original size:112 final size:113

Alignment explanation


    Indices: 326--549  Score: 283
    Period size: 112  Copynumber: 2.0  Consensus size: 113

        316 TTCCTTATAT

                                    *                     * * *              
        326 CATTAGACCACTAACCGCTATTTCGATGCAAAAATGCTTGAACAGGTTTGTAAAATGGATAAAAT
          1 CATTAGACCACTAACCGCTATTTCAATGCAAAAATGCTTGAACAGGGTCGCAAAATGGATAAAAT

                                 * *              *         
        391 TGAATTTTATGAGAGGCAAAGGTTGCATGAATG-AAAAGATTAAAAAC
         66 TGAATTTTATGAGAGGCAAAGCTCGCATGAATGAAAAAAATTAAAAAC

                  *          *              **                   **         *
        438 CATTAGTCCACTAACCGTTATTTCAATGCAAACGTGCTTGAACAGGGTCGCAAGGTGGGA-AAAT
          1 CATTAGACCACTAACCGCTATTTCAATGCAAAAATGCTTGAACAGGGTCGCAAAAT-GGATAAAA

                                                             
        502 TTGAATTTTATTG-GAGGCAAAGCTCGCATGAATGAAAAAAATTAAAAA
         65 TTGAATTTTA-TGAGAGGCAAAGCTCGCATGAATGAAAAAAATTAAAAA

        550 AGACAATCAT


Statistics
Matches: 95,  Mismatches: 14, Indels: 5
        0.83            0.12        0.04

Matches are distributed among these distances:
 112   78  0.82
 113   17  0.18

ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26


Consensus pattern (113 bp):   
CATTAGACCACTAACCGCTATTTCAATGCAAAAATGCTTGAACAGGGTCGCAAAATGGATAAAAT
TGAATTTTATGAGAGGCAAAGCTCGCATGAATGAAAAAAATTAAAAAC

Found at i:875 original size:19 final size:19

Alignment explanation


    Indices: 853--908  Score: 53
    Period size: 19  Copynumber: 2.9  Consensus size: 19

        843 TCACCTCGAG

                                
        853 CTCTCCTTT-TTCTTTTTTC
          1 CTCT-CTTTCTTCTTTTTTC

                *              
        872 CTCTTTTTCTTCTTTTTT-
          1 CTCTCTTTCTTCTTTTTTC

            *   *              
        890 TTCTTTTTCCTTCTTTTTT
          1 CTCTCTTT-CTTCTTTTTT

        909 TTTTTGGGTG


Statistics
Matches: 33,  Mismatches: 2, Indels: 4
        0.85            0.05        0.10

Matches are distributed among these distances:
  18   10  0.30
  19   23  0.70

ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75


Consensus pattern (19 bp):   
CTCTCTTTCTTCTTTTTTC

Found at i:880 original size:9 final size:9

Alignment explanation


    Indices: 858--907  Score: 50
    Period size: 9  Copynumber: 5.7  Consensus size: 9

        848 TCGAGCTCTC

                     
        858 CTTTTT-CT
          1 CTTTTTCCT

                     
        866 -TTTTTCCT
          1 CTTTTTCCT

                   * 
        874 CTTTTTCTT
          1 CTTTTTCCT

                  ** 
        883 CTTTTTTTT
          1 CTTTTTCCT

                      
        892 CTTTTTCCTT
          1 CTTTTTCC-T

                  
        902 CTTTTT
          1 CTTTTT

        908 TTTTTTGGGT


Statistics
Matches: 35,  Mismatches: 4, Indels: 4
        0.81            0.09        0.09

Matches are distributed among these distances:
   7    5  0.14
   8    2  0.06
   9   21  0.60
  10    7  0.20

ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78


Consensus pattern (9 bp):   
CTTTTTCCT

Found at i:909 original size:19 final size:18

Alignment explanation


    Indices: 862--910  Score: 71
    Period size: 19  Copynumber: 2.6  Consensus size: 18

        852 GCTCTCCTTT

                      *        
        862 TTCTTTTTTCCTCTTTTTC
          1 TTCTTTTTT-TTCTTTTTC

                               
        881 TTCTTTTTTTTCTTTTTCC
          1 TTCTTTTTTTTCTTTTT-C

                       
        900 TTCTTTTTTTT
          1 TTCTTTTTTTT

        911 TTTGGGTGAA


Statistics
Matches: 28,  Mismatches: 1, Indels: 2
        0.90            0.03        0.06

Matches are distributed among these distances:
  18    7  0.25
  19   21  0.75

ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80


Consensus pattern (18 bp):   
TTCTTTTTTTTCTTTTTC
Done.