Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013147.1 Corchorus capsularis cultivar CVL-1 contig13168, 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: 11651
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32


Found at i:3786 original size:21 final size:19

Alignment explanation


    Indices: 3757--3807  Score: 57
    Period size: 21  Copynumber: 2.6  Consensus size: 19

       3747 AGCATTTTTA

                *               
       3757 ATTATACCAAAAAAAGATGC
          1 ATTACACCAAAAAAAGAT-C

                        *  *    
       3777 TATTACACCAAATAATGATC
          1 -ATTACACCAAAAAAAGATC

                       
       3797 ATTACACCAAA
          1 ATTACACCAAA

       3808 CAAGGATCAC


Statistics
Matches: 27,  Mismatches: 3, Indels: 2
        0.84            0.09        0.06

Matches are distributed among these distances:
  19   11  0.41
  20    1  0.04
  21   15  0.56

ACGTcount: A:0.51, C:0.20, G:0.06, T:0.24


Consensus pattern (19 bp):   
ATTACACCAAAAAAAGATC

Found at i:3815 original size:19 final size:19

Alignment explanation


    Indices: 3778--3816  Score: 60
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       3768 AAAAGATGCT

                       *  *    
       3778 ATTACACCAAATAATGATC
          1 ATTACACCAAACAAGGATC

                               
       3797 ATTACACCAAACAAGGATC
          1 ATTACACCAAACAAGGATC

             
       3816 A
          1 A

       3817 CTTTCTCATA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  19   18  1.00

ACGTcount: A:0.49, C:0.23, G:0.08, T:0.21


Consensus pattern (19 bp):   
ATTACACCAAACAAGGATC

Found at i:4406 original size:11 final size:11

Alignment explanation


    Indices: 4363--4400  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

       4353 CCTATATATA

                *      
       4363 AAATAAATTAT
          1 AAATTAATTAT

                        
       4374 CAAA-TAATTAT
          1 -AAATTAATTAT

                       
       4385 AAATTAATTAT
          1 AAATTAATTAT

                 
       4396 AAATT
          1 AAATT

       4401 TGTTATGAAT


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  10    3  0.12
  11   18  0.75
  12    3  0.12

ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39


Consensus pattern (11 bp):   
AAATTAATTAT

Found at i:4871 original size:14 final size:14

Alignment explanation


    Indices: 4848--4877  Score: 51
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       4838 ATTATTAAAA

                 *        
       4848 AATTATATTGACCC
          1 AATTACATTGACCC

                          
       4862 AATTACATTGACCC
          1 AATTACATTGACCC

              
       4876 AA
          1 AA

       4878 ATAACCCAAT


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.40, C:0.23, G:0.07, T:0.30


Consensus pattern (14 bp):   
AATTACATTGACCC

Found at i:11637 original size:28 final size:28

Alignment explanation


    Indices: 11592--11651  Score: 75
    Period size: 28  Copynumber: 2.1  Consensus size: 28

      11582 GTAGGAGATC

                   *  *          *     *
      11592 AGAGGCGTTGGAGCGGTGAAGGAGAAGG
          1 AGAGGCGCTGCAGCGGTGAAGCAGAAGA

                         *              
      11620 AGAGGCGCTGCAGTGGTGAAGCAGAAGA
          1 AGAGGCGCTGCAGCGGTGAAGCAGAAGA

                
      11648 AGAG
          1 AGAG


Statistics
Matches: 27,  Mismatches: 5, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  28   27  1.00

ACGTcount: A:0.32, C:0.10, G:0.48, T:0.10


Consensus pattern (28 bp):   
AGAGGCGCTGCAGCGGTGAAGCAGAAGA
Done.