Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021777.1 Corchorus olitorius cultivar O-4 contig21810, 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: 17507
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30


Found at i:7830 original size:15 final size:16

Alignment explanation


    Indices: 7810--7852  Score: 61
    Period size: 15  Copynumber: 2.7  Consensus size: 16

       7800 GCCACCTATT

                            
       7810 TAAATAAATAAAAA-A
          1 TAAATAAATAAAAACA

                            
       7825 TAAATAAATAAAAACA
          1 TAAATAAATAAAAACA

              *         
       7841 TCCAATAAATAA
          1 T-AAATAAATAA

       7853 GCGTCGCCTA


Statistics
Matches: 25,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  15   14  0.56
  16    2  0.08
  17    9  0.36

ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21


Consensus pattern (16 bp):   
TAAATAAATAAAAACA

Found at i:13619 original size:14 final size:13

Alignment explanation


    Indices: 13583--13621  Score: 51
    Period size: 14  Copynumber: 2.8  Consensus size: 13

      13573 ATTTTATATT

                        * 
      13583 TATAATTATATTTA
          1 TATAATTA-ATTAA

                         
      13597 TATAATTAATTAA
          1 TATAATTAATTAA

                        
      13610 TATAATTTAATT
          1 TATAA-TTAATT

      13622 CTTAAAATAA


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

Matches are distributed among these distances:
  13    9  0.39
  14   14  0.61

ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54


Consensus pattern (13 bp):   
TATAATTAATTAA

Found at i:14239 original size:22 final size:22

Alignment explanation


    Indices: 14198--14239  Score: 57
    Period size: 22  Copynumber: 1.9  Consensus size: 22

      14188 TACCGCCCAT

                      *    *      
      14198 TTTTGCTAAATACCGTCTCCCC
          1 TTTTGCTAAACACCGCCTCCCC

                         *      
      14220 TTTTGCTAAACACTGCCTCC
          1 TTTTGCTAAACACCGCCTCC

      14240 TTTTGACAAT


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  22   17  1.00

ACGTcount: A:0.19, C:0.36, G:0.10, T:0.36


Consensus pattern (22 bp):   
TTTTGCTAAACACCGCCTCCCC

Found at i:14648 original size:33 final size:33

Alignment explanation


    Indices: 14610--14674  Score: 94
    Period size: 33  Copynumber: 2.0  Consensus size: 33

      14600 TGCCCTACTG

                   *          **             
      14610 ACCATGGTATGCCACCCTGGGAGGGCGGCACCA
          1 ACCATGGCATGCCACCCTCCGAGGGCGGCACCA

                                *           
      14643 ACCATGGCATGCCACCCTCCTAGGGCGGCACC
          1 ACCATGGCATGCCACCCTCCGAGGGCGGCACC

      14675 GACAATATTT


Statistics
Matches: 28,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  33   28  1.00

ACGTcount: A:0.20, C:0.38, G:0.29, T:0.12


Consensus pattern (33 bp):   
ACCATGGCATGCCACCCTCCGAGGGCGGCACCA

Found at i:15914 original size:13 final size:13

Alignment explanation


    Indices: 15896--15928  Score: 57
    Period size: 13  Copynumber: 2.5  Consensus size: 13

      15886 AATTTCTGAT

                         
      15896 TGACAAATTTGAA
          1 TGACAAATTTGAA

                         
      15909 TGACAAATTTGAA
          1 TGACAAATTTGAA

             *     
      15922 TAACAAA
          1 TGACAAA

      15929 AGAATAAAAA


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  13   19  1.00

ACGTcount: A:0.52, C:0.09, G:0.12, T:0.27


Consensus pattern (13 bp):   
TGACAAATTTGAA
Done.