Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008076.1 Kokia drynarioides strain JFW-HI SEQ_122732, 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: 19249
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:7335 original size:21 final size:21

Alignment explanation


    Indices: 7306--7346  Score: 55
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       7296 TGTAATTTAG

                           *     
       7306 ATTTATAAACTTTATGTTTGA
          1 ATTTATAAACTTTATATTTGA

                *    *          
       7327 ATTTCTAAATTTTATATTTG
          1 ATTTATAAACTTTATATTTG

       7347 GATTATGTTA


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.32, C:0.05, G:0.07, T:0.56


Consensus pattern (21 bp):   
ATTTATAAACTTTATATTTGA

Found at i:8981 original size:29 final size:29

Alignment explanation


    Indices: 8939--9003  Score: 103
    Period size: 29  Copynumber: 2.2  Consensus size: 29

       8929 ATTAAGCACA

                               * **      
       8939 AATACAAAGAAGAACATTTGAGCTAAATG
          1 AATACAAAGAAGAACATTTAAAATAAATG

                                         
       8968 AATACAAAGAAGAACATTTAAAATAAATG
          1 AATACAAAGAAGAACATTTAAAATAAATG

                   
       8997 AATACAA
          1 AATACAA

       9004 TGAAAGCTCA


Statistics
Matches: 33,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  29   33  1.00

ACGTcount: A:0.58, C:0.09, G:0.12, T:0.20


Consensus pattern (29 bp):   
AATACAAAGAAGAACATTTAAAATAAATG

Found at i:9265 original size:20 final size:20

Alignment explanation


    Indices: 9242--9283  Score: 57
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       9232 AGAAGCATAC

                   *      *     
       9242 TTGTATCTGCAGAATTGAAG
          1 TTGTATCGGCAGAAGTGAAG

                     *          
       9262 TTGTATCGGTAGAAGTGAAG
          1 TTGTATCGGCAGAAGTGAAG

              
       9282 TT
          1 TT

       9284 CTATTGGTAA


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36


Consensus pattern (20 bp):   
TTGTATCGGCAGAAGTGAAG

Found at i:9292 original size:20 final size:20

Alignment explanation


    Indices: 9252--9297  Score: 56
    Period size: 20  Copynumber: 2.3  Consensus size: 20

       9242 TTGTATCTGC

                *       *       
       9252 AGAATTGAAGTTGTATCGGT
          1 AGAAGTGAAGTTCTATCGGT

                            *   
       9272 AGAAGTGAAGTTCTATTGGT
          1 AGAAGTGAAGTTCTATCGGT

             *    
       9292 AAAAGT
          1 AGAAGT

       9298 CCAAGGTAGA


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

Matches are distributed among these distances:
  20   22  1.00

ACGTcount: A:0.35, C:0.04, G:0.28, T:0.33


Consensus pattern (20 bp):   
AGAAGTGAAGTTCTATCGGT

Found at i:13097 original size:13 final size:13

Alignment explanation


    Indices: 13079--13103  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

      13069 AAATACAAAT

                         
      13079 ACTTAAACTTAAA
          1 ACTTAAACTTAAA

                        
      13092 ACTTAAACTTAA
          1 ACTTAAACTTAA

      13104 CCTTAAAATT


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32


Consensus pattern (13 bp):   
ACTTAAACTTAAA
Done.