Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003335.1 Kokia drynarioides strain JFW-HI SEQ_116037, 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: 6992
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32


Found at i:58 original size:25 final size:25

Alignment explanation


    Indices: 13--65  Score: 65
    Period size: 25  Copynumber: 2.1  Consensus size: 25

          3 TTTAATTAGT

                          *           
         13 AAATATATTTATTTTTAAAATTTATA
          1 AAATATATTTATTTATAAAATTT-TA

                                      
         39 AAATATA-TTATTTA-ATAAATTTTA
          1 AAATATATTTATTTATA-AAATTTTA

               
         63 AAA
          1 AAA

         66 AATAAACACA


Statistics
Matches: 25,  Mismatches: 1, Indels: 4
        0.83            0.03        0.13

Matches are distributed among these distances:
  24    6  0.24
  25   12  0.48
  26    7  0.28

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (25 bp):   
AAATATATTTATTTATAAAATTTTA

Found at i:66 original size:25 final size:26

Alignment explanation


    Indices: 13--69  Score: 71
    Period size: 26  Copynumber: 2.2  Consensus size: 26

          3 TTTAATTAGT

                          *           
         13 AAATATATTTATTTTTAAAATTTATA
          1 AAATATATTTATTTATAAAATTTATA

                                *    * 
         39 AAATATA-TTATTTAATAAATTTTAAA
          1 AAATATATTTATTT-ATAAAATTTATA

                 
         65 AAATA
          1 AAATA

         70 AACACATAAA


Statistics
Matches: 27,  Mismatches: 3, Indels: 2
        0.84            0.09        0.06

Matches are distributed among these distances:
  25    6  0.22
  26   21  0.78

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


Consensus pattern (26 bp):   
AAATATATTTATTTATAAAATTTATA

Found at i:701 original size:19 final size:19

Alignment explanation


    Indices: 679--723  Score: 56
    Period size: 19  Copynumber: 2.4  Consensus size: 19

        669 TTTTATTAGG

                                
        679 ATTTAATATTTAAGATAT-T
          1 ATTTAATATTTAA-ATATGT

                 *         *   
        698 ATTTATTATTTAAATTTGT
          1 ATTTAATATTTAAATATGT

                   
        717 ATTTAAT
          1 ATTTAAT

        724 TTATGTTTAT


Statistics
Matches: 22,  Mismatches: 3, Indels: 2
        0.81            0.11        0.07

Matches are distributed among these distances:
  18    3  0.14
  19   19  0.86

ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58


Consensus pattern (19 bp):   
ATTTAATATTTAAATATGT

Found at i:3097 original size:21 final size:21

Alignment explanation


    Indices: 3080--3130  Score: 75
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       3070 GAATTTCAGC

                 *               
       3080 AGCAATCTATAGATTTTCAAA
          1 AGCAAACTATAGATTTTCAAA

                    *          * 
       3101 AGCAAACTGTAGATTTTCACA
          1 AGCAAACTATAGATTTTCAAA

                     
       3122 AGCAAACTA
          1 AGCAAACTA

       3131 AGGCATCTAT


Statistics
Matches: 26,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  21   26  1.00

ACGTcount: A:0.43, C:0.18, G:0.12, T:0.27


Consensus pattern (21 bp):   
AGCAAACTATAGATTTTCAAA
Done.