Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010661.1 Corchorus capsularis cultivar CVL-1 contig10682, 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: 11474
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30


Found at i:5237 original size:33 final size:32

Alignment explanation


    Indices: 5200--5306  Score: 126
    Period size: 33  Copynumber: 3.2  Consensus size: 32

       5190 CGCCAAGCGA

                              *   *           
       5200 TGGCCGGTTG-TGGCCGGACATGTCCATGTCGCG
          1 TGGCCGG-TGATGGCCGGGCATCTCCA-GTCGCG

                                             
       5233 TGGCCGGTGATGGCCGGGCATCTCCGAGTCGCG
          1 TGGCCGGTGATGGCCGGGCATCTCC-AGTCGCG

                     *         *            *
       5266 TGGCCGGTGTTGGCCGGGCTTCTCCAAGTCGCA
          1 TGGCCGGTGATGGCCGGGCATCTCC-AGTCGCG

                    
       5299 TGGCCGGT
          1 TGGCCGGT

       5307 CGCTCGCGCC


Statistics
Matches: 66,  Mismatches: 6, Indels: 4
        0.87            0.08        0.05

Matches are distributed among these distances:
  32    2  0.03
  33   63  0.95
  34    1  0.02

ACGTcount: A:0.08, C:0.29, G:0.40, T:0.22


Consensus pattern (32 bp):   
TGGCCGGTGATGGCCGGGCATCTCCAGTCGCG

Found at i:6464 original size:33 final size:32

Alignment explanation


    Indices: 6427--6532  Score: 115
    Period size: 33  Copynumber: 3.2  Consensus size: 32

       6417 GGCGCGAGTG

                    *            *           
       6427 ACCGGCCATGCGACTTGGAGAAGCCCGGCCAAC
          1 ACCGGCCACGCGACTTGGAGATG-CCGGCCAAC

                           *        *     * 
       6460 ACCGGCCACGCGACTCGGAGATGCTGGCCATC
          1 ACCGGCCACGCGACTTGGAGATGCCGGCCAAC

                          *    *             
       6492 ACCGGCCACGCGACATGGACATGTCCGGCC-AC
          1 ACCGGCCACGCGACTTGGAGATG-CCGGCCAAC

                     
       6524 AACCGGCCA
          1 -ACCGGCCA

       6533 TCGCTTGGCG


Statistics
Matches: 61,  Mismatches: 10, Indels: 4
        0.81            0.13        0.05

Matches are distributed among these distances:
  32   28  0.46
  33   33  0.54

ACGTcount: A:0.23, C:0.39, G:0.29, T:0.09


Consensus pattern (32 bp):   
ACCGGCCACGCGACTTGGAGATGCCGGCCAAC

Found at i:6495 original size:32 final size:33

Alignment explanation


    Indices: 6427--6505  Score: 106
    Period size: 32  Copynumber: 2.4  Consensus size: 33

       6417 GGCGCGAGTG

                    *      *                 
       6427 ACCGGCCATGCGACTTGGAGAAGCCCGGCCAAC
          1 ACCGGCCACGCGACTCGGAGAAGCCCGGCCAAC

                                 *   *     * 
       6460 ACCGGCCACGCGACTCGGAGATG-CTGGCCATC
          1 ACCGGCCACGCGACTCGGAGAAGCCCGGCCAAC

                          
       6492 ACCGGCCACGCGAC
          1 ACCGGCCACGCGAC

       6506 ATGGACATGT


Statistics
Matches: 41,  Mismatches: 5, Indels: 1
        0.87            0.11        0.02

Matches are distributed among these distances:
  32   21  0.51
  33   20  0.49

ACGTcount: A:0.22, C:0.39, G:0.30, T:0.09


Consensus pattern (33 bp):   
ACCGGCCACGCGACTCGGAGAAGCCCGGCCAAC

Found at i:10237 original size:11 final size:12

Alignment explanation


    Indices: 10215--10243  Score: 51
    Period size: 11  Copynumber: 2.5  Consensus size: 12

      10205 AGTTATATCG

                        
      10215 AAAAATATAAAA
          1 AAAAATATAAAA

                        
      10227 AAAAATA-AAAA
          1 AAAAATATAAAA

                  
      10238 AAAAAT
          1 AAAAAT

      10244 TTCGACCAGA


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  11   10  0.59
  12    7  0.41

ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14


Consensus pattern (12 bp):   
AAAAATATAAAA
Done.