Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008793.1 Corchorus capsularis cultivar CVL-1 contig08814, 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: 18390
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31


Found at i:3709 original size:13 final size:13

Alignment explanation


    Indices: 3684--3715  Score: 55
    Period size: 13  Copynumber: 2.4  Consensus size: 13

       3674 TGAAGAATAA

                         
       3684 CCTTAAAGAAAGG
          1 CCTTAAAGAAAGG

                         
       3697 CCTTAAAGAAAGG
          1 CCTTAAAGAAAGG

                  
       3710 CGCTTA
          1 C-CTTA

       3716 TTGGGAGGCA


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  13   14  0.78
  14    4  0.22

ACGTcount: A:0.41, C:0.19, G:0.22, T:0.19


Consensus pattern (13 bp):   
CCTTAAAGAAAGG

Found at i:9956 original size:33 final size:32

Alignment explanation


    Indices: 9859--9963  Score: 129
    Period size: 33  Copynumber: 3.2  Consensus size: 32

       9849 TTGAAAAGAG

                                           * 
       9859 TGTTTTAGATGTTGTTTGCGATGATACTAAACC
          1 TGTTTTAG-TGTTGTTTGCGATGATACTAAATC

              *   *            *    *        
       9892 TAATTTGAGTGTTGTTTGCAATGACACTAAATC
          1 T-GTTTTAGTGTTGTTTGCGATGATACTAAATC

                              *              
       9925 TGTTTTAAGTGTTGTTTGTGATGATACTAAATC
          1 TGTTTT-AGTGTTGTTTGCGATGATACTAAATC

                  
       9958 TGTTTT
          1 TGTTTT

       9964 GGATGCTAAT


Statistics
Matches: 60,  Mismatches: 10, Indels: 4
        0.81            0.14        0.05

Matches are distributed among these distances:
  32    3  0.05
  33   52  0.87
  34    5  0.08

ACGTcount: A:0.25, C:0.10, G:0.20, T:0.46


Consensus pattern (32 bp):   
TGTTTTAGTGTTGTTTGCGATGATACTAAATC

Found at i:13822 original size:12 final size:12

Alignment explanation


    Indices: 13802--13831  Score: 51
    Period size: 12  Copynumber: 2.5  Consensus size: 12

      13792 GACCGGCCAA

                *       
      13802 CGCATGGGACAT
          1 CGCACGGGACAT

                        
      13814 CGCACGGGACAT
          1 CGCACGGGACAT

                  
      13826 CGCACG
          1 CGCACG

      13832 AGCCATCCGG


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

Matches are distributed among these distances:
  12   17  1.00

ACGTcount: A:0.23, C:0.33, G:0.33, T:0.10


Consensus pattern (12 bp):   
CGCACGGGACAT

Found at i:13859 original size:30 final size:30

Alignment explanation


    Indices: 13823--13885  Score: 108
    Period size: 30  Copynumber: 2.1  Consensus size: 30

      13813 TCGCACGGGA

                                          
      13823 CATCGCACGAGCCATCCGGCCACAACCGGC
          1 CATCGCACGAGCCATCCGGCCACAACCGGC

                   * *                    
      13853 CATCGCATGGGCCATCCGGCCACAACCGGC
          1 CATCGCACGAGCCATCCGGCCACAACCGGC

               
      13883 CAT
          1 CAT

      13886 TCGACCCTTT


Statistics
Matches: 31,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  30   31  1.00

ACGTcount: A:0.22, C:0.44, G:0.24, T:0.10


Consensus pattern (30 bp):   
CATCGCACGAGCCATCCGGCCACAACCGGC
Done.