Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000681.1 Kokia drynarioides strain JFW-HI SEQ_111676, 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: 4977
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36


Found at i:425 original size:69 final size:69

Alignment explanation


    Indices: 314--455  Score: 275
    Period size: 69  Copynumber: 2.1  Consensus size: 69

        304 CCCCGCGGAG

                                                                             
        314 TTTATGGAAACGAAGTCGTGACGTTCGGGTTTCTGAAGAAAAGAATTGAATAAATTTTTGTTATG
          1 TTTATGGAAACGAAGTCGTGACGTTCGGGTTTCTGAAGAAAAGAATTGAATAAATTTTTGTTATG

                
        379 GACT
         66 GACT

                                                                             
        383 TTTATGGAAACGAAGTCGTGACGTTCGGGTTTCTGAAGAAAAGAATTGAATAAATTTTTGTTATG
          1 TTTATGGAAACGAAGTCGTGACGTTCGGGTTTCTGAAGAAAAGAATTGAATAAATTTTTGTTATG

             *  
        448 GGCT
         66 GACT

                
        452 TTTA
          1 TTTA

        456 GTAACCTCTA


Statistics
Matches: 72,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  69   72  1.00

ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36


Consensus pattern (69 bp):   
TTTATGGAAACGAAGTCGTGACGTTCGGGTTTCTGAAGAAAAGAATTGAATAAATTTTTGTTATG
GACT

Found at i:2984 original size:22 final size:22

Alignment explanation


    Indices: 2942--2985  Score: 63
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       2932 AGTGCTTTTT

                           *      
       2942 AAAAACACTTTTGACGTAAAAA
          1 AAAAACACTTTTGACATAAAAA

                             *    
       2964 AAAAACACTTTTGA-ATCAAAA
          1 AAAAACACTTTTGACATAAAAA

             
       2985 A
          1 A

       2986 CAGTACTAAA


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  21    6  0.30
  22   14  0.70

ACGTcount: A:0.57, C:0.14, G:0.07, T:0.23


Consensus pattern (22 bp):   
AAAAACACTTTTGACATAAAAA

Found at i:3946 original size:23 final size:23

Alignment explanation


    Indices: 3920--3999  Score: 124
    Period size: 23  Copynumber: 3.5  Consensus size: 23

       3910 TAGCGCAAAT

                 *     *  *   *    
       3920 CAGTAGGCACAAGAGGTGTGAAA
          1 CAGTAAGCACATGAAGTGCGAAA

                                   
       3943 CAGTAAGCACATGAAGTGCGAAA
          1 CAGTAAGCACATGAAGTGCGAAA

                                   
       3966 CAGTAAGCACATGAAGTGCGAAA
          1 CAGTAAGCACATGAAGTGCGAAA

                       
       3989 CAGTAAGCACA
          1 CAGTAAGCACA

       4000 CACAGTGCTG


Statistics
Matches: 53,  Mismatches: 4, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  23   53  1.00

ACGTcount: A:0.42, C:0.17, G:0.28, T:0.12


Consensus pattern (23 bp):   
CAGTAAGCACATGAAGTGCGAAA

Found at i:4006 original size:23 final size:22

Alignment explanation


    Indices: 3826--4019  Score: 121
    Period size: 23  Copynumber: 8.5  Consensus size: 22

       3816 CGAAGTACTT

                                      
       3826 AACAGTAAGCACACAAGTGCTGGGGA
          1 AACAGTAAGCACACAAGTGC----GA

                                  
       3852 AACAGTAAGCACAC-AGTGC-A
          1 AACAGTAAGCACACAAGTGCGA

             *      *               
       3872 ATCTAGTAGGCACACACAGTGC-A
          1 AAC-AGTAAGCACACA-AGTGCGA

             *     *  **      *    
       3895 ATCAGTAGGCGTACATAGCGC-A
          1 AACAGTAAGCACACA-AGTGCGA

                    *             *  
       3917 AATCAGTAGGCACA-AGAGGTGTGA
          1 AA-CAGTAAGCACACA-A-GTGCGA

                          *        
       3941 AACAGTAAGCACATGAAGTGCGA
          1 AACAGTAAGCACA-CAAGTGCGA

                          *        
       3964 AACAGTAAGCACATGAAGTGCGA
          1 AACAGTAAGCACA-CAAGTGCGA

                                    
       3987 AACAGTAAGCACACACAGTGCTG-
          1 AACAGTAAGCACACA-AGTGC-GA

                      
       4010 AACAGTAAGC
          1 AACAGTAAGC

       4020 GCGCTAACGT


Statistics
Matches: 143,  Mismatches: 15, Indels: 23
        0.79            0.08        0.13

Matches are distributed among these distances:
  20    3  0.02
  21   10  0.07
  22   19  0.13
  23   86  0.60
  24    5  0.03
  25    6  0.04
  26   14  0.10

ACGTcount: A:0.40, C:0.21, G:0.26, T:0.14


Consensus pattern (22 bp):   
AACAGTAAGCACACAAGTGCGA

Done.