Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017657.1 Corchorus olitorius cultivar O-4 contig17690, 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: 18305
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32


Found at i:3547 original size:16 final size:17

Alignment explanation


    Indices: 3521--3552  Score: 57
    Period size: 16  Copynumber: 1.9  Consensus size: 17

       3511 AGTGCAAATT

                             
       3521 AAAATAGAAAAATAAAG
          1 AAAATAGAAAAATAAAG

                            
       3538 AAAA-AGAAAAATAAA
          1 AAAATAGAAAAATAAA

       3553 ACGCAATCTC


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  16   11  0.73
  17    4  0.27

ACGTcount: A:0.81, C:0.00, G:0.09, T:0.09


Consensus pattern (17 bp):   
AAAATAGAAAAATAAAG

Found at i:12705 original size:39 final size:39

Alignment explanation


    Indices: 12662--12744  Score: 166
    Period size: 39  Copynumber: 2.1  Consensus size: 39

      12652 TAAGATCCAA

                                                   
      12662 AATTTTCCATCAAAAATCCAAACTTTAAACAAGATTGTC
          1 AATTTTCCATCAAAAATCCAAACTTTAAACAAGATTGTC

                                                   
      12701 AATTTTCCATCAAAAATCCAAACTTTAAACAAGATTGTC
          1 AATTTTCCATCAAAAATCCAAACTTTAAACAAGATTGTC

                 
      12740 AATTT
          1 AATTT

      12745 AATCATTGGA


Statistics
Matches: 44,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  39   44  1.00

ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33


Consensus pattern (39 bp):   
AATTTTCCATCAAAAATCCAAACTTTAAACAAGATTGTC

Found at i:14122 original size:39 final size:39

Alignment explanation


    Indices: 14068--14181  Score: 210
    Period size: 39  Copynumber: 2.9  Consensus size: 39

      14058 GATAGTGAAC

                 *                                 
      14068 TGAAAGATGCATATGGCTAAGTTTTGAGATGCAGTGGAT
          1 TGAAAAATGCATATGGCTAAGTTTTGAGATGCAGTGGAT

                                      *            
      14107 TGAAAAATGCATATGGCTAAGTTTTGTGATGCAGTGGAT
          1 TGAAAAATGCATATGGCTAAGTTTTGAGATGCAGTGGAT

                                                
      14146 TGAAAAATGCATATGGCTAAGTTTTGAGATGCAGTG
          1 TGAAAAATGCATATGGCTAAGTTTTGAGATGCAGTG

      14182 AACTTCCATT


Statistics
Matches: 72,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  39   72  1.00

ACGTcount: A:0.32, C:0.08, G:0.29, T:0.32


Consensus pattern (39 bp):   
TGAAAAATGCATATGGCTAAGTTTTGAGATGCAGTGGAT

Found at i:15702 original size:28 final size:28

Alignment explanation


    Indices: 15669--15793  Score: 106
    Period size: 28  Copynumber: 4.5  Consensus size: 28

      15659 AGTGCACTTG

                                  *   * 
      15669 AAATGACCAAAATACCCCTAGATGTGTA
          1 AAATGACCAAAATACCCCTAGACGTGCA

                         *     *        
      15697 AAATGACCAAAATGCCCCTGGACGTGCA
          1 AAATGACCAAAATACCCCTAGACGTGCA

                         *   * * * *    
      15725 AAATGACCAAAATGCCCTTGGTCATGCA
          1 AAATGACCAAAATACCCCTAGACGTGCA

                  *      *   * * * *    
      15753 AAATGATCAAAATGCCCTTGGTCATGCA
          1 AAATGACCAAAATACCCCTAGACGTGCA

                  *      
      15781 AAATGATCAAAAT
          1 AAATGACCAAAAT

      15794 GCCCTCTTAA


Statistics
Matches: 89,  Mismatches: 8, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  28   89  1.00

ACGTcount: A:0.40, C:0.22, G:0.17, T:0.21


Consensus pattern (28 bp):   
AAATGACCAAAATACCCCTAGACGTGCA

Found at i:15736 original size:56 final size:56

Alignment explanation


    Indices: 15669--15798  Score: 145
    Period size: 56  Copynumber: 2.3  Consensus size: 56

      15659 AGTGCACTTG

                                    *  *                        *    
      15669 AAATGACCAAAATACCCCTAGAT-GTGTAAAATGACCAAAATGCCCCTGGACGTGCA
          1 AAATGACCAAAAT-CCCCTAGATCATGCAAAATGACCAAAATGCCCCTGGACATGCA

                         *    * *             *          *   *      
      15725 AAATGACCAAAATGCCCTTGGTCATGCAAAATGATCAAAATGCCCTTGGTCATGCA
          1 AAATGACCAAAATCCCCTAGATCATGCAAAATGACCAAAATGCCCCTGGACATGCA

                  *      *    
      15781 AAATGATCAAAATGCCCT
          1 AAATGACCAAAATCCCCT

      15799 CTTAAATGAT


Statistics
Matches: 63,  Mismatches: 10, Indels: 2
        0.84            0.13        0.03

Matches are distributed among these distances:
  55    6  0.10
  56   57  0.90

ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21


Consensus pattern (56 bp):   
AAATGACCAAAATCCCCTAGATCATGCAAAATGACCAAAATGCCCCTGGACATGCA

Found at i:15794 original size:28 final size:28

Alignment explanation


    Indices: 15696--15798  Score: 161
    Period size: 28  Copynumber: 3.7  Consensus size: 28

      15686 CTAGATGTGT

                              *   * *   
      15696 AAAATGACCAAAATGCCCCTGGACGTGC
          1 AAAATGACCAAAATGCCCTTGGTCATGC

                                        
      15724 AAAATGACCAAAATGCCCTTGGTCATGC
          1 AAAATGACCAAAATGCCCTTGGTCATGC

                   *                    
      15752 AAAATGATCAAAATGCCCTTGGTCATGC
          1 AAAATGACCAAAATGCCCTTGGTCATGC

                   *           
      15780 AAAATGATCAAAATGCCCT
          1 AAAATGACCAAAATGCCCT

      15799 CTTAAATGAT


Statistics
Matches: 71,  Mismatches: 4, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  28   71  1.00

ACGTcount: A:0.38, C:0.24, G:0.17, T:0.20


Consensus pattern (28 bp):   
AAAATGACCAAAATGCCCTTGGTCATGC
Done.