Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009353.1 Corchorus capsularis cultivar CVL-1 contig09374, 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: 4712
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.29


Found at i:4498 original size:33 final size:33

Alignment explanation


    Indices: 4460--4538  Score: 115
    Period size: 33  Copynumber: 2.4  Consensus size: 33

       4450 AGCACGAGTG

                           *                 
       4460 ACCGGCCACGCGACTTGGAGAAGCCCGACCAAC
          1 ACCGGCCACGCGACTCGGAGAAGCCCGACCAAC

                                 *     *   * 
       4493 ACCGGCCACGCGACTCGGAGATGCCCGGCCATC
          1 ACCGGCCACGCGACTCGGAGAAGCCCGACCAAC

                          
       4526 A-CGGCCACGCGAC
          1 ACCGGCCACGCGAC

       4539 ATGACATGCC


Statistics
Matches: 42,  Mismatches: 4, Indels: 1
        0.89            0.09        0.02

Matches are distributed among these distances:
  32   12  0.29
  33   30  0.71

ACGTcount: A:0.23, C:0.42, G:0.29, T:0.06


Consensus pattern (33 bp):   
ACCGGCCACGCGACTCGGAGAAGCCCGACCAAC

Found at i:4563 original size:10 final size:10

Alignment explanation


    Indices: 4548--4597  Score: 66
    Period size: 10  Copynumber: 4.9  Consensus size: 10

       4538 CATGACATGC

                      
       4548 CCGGCCACAA
          1 CCGGCCACAA

                       
       4558 CCGGCCATC-A
          1 CCGGCCA-CAA

                     * 
       4568 CTCGGCCACCA
          1 C-CGGCCACAA

                      
       4579 CCGGCCACAA
          1 CCGGCCACAA

                     
       4589 CCGGCCACA
          1 CCGGCCACA

       4598 TGAGCCATCC


Statistics
Matches: 36,  Mismatches: 1, Indels: 6
        0.84            0.02        0.14

Matches are distributed among these distances:
  10   27  0.75
  11    9  0.25

ACGTcount: A:0.24, C:0.52, G:0.20, T:0.04


Consensus pattern (10 bp):   
CCGGCCACAA

Found at i:4563 original size:32 final size:32

Alignment explanation


    Indices: 4460--4564  Score: 110
    Period size: 33  Copynumber: 3.2  Consensus size: 32

       4450 AGCACGAGTG

                                 *     *     
       4460 ACCGGCCACGCGACTTGGAGAAGCCCGACCA-A
          1 ACCGGCCACGCGAC-TGGAGATGCCCGGCCACA

                                               
       4492 CACCGGCCACGCGACTCGGAGATGCCCGGCCATC-
          1 -ACCGGCCACGCGACT-GGAGATGCCCGGCCA-CA

                               *             
       4526 A-CGGCCACGCGACAT-GACATGCCCGGCCACA
          1 ACCGGCCACGCGAC-TGGAGATGCCCGGCCACA

                    
       4557 ACCGGCCA
          1 ACCGGCCA

       4565 TCACTCGGCC


Statistics
Matches: 63,  Mismatches: 3, Indels: 13
        0.80            0.04        0.16

Matches are distributed among these distances:
  30    1  0.02
  31   14  0.22
  32   19  0.30
  33   29  0.46

ACGTcount: A:0.24, C:0.42, G:0.28, T:0.07


Consensus pattern (32 bp):   
ACCGGCCACGCGACTGGAGATGCCCGGCCACA

Found at i:4575 original size:21 final size:20

Alignment explanation


    Indices: 4548--4597  Score: 66
    Period size: 21  Copynumber: 2.5  Consensus size: 20

       4538 CATGACATGC

                                 
       4548 CCGGCCACAACCGGCCATC-A
          1 CCGGCCACAACCGGCCA-CAA

                     *           
       4568 CTCGGCCACCACCGGCCACAA
          1 C-CGGCCACAACCGGCCACAA

                     
       4589 CCGGCCACA
          1 CCGGCCACA

       4598 TGAGCCATCC


Statistics
Matches: 26,  Mismatches: 2, Indels: 4
        0.81            0.06        0.12

Matches are distributed among these distances:
  20    9  0.35
  21   17  0.65

ACGTcount: A:0.24, C:0.52, G:0.20, T:0.04


Consensus pattern (20 bp):   
CCGGCCACAACCGGCCACAA
Done.