Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009643.1 Corchorus capsularis cultivar CVL-1 contig09664, 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: 11456
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31


Found at i:3011 original size:36 final size:36

Alignment explanation


    Indices: 2960--3029  Score: 104
    Period size: 36  Copynumber: 1.9  Consensus size: 36

       2950 CAAGTCGATC

                                  *             
       2960 ATACTCATATCCTAGCAATCCTTCTTCTAAATGATT
          1 ATACTCATATCCTAGCAATCCTGCTTCTAAATGATT

                  *   *      *                
       2996 ATACTCGTATTCTAGCACTCCTGCTTCTAAATGA
          1 ATACTCATATCCTAGCAATCCTGCTTCTAAATGA

       3030 ACAACTGTCA


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  36   30  1.00

ACGTcount: A:0.29, C:0.26, G:0.09, T:0.37


Consensus pattern (36 bp):   
ATACTCATATCCTAGCAATCCTGCTTCTAAATGATT

Found at i:4673 original size:45 final size:45

Alignment explanation


    Indices: 4623--4712  Score: 153
    Period size: 45  Copynumber: 2.0  Consensus size: 45

       4613 TAATGGAGTA

                                                         
       4623 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGG
          1 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGG

                                     *  *         *      
       4668 GTGGAATTACTAAAAGATCCCTACCTCGGATTAATGATGAGCTGG
          1 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGG

       4713 AGAAGTAATC


Statistics
Matches: 42,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  45   42  1.00

ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26


Consensus pattern (45 bp):   
GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGG

Found at i:8363 original size:28 final size:28

Alignment explanation


    Indices: 8332--8385  Score: 108
    Period size: 28  Copynumber: 1.9  Consensus size: 28

       8322 ACTACTACAC

                                        
       8332 TTGGCAATTGGCTTATGTTTGGGCACTG
          1 TTGGCAATTGGCTTATGTTTGGGCACTG

                                      
       8360 TTGGCAATTGGCTTATGTTTGGGCAC
          1 TTGGCAATTGGCTTATGTTTGGGCAC

       8386 ACAGTTCGAT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  28   26  1.00

ACGTcount: A:0.15, C:0.15, G:0.31, T:0.39


Consensus pattern (28 bp):   
TTGGCAATTGGCTTATGTTTGGGCACTG

Found at i:10820 original size:73 final size:73

Alignment explanation


    Indices: 10696--10842  Score: 267
    Period size: 73  Copynumber: 2.0  Consensus size: 73

      10686 ATAATTTCAG

                                   *                                         
      10696 TGATAAGATTCAAATTCTGACAATCTTAAGTAATCAGAGTTTCTCTCAAAATATCGGCAACTAAA
          1 TGATAAGATTCAAATTCTGACAACCTTAAGTAATCAGAGTTTCTCTCAAAATATCGGCAACTAAA

                    
      10761 CTACCATC
         66 CTACCATC

                *     *                                                      
      10769 TGATCAGATTTAAATTCTGACAACCTTAAGTAATCAGAGTTTCTCTCAAAATATCGGCAACTAAA
          1 TGATAAGATTCAAATTCTGACAACCTTAAGTAATCAGAGTTTCTCTCAAAATATCGGCAACTAAA

                    
      10834 CTACCATC
         66 CTACCATC

             
      10842 T
          1 T

      10843 AGATTTCGCT


Statistics
Matches: 71,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  73   71  1.00

ACGTcount: A:0.37, C:0.21, G:0.11, T:0.31


Consensus pattern (73 bp):   
TGATAAGATTCAAATTCTGACAACCTTAAGTAATCAGAGTTTCTCTCAAAATATCGGCAACTAAA
CTACCATC

Found at i:10935 original size:42 final size:42

Alignment explanation


    Indices: 10874--10959  Score: 111
    Period size: 42  Copynumber: 2.0  Consensus size: 42

      10864 TTTTTTATTT

                                                  *    
      10874 TAGTGATTGGGTTCGAATTAAGACAA-TCTTAGGTAATTAGAG
          1 TAGTGATTGGGTTCGAATTAAGACAACT-TTAGGTAATCAGAG

                         **     *          *          
      10916 TAGTGATTGGGTTTTAATTATGACAACTTTATGTAATCAGAG
          1 TAGTGATTGGGTTCGAATTAAGACAACTTTAGGTAATCAGAG

              
      10958 TA
          1 TA

      10960 TCTTCTTTCA


Statistics
Matches: 38,  Mismatches: 5, Indels: 2
        0.84            0.11        0.04

Matches are distributed among these distances:
  42   37  0.97
  43    1  0.03

ACGTcount: A:0.33, C:0.07, G:0.23, T:0.37


Consensus pattern (42 bp):   
TAGTGATTGGGTTCGAATTAAGACAACTTTAGGTAATCAGAG
Done.