Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006044.1 Kokia drynarioides strain JFW-HI SEQ_120510, 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: 1942
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33


Found at i:40 original size:22 final size:22

Alignment explanation


    Indices: 14--99  Score: 84
    Period size: 22  Copynumber: 3.7  Consensus size: 22

          4 ATTATTTAAT

                    *             
         14 AATTTTATTATTTTAAAAAATA
          1 AATTTTATAATTTTAAAAAATA

                                     * 
         36 AATTTTATAATTTTATAATTTCAAAAA
          1 AATTTTATAATTTTA-AA----AAATA

              *                   
         63 AAATTTAT-ATTTTAAAAAATA
          1 AATTTTATAATTTTAAAAAATA

                 *          
         84 AATTTAATAATTTTAA
          1 AATTTTATAATTTTAA

        100 TATTTTAAAA


Statistics
Matches: 52,  Mismatches: 6, Indels: 12
        0.74            0.09        0.17

Matches are distributed among these distances:
  21   10  0.19
  22   21  0.40
  23    2  0.04
  25    2  0.04
  26    6  0.12
  27   11  0.21

ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48


Consensus pattern (22 bp):   
AATTTTATAATTTTAAAAAATA

Found at i:46 original size:30 final size:30

Alignment explanation


    Indices: 7--63  Score: 87
    Period size: 30  Copynumber: 1.9  Consensus size: 30

          1 AAAATT

                           *    *         
          7 ATTTAATAATTTTATTATTTTAAAAAATAA
          1 ATTTAATAATTTTATAATTTCAAAAAATAA

                *                      
         37 ATTTTATAATTTTATAATTTCAAAAAA
          1 ATTTAATAATTTTATAATTTCAAAAAA

         64 AATTTATATT


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  30   24  1.00

ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49


Consensus pattern (30 bp):   
ATTTAATAATTTTATAATTTCAAAAAATAA

Found at i:71 original size:19 final size:20

Alignment explanation


    Indices: 42--96  Score: 67
    Period size: 19  Copynumber: 2.8  Consensus size: 20

         32 AATAAATTTT

                *          *    
         42 ATAATTTTATAATTTCAAAA
          1 ATAAATTTATAATTTAAAAA

                       *        
         62 A-AAATTTATATTTTAAAAA
          1 ATAAATTTATAATTTAAAAA

                            
         81 ATAAATTTAATAATTT
          1 ATAAATTT-ATAATTT

         97 TAATATTTTA


Statistics
Matches: 29,  Mismatches: 4, Indels: 3
        0.81            0.11        0.08

Matches are distributed among these distances:
  19   16  0.55
  20    7  0.24
  21    6  0.21

ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45


Consensus pattern (20 bp):   
ATAAATTTATAATTTAAAAA

Found at i:81 original size:20 final size:22

Alignment explanation


    Indices: 58--99  Score: 61
    Period size: 20  Copynumber: 2.0  Consensus size: 22

         48 TTATAATTTC

                                  
         58 AAAAAAAATTT-AT-ATTTTAA
          1 AAAAAAAATTTAATAATTTTAA

                *                 
         78 AAAATAAATTTAATAATTTTAA
          1 AAAAAAAATTTAATAATTTTAA

        100 TATTTTAAAA


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  20   10  0.53
  21    2  0.11
  22    7  0.37

ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40


Consensus pattern (22 bp):   
AAAAAAAATTTAATAATTTTAA

Found at i:87 original size:48 final size:49

Alignment explanation


    Indices: 17--111  Score: 149
    Period size: 48  Copynumber: 2.0  Consensus size: 49

          7 ATTTAATAAT

                                    *                         
         17 TTTATTATTTTAAAAAATAAATTTTATAATTTT-ATAATTTCAAAAAAAA
          1 TTTATTATTTTAAAAAATAAATTTAATAATTTTAAT-ATTTCAAAAAAAA

                                                    *      
         66 TTTA-TATTTTAAAAAATAAATTTAATAATTTTAATATTTTAAAAAA
          1 TTTATTATTTTAAAAAATAAATTTAATAATTTTAATATTTCAAAAAA

        112 TATAAGCAAA


Statistics
Matches: 43,  Mismatches: 2, Indels: 3
        0.90            0.04        0.06

Matches are distributed among these distances:
  48   37  0.86
  49    6  0.14

ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47


Consensus pattern (49 bp):   
TTTATTATTTTAAAAAATAAATTTAATAATTTTAATATTTCAAAAAAAA
Done.