Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000429.1 Kokia drynarioides strain JFW-HI SEQ_111261, 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: 20780
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:8049 original size:21 final size:21

Alignment explanation


    Indices: 8025--8081  Score: 60
    Period size: 23  Copynumber: 2.6  Consensus size: 21

       8015 AATTATATTT

                                 
       8025 TAATTTTTTATATTTAAAATA
          1 TAATTTTTTATATTTAAAATA

                     *          *  
       8046 TAATGTTTTAATCATTTAAATTA
          1 TAAT-TTTTTAT-ATTTAAAATA

             *           
       8069 TTATTTTATTATA
          1 TAATTTT-TTATA

       8082 AAATAATCAT


Statistics
Matches: 29,  Mismatches: 4, Indels: 5
        0.76            0.11        0.13

Matches are distributed among these distances:
  21    4  0.14
  22   10  0.34
  23   15  0.52

ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58


Consensus pattern (21 bp):   
TAATTTTTTATATTTAAAATA

Found at i:8217 original size:18 final size:18

Alignment explanation


    Indices: 8194--8236  Score: 61
    Period size: 18  Copynumber: 2.4  Consensus size: 18

       8184 GAATAAAATT

                               
       8194 TTAATTAAATAAATTT-AA
          1 TTAATTAAA-AAATTTAAA

                       *      
       8212 TTAATTAAAAATTTTAAA
          1 TTAATTAAAAAATTTAAA

                   
       8230 TTAATTA
          1 TTAATTA

       8237 CAATTAAAAA


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  17    5  0.22
  18   18  0.78

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (18 bp):   
TTAATTAAAAAATTTAAA

Found at i:8253 original size:31 final size:31

Alignment explanation


    Indices: 8188--8253  Score: 73
    Period size: 31  Copynumber: 2.1  Consensus size: 31

       8178 GAATGAGAAT

                                     *   * 
       8188 AAAATTTTAATTAAATAAATTTAATTAATTA
          1 AAAATTTTAATTAAATAAATTTAATAAATAA

                           *                 
       8219 AAAATTTTAAATTAATTACAA-TTAA-AAATAA
          1 AAAATTTT-AATTAAATA-AATTTAATAAATAA

                
       8250 AAAA
          1 AAAA

       8254 CCCAATTGGA


Statistics
Matches: 30,  Mismatches: 3, Indels: 4
        0.81            0.08        0.11

Matches are distributed among these distances:
  31   16  0.53
  32   12  0.40
  33    2  0.07

ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38


Consensus pattern (31 bp):   
AAAATTTTAATTAAATAAATTTAATAAATAA

Found at i:14746 original size:38 final size:38

Alignment explanation


    Indices: 14695--14771  Score: 136
    Period size: 38  Copynumber: 2.0  Consensus size: 38

      14685 GAATAGCAAA

                                                  
      14695 ACAAAGGTTGAGTAGTTTCCCTTTCTCATGCATCCTAT
          1 ACAAAGGTTGAGTAGTTTCCCTTTCTCATGCATCCTAT

                  *                          *    
      14733 ACAAAGTTTGAGTAGTTTCCCTTTCTCATGCATGCTAT
          1 ACAAAGGTTGAGTAGTTTCCCTTTCTCATGCATCCTAT

             
      14771 A
          1 A

      14772 TTTGTCAAGA


Statistics
Matches: 37,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  38   37  1.00

ACGTcount: A:0.25, C:0.22, G:0.16, T:0.38


Consensus pattern (38 bp):   
ACAAAGGTTGAGTAGTTTCCCTTTCTCATGCATCCTAT
Done.