Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015553.1 Corchorus olitorius cultivar O-4 contig15586, 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: 21062
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.26


Found at i:65 original size:27 final size:29

Alignment explanation


    Indices: 5--66  Score: 74
    Period size: 29  Copynumber: 2.2  Consensus size: 29

          1 GTAG

                                 *     **
          5 CAATTTATATAATATTTATTCTTATTTGG
          1 CAATTTATATAATATTTATTCATATTTAA

                                         
         34 CAATTTATATAATATTTA-T-ATATTTAA
          1 CAATTTATATAATATTTATTCATATTTAA

            *     
         61 TAATTT
          1 CAATTT

         67 TGGCTTCTTT


Statistics
Matches: 29,  Mismatches: 4, Indels: 2
        0.83            0.11        0.06

Matches are distributed among these distances:
  27   10  0.34
  28    1  0.03
  29   18  0.62

ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55


Consensus pattern (29 bp):   
CAATTTATATAATATTTATTCATATTTAA

Found at i:6323 original size:33 final size:33

Alignment explanation


    Indices: 6281--6346  Score: 114
    Period size: 33  Copynumber: 2.0  Consensus size: 33

       6271 CTCCTGACAT

                                       *     
       6281 GAGTAGAGAGGAGGACAATGAGATAGGTGGCGA
          1 GAGTAGAGAGGAGGACAATGAGATAGGCGGCGA

                           *                 
       6314 GAGTAGAGAGGAGGAGAATGAGATAGGCGGCGA
          1 GAGTAGAGAGGAGGACAATGAGATAGGCGGCGA

       6347 TGTCCCTCCC


Statistics
Matches: 31,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  33   31  1.00

ACGTcount: A:0.36, C:0.06, G:0.47, T:0.11


Consensus pattern (33 bp):   
GAGTAGAGAGGAGGACAATGAGATAGGCGGCGA

Found at i:6394 original size:81 final size:81

Alignment explanation


    Indices: 6243--6394  Score: 241
    Period size: 81  Copynumber: 1.9  Consensus size: 81

       6233 TAGAGGTAGA

                                       *    *                        *      *
       6243 GAGGAGAATGAGATAGGCAGCGATGTCTCTCCTGACATGAGTAGAGAGGAGGACAATGAGATAGG
          1 GAGGAGAATGAGATAGGCAGCGATGTCCCTCCCGACATGAGTAGAGAGGAGGACAATAAGATAGA

            *               
       6308 TGGCGAGAGTAGAGAG
         66 CGGCGAGAGTAGAGAG

                              *                                  *           
       6324 GAGGAGAATGAGATAGGCGGCGATGTCCCTCCCGACATGAGTAGAGAGGAGGAGAATAAGATAGA
          1 GAGGAGAATGAGATAGGCAGCGATGTCCCTCCCGACATGAGTAGAGAGGAGGACAATAAGATAGA

                  
       6389 CGGCGA
         66 CGGCGA

       6395 TGTCCCGCCT


Statistics
Matches: 64,  Mismatches: 7, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  81   64  1.00

ACGTcount: A:0.34, C:0.13, G:0.39, T:0.14


Consensus pattern (81 bp):   
GAGGAGAATGAGATAGGCAGCGATGTCCCTCCCGACATGAGTAGAGAGGAGGACAATAAGATAGA
CGGCGAGAGTAGAGAG

Found at i:6450 original size:42 final size:39

Alignment explanation


    Indices: 6371--6450  Score: 97
    Period size: 42  Copynumber: 2.0  Consensus size: 39

       6361 TGAGTAGAGA

                                            *      
       6371 GGAGGAGAATAAGATAGACGGCGATGTCCCGCCTGACAG
          1 GGAGGAGAATAAGATAGACGGCGATGTCCCGCATGACAG

                                *         *  *       
       6410 GGAGGAGAATGATGAGATAGGCGGCGATGTTCCTCATGACA
          1 GGAGGAGAAT-A--AGATAGACGGCGATGTCCCGCATGACA

       6451 TGGTTAATTG


Statistics
Matches: 34,  Mismatches: 4, Indels: 3
        0.83            0.10        0.07

Matches are distributed among these distances:
  39   10  0.29
  40    1  0.03
  42   23  0.68

ACGTcount: A:0.30, C:0.17, G:0.36, T:0.16


Consensus pattern (39 bp):   
GGAGGAGAATAAGATAGACGGCGATGTCCCGCATGACAG

Found at i:20976 original size:23 final size:22

Alignment explanation


    Indices: 20950--20992  Score: 68
    Period size: 23  Copynumber: 1.9  Consensus size: 22

      20940 TATTAAAAGA

                                   
      20950 TAAAAAGAAATTGAAAAAAAATC
          1 TAAAAAGAAATT-AAAAAAAATC

                    *           
      20973 TAAAAAGATATTAAAAAAAA
          1 TAAAAAGAAATTAAAAAAAA

      20993 CCGCAGAAAA


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  22    8  0.42
  23   11  0.58

ACGTcount: A:0.72, C:0.02, G:0.07, T:0.19


Consensus pattern (22 bp):   
TAAAAAGAAATTAAAAAAAATC
Done.