Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018589.1 Corchorus olitorius cultivar O-4 contig18622, 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: 28679
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31


Found at i:9602 original size:2 final size:2

Alignment explanation


    Indices: 9595--9630  Score: 72
    Period size: 2  Copynumber: 18.0  Consensus size: 2

       9585 GTTGGTAATA

                                                                 
       9595 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
          1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT

       9631 TTTATTTTTA


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   34  1.00

ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50


Consensus pattern (2 bp):   
GT

Found at i:10751 original size:109 final size:109

Alignment explanation


    Indices: 10554--10771  Score: 391
    Period size: 109  Copynumber: 2.0  Consensus size: 109

      10544 ATTATCTTGG

                                      *                                  *   
      10554 TATTCCAAATTTAGGATAAATATGGGGTTCTACAACTTGTGGCTACAAAATTCAAGATTCAGGGA
          1 TATTCCAAATTTAGGATAAATATGGGCTTCTACAACTTGTGGCTACAAAATTCAAGATTCAAGGA

                                                        
      10619 GAACATTATTCGAGAGAGAATTTATTAAAGGCTCCATAGGTATA
         66 GAACATTATTCGAGAGAGAATTTATTAAAGGCTCCATAGGTATA

                *                *                                           
      10663 TATTTCAAATTTAGGATAAATTTGGGCTTCTACAACTTGTGGCTACAAAATTCAAGATTCAAGGA
          1 TATTCCAAATTTAGGATAAATATGGGCTTCTACAACTTGTGGCTACAAAATTCAAGATTCAAGGA

                              *                         
      10728 GAACATTATTCGAGAGAGGATTTATTAAAGGCTCCATAGGTATA
         66 GAACATTATTCGAGAGAGAATTTATTAAAGGCTCCATAGGTATA

      10772 GGTCTTAGTA


Statistics
Matches: 104,  Mismatches: 5, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
 109  104  1.00

ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31


Consensus pattern (109 bp):   
TATTCCAAATTTAGGATAAATATGGGCTTCTACAACTTGTGGCTACAAAATTCAAGATTCAAGGA
GAACATTATTCGAGAGAGAATTTATTAAAGGCTCCATAGGTATA

Found at i:20524 original size:25 final size:24

Alignment explanation


    Indices: 20489--20539  Score: 93
    Period size: 25  Copynumber: 2.1  Consensus size: 24

      20479 ATAAATTTGA

                                    
      20489 AAATCTCCATTCACTTTTACATGC
          1 AAATCTCCATTCACTTTTACATGC

                                     
      20513 AAATCTTCCATTCACTTTTACATGC
          1 AAATC-TCCATTCACTTTTACATGC

              
      20538 AA
          1 AA

      20540 GACAAACACT


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  24    5  0.19
  25   21  0.81

ACGTcount: A:0.31, C:0.27, G:0.04, T:0.37


Consensus pattern (24 bp):   
AAATCTCCATTCACTTTTACATGC

Found at i:20689 original size:13 final size:14

Alignment explanation


    Indices: 20654--20692  Score: 53
    Period size: 13  Copynumber: 2.8  Consensus size: 14

      20644 CCTGCAATTT

                     *     
      20654 AGAAAAGAAAAGAAA
          1 AGAAAAG-AGAGAAA

                          
      20669 AGAAAAGAGAGAAA
          1 AGAAAAGAGAGAAA

                       
      20683 A-AAAAGAGAG
          1 AGAAAAGAGAG

      20693 TATATTTGAA


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

Matches are distributed among these distances:
  13    9  0.39
  14    7  0.30
  15    7  0.30

ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00


Consensus pattern (14 bp):   
AGAAAAGAGAGAAA

Found at i:23008 original size:123 final size:126

Alignment explanation


    Indices: 22789--23040  Score: 404
    Period size: 123  Copynumber: 2.0  Consensus size: 126

      22779 ATTTAAGAAA

                                                                             
      22789 TATATTTAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAAT
          1 TATATTTAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT---AT

                                                         *            *      
      22854 AGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAAG
         63 A-GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAATTGAGTAAAACTATAAAAG

                                                                             
      22919 TATATTTAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAAT-TA-
          1 TATATTTAAAAATTCTAATATATATAAG-TTTTTTAATTAAAATAGTAAAATGGTAAAAATATAG

                                              *                          
      22982 TA-AA-GATATTAGATTTAATTAAATAAAAATAGTGTTTTTAATTGAGTAAAACTATAAAA
         65 TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAATTGAGTAAAACTATAAAA

      23041 AGTTTAAACA


Statistics
Matches: 118,  Mismatches: 3, Indels: 9
        0.91            0.02        0.07

Matches are distributed among these distances:
 123   52  0.44
 124    2  0.02
 125    2  0.02
 127    2  0.02
 130   28  0.24
 131   32  0.27

ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38


Consensus pattern (126 bp):   
TATATTTAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAGT
ATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAATTGAGTAAAACTATAAAAG
Done.