Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006335.1 Kokia drynarioides strain JFW-HI SEQ_120910, 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: 5376
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37


Found at i:887 original size:31 final size:31

Alignment explanation


    Indices: 847--905  Score: 73
    Period size: 31  Copynumber: 1.9  Consensus size: 31

        837 TTTAAATGTG

                      * *                  
        847 TATAGTTGAATCGCAATCAAAATTTCATTTA
          1 TATAGTTGAACCACAATCAAAATTTCATTTA

                *        *   *          
        878 TATATTTGAACCATAATTAAAATTTCAT
          1 TATAGTTGAACCACAATCAAAATTTCAT

        906 GTGTATAATT


Statistics
Matches: 23,  Mismatches: 5, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  31   23  1.00

ACGTcount: A:0.41, C:0.12, G:0.07, T:0.41


Consensus pattern (31 bp):   
TATAGTTGAACCACAATCAAAATTTCATTTA

Found at i:946 original size:30 final size:31

Alignment explanation


    Indices: 865--939  Score: 84
    Period size: 31  Copynumber: 2.5  Consensus size: 31

        855 AATCGCAATC

                      *      *              
        865 AAAATTTCATTTATATATTTGA-ACCATAATT
          1 AAAATTTCATGTATATAATT-ACACCATAATT

                        *                  
        896 AAAATTTCATGTGTATAATTACACCA-AATT
          1 AAAATTTCATGTATATAATTACACCATAATT

                           
        926 AAAA-TTCATAGTAT
          1 AAAATTTCAT-GTAT

        940 CAAATTATAC


Statistics
Matches: 38,  Mismatches: 4, Indels: 5
        0.81            0.09        0.11

Matches are distributed among these distances:
  29    5  0.13
  30   12  0.32
  31   21  0.55

ACGTcount: A:0.44, C:0.11, G:0.05, T:0.40


Consensus pattern (31 bp):   
AAAATTTCATGTATATAATTACACCATAATT

Found at i:1795 original size:17 final size:18

Alignment explanation


    Indices: 1773--1830  Score: 66
    Period size: 17  Copynumber: 3.3  Consensus size: 18

       1763 TTTATTTACT

                              
       1773 TAAATTTAATT-TAAAAA
          1 TAAATTTAATTATAAAAA

                   *     *   *
       1790 TAAATTTCATTATTAAAT
          1 TAAATTTAATTATAAAAA

                              
       1808 TAAA-TTAATTATAAAAA
          1 TAAATTTAATTATAAAAA

            *     
       1825 GAAATT
          1 TAAATT

       1831 GCAAATCCCC


Statistics
Matches: 32,  Mismatches: 7, Indels: 3
        0.76            0.17        0.07

Matches are distributed among these distances:
  17   23  0.72
  18    9  0.28

ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41


Consensus pattern (18 bp):   
TAAATTTAATTATAAAAA

Found at i:3529 original size:31 final size:31

Alignment explanation


    Indices: 3494--3552  Score: 109
    Period size: 31  Copynumber: 1.9  Consensus size: 31

       3484 ATAGTTATTG

                             *             
       3494 AACTATTCAAAAGTTTTTATTTAAGTCATTA
          1 AACTATTCAAAAGTTTTCATTTAAGTCATTA

                                        
       3525 AACTATTCAAAAGTTTTCATTTAAGTCA
          1 AACTATTCAAAAGTTTTCATTTAAGTCA

       3553 CCAGGTTGTT


Statistics
Matches: 27,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  31   27  1.00

ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42


Consensus pattern (31 bp):   
AACTATTCAAAAGTTTTCATTTAAGTCATTA
Done.