Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007301.1 Corchorus capsularis cultivar CVL-1 contig07322, 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: 27297
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:5796 original size:33 final size:30

Alignment explanation


    Indices: 5728--5829  Score: 125
    Period size: 30  Copynumber: 3.3  Consensus size: 30

       5718 AATGGATCAA

                         *                
       5728 ATGGCCGGTTGTGCCCGGATGGCCCATGCG
          1 ATGGCCGGTTGTGGCCGGATGGCCCATGCG

                              *              
       5758 ATGGCCGGTTGTGGCCGGTTGGTGCCTCATGCG
          1 ATGGCCGGTTGTGGCCGGAT-G-GCC-CATGCG

            *                              
       5791 TTGGCCGGTTGTGGCCGGAT-GCTCCATGCG
          1 ATGGCCGGTTGTGGCCGGATGGC-CCATGCG

               *     
       5821 ATGTCCGGT
          1 ATGGCCGGT

       5830 CAAGTGGCCG


Statistics
Matches: 62,  Mismatches: 6, Indels: 8
        0.82            0.08        0.11

Matches are distributed among these distances:
  30   33  0.53
  31    2  0.03
  32    3  0.05
  33   24  0.39

ACGTcount: A:0.08, C:0.26, G:0.40, T:0.25


Consensus pattern (30 bp):   
ATGGCCGGTTGTGGCCGGATGGCCCATGCG

Found at i:22391 original size:33 final size:33

Alignment explanation


    Indices: 22353--22437  Score: 125
    Period size: 33  Copynumber: 2.6  Consensus size: 33

      22343 GGCGCGAGTG

                    *                        
      22353 ACCGGCCATGCGACTTGGAGAAGCCCGGCCAAC
          1 ACCGGCCACGCGACTTGGAGAAGCCCGGCCAAC

                           *   * *           
      22386 ACCGGCCACGCGACTCGGATATGCCCGGCCAAC
          1 ACCGGCCACGCGACTTGGAGAAGCCCGGCCAAC

                          *    
      22419 ACCGGCCACGCGACATGGA
          1 ACCGGCCACGCGACTTGGA

      22438 CATGTCCGGC


Statistics
Matches: 46,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  33   46  1.00

ACGTcount: A:0.24, C:0.39, G:0.29, T:0.08


Consensus pattern (33 bp):   
ACCGGCCACGCGACTTGGAGAAGCCCGGCCAAC

Found at i:22456 original size:33 final size:32

Alignment explanation


    Indices: 22353--22449  Score: 122
    Period size: 33  Copynumber: 2.9  Consensus size: 32

      22343 GGCGCGAGTG

                    *          * *           
      22353 ACCGGCCATGCGACTTGGAGAAGCCCGGCCAAC
          1 ACCGGCCACGCGAC-TGGACATGCCCGGCCAAC

                               *             
      22386 ACCGGCCACGCGACTCGGATATGCCCGGCCAAC
          1 ACCGGCCACGCGACT-GGACATGCCCGGCCAAC

                                   *       
      22419 ACCGGCCACGCGACATGGACATGTCCGGCCA
          1 ACCGGCCACGCGAC-TGGACATGCCCGGCCA

      22450 CAACCGGTCA


Statistics
Matches: 57,  Mismatches: 5, Indels: 4
        0.86            0.08        0.06

Matches are distributed among these distances:
  32    1  0.02
  33   55  0.96
  34    1  0.02

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


Consensus pattern (32 bp):   
ACCGGCCACGCGACTGGACATGCCCGGCCAAC

Found at i:26513 original size:27 final size:27

Alignment explanation


    Indices: 26483--26556  Score: 105
    Period size: 26  Copynumber: 2.8  Consensus size: 27

      26473 AAGTAGACTC

                     *                 
      26483 CAAATGACCTAAATGCCCCTAAATGTG
          1 CAAATGACCAAAATGCCCCTAAATGTG

                                * *    
      26510 CAAATGACCAAAATG-CCCTTAGTGTG
          1 CAAATGACCAAAATGCCCCTAAATGTG

            *                    
      26536 AAAATGACCAAAATGCCCCTA
          1 CAAATGACCAAAATGCCCCTA

      26557 TGTGACCCTA


Statistics
Matches: 41,  Mismatches: 5, Indels: 2
        0.85            0.10        0.04

Matches are distributed among these distances:
  26   23  0.56
  27   18  0.44

ACGTcount: A:0.39, C:0.26, G:0.15, T:0.20


Consensus pattern (27 bp):   
CAAATGACCAAAATGCCCCTAAATGTG

Found at i:27266 original size:2 final size:2

Alignment explanation


    Indices: 27259--27297  Score: 78
    Period size: 2  Copynumber: 19.5  Consensus size: 2

      27249 GATTGGTGGG

                                                                      
      27259 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   37  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Done.