Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008051.1 Corchorus capsularis cultivar CVL-1 contig08072, 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: 7068
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.32


Found at i:5837 original size:33 final size:32

Alignment explanation


    Indices: 5734--5872  Score: 118
    Period size: 33  Copynumber: 4.2  Consensus size: 32

       5724 AATTTGAGAT

                         *    *          *   
       5734 CCGGCCACACGACTTGGAGATGCCCGCGCAACA
          1 CCGGCCACACGACATGGACATGCCCG-GCCACA

               *   **         *       *      
       5767 CCGACCATGCGACATGGAGATGCCCGACCATCA
          1 CCGGCCACACGACATGGACATGCCCGGCCA-CA

                    *        *              
       5800 CCGGCCACGCGACATGGCCATGCCCGGCCACA
          1 CCGGCCACACGACATGGACATGCCCGGCCACA

                      *        *               
       5832 CCCGGCCACATGAC-TCGGCCATGCCCGGCCACAA
          1 -CCGGCCACACGACAT-GGACATGCCCGGCCAC-A

                   
       5866 CCGGCCA
          1 CCGGCCA

       5873 TATGATCCTT


Statistics
Matches: 89,  Mismatches: 13, Indels: 8
        0.81            0.12        0.07

Matches are distributed among these distances:
  32    5  0.06
  33   83  0.93
  34    1  0.01

ACGTcount: A:0.22, C:0.43, G:0.26, T:0.09


Consensus pattern (32 bp):   
CCGGCCACACGACATGGACATGCCCGGCCACA

Found at i:6808 original size:8 final size:8

Alignment explanation


    Indices: 6795--6828  Score: 50
    Period size: 8  Copynumber: 4.1  Consensus size: 8

       6785 CACCTTCTTG

                    
       6795 AAAAATTC
          1 AAAAATTC

                    
       6803 AAAAATTC
          1 AAAAATTC

                 *   
       6811 AGAAACTTC
          1 A-AAAATTC

                    
       6820 AAAAATTC
          1 AAAAATTC

             
       6828 A
          1 A

       6829 TAGCCGATTC


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
   8   16  0.70
   9    7  0.30

ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24


Consensus pattern (8 bp):   
AAAAATTC

Found at i:6916 original size:10 final size:10

Alignment explanation


    Indices: 6901--6933  Score: 66
    Period size: 10  Copynumber: 3.3  Consensus size: 10

       6891 AGTTATATCG

                      
       6901 AAAAATAAAA
          1 AAAAATAAAA

                      
       6911 AAAAATAAAA
          1 AAAAATAAAA

                      
       6921 AAAAATAAAA
          1 AAAAATAAAA

               
       6931 AAA
          1 AAA

       6934 TTTCGACCAG


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   23  1.00

ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09


Consensus pattern (10 bp):   
AAAAATAAAA
Done.