Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013890.1 Kokia drynarioides strain JFW-HI SEQ_128918, 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: 9459
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34


Found at i:4552 original size:53 final size:53

Alignment explanation


    Indices: 4443--4572  Score: 181
    Period size: 53  Copynumber: 2.5  Consensus size: 53

       4433 CACACGGACG

                                                             * **
       4443 TGTGTCAAGGTGTGTGTATATTG-TCTAAGACACATGGGCTGACACATGGGGG
          1 TGTGTCAAGGTGTGTGTATATTGTTCTAAGACACATGGGCTGACACATGAGCA

                   *            *       * *  *                   
       4495 TGTGTCAGGGTGTGTGTATACTGTTCTAGGGCATATGGGCTGACACATGAGCA
          1 TGTGTCAAGGTGTGTGTATATTGTTCTAAGACACATGGGCTGACACATGAGCA

                                     
       4548 TGTGTCAAGGTGTGTGTATATTGTT
          1 TGTGTCAAGGTGTGTGTATATTGTT

       4573 TTCAGACGCA


Statistics
Matches: 67,  Mismatches: 10, Indels: 1
        0.86            0.13        0.01

Matches are distributed among these distances:
  52   21  0.31
  53   46  0.69

ACGTcount: A:0.21, C:0.12, G:0.34, T:0.33


Consensus pattern (53 bp):   
TGTGTCAAGGTGTGTGTATATTGTTCTAAGACACATGGGCTGACACATGAGCA

Found at i:5869 original size:33 final size:32

Alignment explanation


    Indices: 5823--5891  Score: 102
    Period size: 33  Copynumber: 2.1  Consensus size: 32

       5813 AAAAAAGATA

                            *          *    
       5823 AATTCTATTAGGATTTGAAAAGGAGTAGTTTG
          1 AATTCTATTAGGATTTAAAAAGGAGTAATTTG

                                     *       
       5855 AATTCTAGTTAGGATTTAAAAAGGATTAATTTG
          1 AATTCTA-TTAGGATTTAAAAAGGAGTAATTTG

                
       5888 AATT
          1 AATT

       5892 TCAAATTAAA


Statistics
Matches: 33,  Mismatches: 3, Indels: 1
        0.89            0.08        0.03

Matches are distributed among these distances:
  32    7  0.21
  33   26  0.79

ACGTcount: A:0.38, C:0.03, G:0.20, T:0.39


Consensus pattern (32 bp):   
AATTCTATTAGGATTTAAAAAGGAGTAATTTG

Found at i:6850 original size:21 final size:21

Alignment explanation


    Indices: 6809--6852  Score: 54
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       6799 AGAGTTTTTA

                            *    
       6809 GTTTCGGTAGAAGTAAGACTT
          1 GTTTCGGTAGAAGTAACACTT

                *                 
       6830 GTTTTGGTAGAAG-AGACACTT
          1 GTTTCGGTAGAAGTA-ACACTT

              
       6851 GT
          1 GT

       6853 ATCTATCGAA


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  20    1  0.05
  21   19  0.95

ACGTcount: A:0.27, C:0.09, G:0.30, T:0.34


Consensus pattern (21 bp):   
GTTTCGGTAGAAGTAACACTT
Done.