Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011643.1 Kokia drynarioides strain JFW-HI SEQ_126635, 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, 868

Length: 1448
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.33


Found at i:676 original size:13 final size:14

Alignment explanation


    Indices: 647--679  Score: 50
    Period size: 13  Copynumber: 2.4  Consensus size: 14

        637 AAGTAAGAGG

                      *   
        647 TATATGATGATAAA
          1 TATATGATGAAAAA

                          
        661 TATATGA-GAAAAA
          1 TATATGATGAAAAA

                  
        674 TATATG
          1 TATATG

        680 TGTAAGATAT


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  13   11  0.61
  14    7  0.39

ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33


Consensus pattern (14 bp):   
TATATGATGAAAAA

Found at i:827 original size:24 final size:26

Alignment explanation


    Indices: 800--847  Score: 66
    Period size: 24  Copynumber: 1.9  Consensus size: 26

        790 AGAGAAATGT

                                       
        800 AAATG-TGATATATGA-A-ATTATGAG
          1 AAATGATGA-ATATGAGAGATTATGAG

                                    
        824 AAATGATGAATATGAGAGATTATG
          1 AAATGATGAATATGAGAGATTATG

        848 CCCATGTAGA


Statistics
Matches: 21,  Mismatches: 0, Indels: 4
        0.84            0.00        0.16

Matches are distributed among these distances:
  24   11  0.52
  25    4  0.19
  26    6  0.29

ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31


Consensus pattern (26 bp):   
AAATGATGAATATGAGAGATTATGAG

Found at i:936 original size:23 final size:23

Alignment explanation


    Indices: 910--1005  Score: 149
    Period size: 23  Copynumber: 4.2  Consensus size: 23

        900 ACACTAGCGC

                                   
        910 GCTCTCTGATTAGCACTGTGTGT
          1 GCTCTCTGATTAGCACTGTGTGT

                    *   *           
        933 GCTCTCTGTTTAACACT-TCGTGT
          1 GCTCTCTGATTAGCACTGT-GTGT

                 *                 
        956 GCTCTTTGATTAGCACTGTGTGT
          1 GCTCTCTGATTAGCACTGTGTGT

                                   
        979 GCTCTCTGATTAGCACTGTGTGT
          1 GCTCTCTGATTAGCACTGTGTGT

                
       1002 GCTC
          1 GCTC

       1006 AGTACTTTGT


Statistics
Matches: 65,  Mismatches: 6, Indels: 4
        0.87            0.08        0.05

Matches are distributed among these distances:
  22    1  0.02
  23   63  0.97
  24    1  0.02

ACGTcount: A:0.12, C:0.23, G:0.24, T:0.41


Consensus pattern (23 bp):   
GCTCTCTGATTAGCACTGTGTGT

Done.