Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012450.1 Corchorus capsularis cultivar CVL-1 contig12471, 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: 22373
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34


Found at i:778 original size:11 final size:11

Alignment explanation


    Indices: 735--772  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

        725 TTCCTATATA

                *      
        735 AAATAAATTAT
          1 AAATTAATTAT

                        
        746 CAAA-TAATTAT
          1 -AAATTAATTAT

                       
        757 AAATTAATTAT
          1 AAATTAATTAT

                 
        768 AAATT
          1 AAATT

        773 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:5725 original size:31 final size:32

Alignment explanation


    Indices: 5690--5758  Score: 97
    Period size: 31  Copynumber: 2.2  Consensus size: 32

       5680 TAAATCTTTT

                              *             
       5690 ATTTTAGGAGGA-CCAATGTGATAAAACTTCA
          1 ATTTTAGGAGGAGCCAATATGATAAAACTTCA

                    *    *                  
       5721 ATTTTA-GTGGAGTCAATATGATAAAACTTCA
          1 ATTTTAGGAGGAGCCAATATGATAAAACTTCA

                   
       5752 ATTTTAG
          1 ATTTTAG

       5759 TAGGGTCAAT


Statistics
Matches: 33,  Mismatches: 3, Indels: 3
        0.85            0.08        0.08

Matches are distributed among these distances:
  30    4  0.12
  31   29  0.88

ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35


Consensus pattern (32 bp):   
ATTTTAGGAGGAGCCAATATGATAAAACTTCA

Found at i:5759 original size:31 final size:31

Alignment explanation


    Indices: 5703--5768  Score: 107
    Period size: 31  Copynumber: 2.1  Consensus size: 31

       5693 TTAGGAGGAC

                *                           
       5703 CAATGTGATAAAACTTCAATTTTAGT-GGAGT
          1 CAATATGATAAAACTTCAATTTTAGTAGG-GT

                                           
       5734 CAATATGATAAAACTTCAATTTTAGTAGGGT
          1 CAATATGATAAAACTTCAATTTTAGTAGGGT

                
       5765 CAAT
          1 CAAT

       5769 TGGTAATTTT


Statistics
Matches: 33,  Mismatches: 1, Indels: 2
        0.92            0.03        0.06

Matches are distributed among these distances:
  31   31  0.94
  32    2  0.06

ACGTcount: A:0.38, C:0.11, G:0.17, T:0.35


Consensus pattern (31 bp):   
CAATATGATAAAACTTCAATTTTAGTAGGGT

Found at i:6099 original size:2 final size:2

Alignment explanation


    Indices: 6092--6116  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       6082 TGAATACTTT

                                                 
       6092 AG AG AG AG AG AG AG AG AG AG AG AG A
          1 AG AG AG AG AG AG AG AG AG AG AG AG A

       6117 TTAAATATAC


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:0.48, T:0.00


Consensus pattern (2 bp):   
AG

Found at i:22250 original size:2 final size:2

Alignment explanation


    Indices: 22243--22277  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

      22233 CAGATATTGA

                                                                
      22243 AT AT AT AT AT 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 AT AT AT AT AT A

      22278 GAGAGAGAGA


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

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:22282 original size:2 final size:2

Alignment explanation


    Indices: 22277--22301  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

      22267 ATATATATAT

                                                 
      22277 AG AG AG AG AG AG AG AG AG AG AG AG A
          1 AG AG AG AG AG AG AG AG AG AG AG AG A

      22302 ATTCTCTAGG


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:0.48, T:0.00


Consensus pattern (2 bp):   
AG

Done.