Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017695.1 Corchorus olitorius cultivar O-4 contig17728, 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: 12681
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33


Found at i:6948 original size:54 final size:54

Alignment explanation


    Indices: 6889--6997  Score: 200
    Period size: 54  Copynumber: 2.0  Consensus size: 54

       6879 TATATCTATT

                                    *   *                         
       6889 TCTATACTATATTAAAGAGTACGATCTCTTGTAAAACTTTTGAATCGCCCATTA
          1 TCTATACTATATTAAAGAGTACGACCTCCTGTAAAACTTTTGAATCGCCCATTA

                                                                  
       6943 TCTATACTATATTAAAGAGTACGACCTCCTGTAAAACTTTTGAATCGCCCATTA
          1 TCTATACTATATTAAAGAGTACGACCTCCTGTAAAACTTTTGAATCGCCCATTA

             
       6997 T
          1 T

       6998 ACCCTTAATT


Statistics
Matches: 53,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  54   53  1.00

ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36


Consensus pattern (54 bp):   
TCTATACTATATTAAAGAGTACGACCTCCTGTAAAACTTTTGAATCGCCCATTA

Found at i:10843 original size:32 final size:32

Alignment explanation


    Indices: 10802--10866  Score: 130
    Period size: 32  Copynumber: 2.0  Consensus size: 32

      10792 CACGCCTTAC

                                            
      10802 ACAAAATACTTACCACTTATATTATATGTAAA
          1 ACAAAATACTTACCACTTATATTATATGTAAA

                                            
      10834 ACAAAATACTTACCACTTATATTATATGTAAA
          1 ACAAAATACTTACCACTTATATTATATGTAAA

             
      10866 A
          1 A

      10867 TGGTACCTCA


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  32   33  1.00

ACGTcount: A:0.48, C:0.15, G:0.03, T:0.34


Consensus pattern (32 bp):   
ACAAAATACTTACCACTTATATTATATGTAAA

Found at i:12361 original size:8 final size:8

Alignment explanation


    Indices: 12350--12401  Score: 54
    Period size: 8  Copynumber: 6.8  Consensus size: 8

      12340 CTATGCTGCT

                  * 
      12350 ATATATGC
          1 ATATATAC

                    
      12358 ATATATAC
          1 ATATATAC

                    
      12366 --ATATAC
          1 ATATATAC

                   *
      12372 ATATATAT
          1 ATATATAC

                   *
      12380 ATATATAT
          1 ATATATAC

                   *
      12388 ATATATAT
          1 ATATATAC

                  
      12396 ATATAT
          1 ATATAT

      12402 GGAATTTGAT


Statistics
Matches: 40,  Mismatches: 2, Indels: 4
        0.87            0.04        0.09

Matches are distributed among these distances:
   6    6  0.15
   8   34  0.85

ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44


Consensus pattern (8 bp):   
ATATATAC

Found at i:12363 original size:2 final size:2

Alignment explanation


    Indices: 12358--12401  Score: 70
    Period size: 2  Copynumber: 22.0  Consensus size: 2

      12348 CTATATATGC

                      *        *                                          
      12358 AT AT AT AC AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

              
      12400 AT
          1 AT

      12402 GGAATTTGAT


Statistics
Matches: 38,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
   2   38  1.00

ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45


Consensus pattern (2 bp):   
AT

Done.