Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011618.1 Corchorus capsularis cultivar CVL-1 contig11639, 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: 12574
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:501 original size:27 final size:27

Alignment explanation


    Indices: 444--503  Score: 75
    Period size: 27  Copynumber: 2.2  Consensus size: 27

        434 AAGTGACCTT

                   *                 **
        444 AAAATGACCAAAATGCCCCTAAATGTG
          1 AAAATGAACAAAATGCCCCTAAATGAA

                              * *      
        471 AAAATGAACAAAATGCCCTTGAATGAA
          1 AAAATGAACAAAATGCCCCTAAATGAA

                  
        498 AAAATG
          1 AAAATG

        504 CCCCTAGGTG


Statistics
Matches: 28,  Mismatches: 5, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  27   28  1.00

ACGTcount: A:0.50, C:0.17, G:0.15, T:0.18


Consensus pattern (27 bp):   
AAAATGAACAAAATGCCCCTAAATGAA

Found at i:4075 original size:33 final size:33

Alignment explanation


    Indices: 4038--4134  Score: 122
    Period size: 33  Copynumber: 2.9  Consensus size: 33

       4028 AGCACAAGTG

                              *              
       4038 ACCGGCCATGCGACTTGGGGATGCCCGGCCAAC
          1 ACCGGCCATGCGACTTGGAGATGCCCGGCCAAC

                                       *   * 
       4071 ACCGGCCATGCGACTTGGAGATGCCCGACCATC
          1 ACCGGCCATGCGACTTGGAGATGCCCGGCCAAC

                    * *   *   **           
       4104 ACCGGCCACGAGACATGGCCATGCCCGGCCA
          1 ACCGGCCATGCGACTTGGAGATGCCCGGCCA

       4135 CAACCGGTCA


Statistics
Matches: 55,  Mismatches: 9, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  33   55  1.00

ACGTcount: A:0.21, C:0.38, G:0.30, T:0.11


Consensus pattern (33 bp):   
ACCGGCCATGCGACTTGGAGATGCCCGGCCAAC

Found at i:4141 original size:33 final size:32

Alignment explanation


    Indices: 4058--4178  Score: 104
    Period size: 33  Copynumber: 3.7  Consensus size: 32

       4048 CGACTTGGGG

                                  * *       **
       4058 ATGCCCGGCCA-ACACCGGCCATGCGACTTGGAG
          1 ATGCCCGGCCACA-ACCGGCCACGAGAC-TGGCC

                   *                          
       4091 ATGCCCGACCATC-ACCGGCCACGAGACATGGCC
          1 ATGCCCGGCCA-CAACCGGCCACGAGAC-TGGCC

                              *               
       4124 ATGCCCGGCCACAACCGGTCAC-ATGACTCGGCC
          1 ATGCCCGGCCACAACCGGCCACGA-GACT-GGCC

                       *          
       4157 ATGCCCGGCCATAACCGGCCAC
          1 ATGCCCGGCCACAACCGGCCAC

       4179 ATGCTATACC


Statistics
Matches: 73,  Mismatches: 10, Indels: 10
        0.78            0.11        0.11

Matches are distributed among these distances:
  32    3  0.04
  33   70  0.96

ACGTcount: A:0.22, C:0.41, G:0.26, T:0.11


Consensus pattern (32 bp):   
ATGCCCGGCCACAACCGGCCACGAGACTGGCC

Found at i:4180 original size:33 final size:33

Alignment explanation


    Indices: 4091--4181  Score: 114
    Period size: 33  Copynumber: 2.8  Consensus size: 33

       4081 CGACTTGGAG

                   *    *                     
       4091 ATGCCCGACCATCACCGGCCACGA-GACATGGCC
          1 ATGCCCGGCCATAACCGGCCAC-ATGACATGGCC

                       *      *               
       4124 ATGCCCGGCCACAACCGGTCACATGAC-TCGGCC
          1 ATGCCCGGCCATAACCGGCCACATGACAT-GGCC

                                     
       4157 ATGCCCGGCCATAACCGGCCACATG
          1 ATGCCCGGCCATAACCGGCCACATG

       4182 CTATACCGTT


Statistics
Matches: 50,  Mismatches: 6, Indels: 4
        0.83            0.10        0.07

Matches are distributed among these distances:
  32    2  0.04
  33   48  0.96

ACGTcount: A:0.23, C:0.42, G:0.24, T:0.11


Consensus pattern (33 bp):   
ATGCCCGGCCATAACCGGCCACATGACATGGCC

Found at i:7255 original size:30 final size:31

Alignment explanation


    Indices: 7201--7259  Score: 102
    Period size: 31  Copynumber: 1.9  Consensus size: 31

       7191 GGCATCTTAA

                           *               
       7201 TGGCATCTCCATGAGGCTTTTGCGATTCCAT
          1 TGGCATCTCCATGAGACTTTTGCGATTCCAT

                                         
       7232 TGGCATCTCCATGAGAC-TTTGCGATTCC
          1 TGGCATCTCCATGAGACTTTTGCGATTCC

       7260 TTCCTCTCCT


Statistics
Matches: 27,  Mismatches: 1, Indels: 1
        0.93            0.03        0.03

Matches are distributed among these distances:
  30   11  0.41
  31   16  0.59

ACGTcount: A:0.17, C:0.27, G:0.22, T:0.34


Consensus pattern (31 bp):   
TGGCATCTCCATGAGACTTTTGCGATTCCAT

Found at i:10545 original size:33 final size:33

Alignment explanation


    Indices: 10474--10592  Score: 125
    Period size: 33  Copynumber: 3.5  Consensus size: 33

      10464 AAAGGATCGT

                              *    *         *
      10474 GTGGCCGGTTGTGGCCGGGCATGGCCGA-GTCGT
          1 GTGGCCGGTTGTGGCCGGACATGTCC-ATGTCGC

            *           *     *              
      10507 TTGGCCGGTTGTAGCCGGCCATGTCCATGTCGC
          1 GTGGCCGGTTGTGGCCGGACATGTCCATGTCGC

                                              
      10540 GTGGCCGG-TGATGGCCGGACATGTCCATGTCGC
          1 GTGGCCGGTTG-TGGCCGGACATGTCCATGTCGC

                *               
      10573 GTGGTCGGTCTTGTGGCCGG
          1 GTGGCCGG--TTGTGGCCGG

      10593 TGTTGCGCGG


Statistics
Matches: 72,  Mismatches: 9, Indels: 8
        0.81            0.10        0.09

Matches are distributed among these distances:
  32    3  0.04
  33   60  0.83
  35    7  0.10
  36    2  0.03

ACGTcount: A:0.08, C:0.26, G:0.42, T:0.24


Consensus pattern (33 bp):   
GTGGCCGGTTGTGGCCGGACATGTCCATGTCGC
Done.