Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004168.1 Corchorus capsularis cultivar CVL-1 contig04176, 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: 14424
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.26


Found at i:4409 original size:2 final size:2

Alignment explanation


    Indices: 4404--4428  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       4394 ACACACACAC

                                                 
       4404 AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT A

       4429 CACACACACC


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

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:12545 original size:83 final size:83

Alignment explanation


    Indices: 12406--12580  Score: 278
    Period size: 83  Copynumber: 2.1  Consensus size: 83

      12396 CAAGTTCAAG

                                                 * *                   *     
      12406 CTGGTCGTGCGCCGTAACACCCCGCTGAGGTTGGCCAGGGCAGTCTCCGCTAATGAGACTGTCTC
          1 CTGGTCGTGCGCCGTAACACCCCGCTGAGGTTGGCCACGACAGTCTCCGCTAATGAGACCGTCTC

                              
      12471 CGCTAATGGGACGTTAAA
         66 CGCTAATGGGACGTTAAA

                 *                *           *           *                  
      12489 CTGGTTGTGCGCCGTAACACCCTGCTGAGGTTGGTCACGACAGTCTTCGCTAATGAGACCGTCTC
          1 CTGGTCGTGCGCCGTAACACCCCGCTGAGGTTGGCCACGACAGTCTCCGCTAATGAGACCGTCTC

                              
      12554 CGCTAATGGGACGTTAAA
         66 CGCTAATGGGACGTTAAA

              *      
      12572 CTAGTCGTG
          1 CTGGTCGTG

      12581 ATGTCAGCCA


Statistics
Matches: 83,  Mismatches: 9, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  83   83  1.00

ACGTcount: A:0.19, C:0.27, G:0.29, T:0.24


Consensus pattern (83 bp):   
CTGGTCGTGCGCCGTAACACCCCGCTGAGGTTGGCCACGACAGTCTCCGCTAATGAGACCGTCTC
CGCTAATGGGACGTTAAA

Found at i:13386 original size:22 final size:22

Alignment explanation


    Indices: 13361--13412  Score: 67
    Period size: 19  Copynumber: 2.5  Consensus size: 22

      13351 GAAGTTTGTG

                                  
      13361 ATTTGAAGAATTCTTGAAGATA
          1 ATTTGAAGAATTCTTGAAGATA

                                 *
      13383 ATTTGAAG-A--CTTGAAGATC
          1 ATTTGAAGAATTCTTGAAGATA

                        
      13402 A-TTGAAGAATT
          1 ATTTGAAGAATT

      13413 ATTTCAAGGA


Statistics
Matches: 26,  Mismatches: 1, Indels: 7
        0.76            0.03        0.21

Matches are distributed among these distances:
  18    6  0.23
  19   11  0.42
  21    1  0.04
  22    8  0.31

ACGTcount: A:0.40, C:0.06, G:0.19, T:0.35


Consensus pattern (22 bp):   
ATTTGAAGAATTCTTGAAGATA

Done.