Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010575.1 Corchorus capsularis cultivar CVL-1 contig10596, 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: 8213
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:13 original size:2 final size:2

Alignment explanation


    Indices: 7--38  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

          1 TTTTCT

                                                           
          7 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

         39 ATACTTTTTT


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:326 original size:21 final size:22

Alignment explanation


    Indices: 300--341  Score: 77
    Period size: 22  Copynumber: 2.0  Consensus size: 22

        290 CCAGGTTACA

                                  
        300 TAAACCCT-AATTAGTTTAATC
          1 TAAACCCTAAATTAGTTTAATC

                                 
        321 TAAACCCTAAATTAGTTTAAT
          1 TAAACCCTAAATTAGTTTAAT

        342 ACCCATTATT


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  21    8  0.40
  22   12  0.60

ACGTcount: A:0.40, C:0.17, G:0.05, T:0.38


Consensus pattern (22 bp):   
TAAACCCTAAATTAGTTTAATC

Found at i:392 original size:19 final size:21

Alignment explanation


    Indices: 349--396  Score: 64
    Period size: 22  Copynumber: 2.3  Consensus size: 21

        339 AATACCCATT

                     *            
        349 ATTATTTTACTCTAATCACCCC
          1 ATTATTTTAATCTAA-CACCCC

                                 
        371 ATTATTTTAATCTAA-A-CCC
          1 ATTATTTTAATCTAACACCCC

                   
        390 ATTATTT
          1 ATTATTT

        397 AACCGCTAAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 3
        0.86            0.03        0.10

Matches are distributed among these distances:
  19   10  0.40
  20    1  0.04
  22   14  0.56

ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46


Consensus pattern (21 bp):   
ATTATTTTAATCTAACACCCC

Found at i:662 original size:12 final size:12

Alignment explanation


    Indices: 641--670  Score: 51
    Period size: 12  Copynumber: 2.5  Consensus size: 12

        631 GAAATGCACT

                 *      
        641 AGAGATGGAGAG
          1 AGAGAAGGAGAG

                        
        653 AGAGAAGGAGAG
          1 AGAGAAGGAGAG

                  
        665 AGAGAA
          1 AGAGAA

        671 AACGTCAAGA


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:0.50, C:0.00, G:0.47, T:0.03


Consensus pattern (12 bp):   
AGAGAAGGAGAG

Found at i:2122 original size:21 final size:21

Alignment explanation


    Indices: 2098--2139  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       2088 AGGAAATGAG

                   *             
       2098 GGAGTTGGAGAAGAAAGCGGA
          1 GGAGTTGCAGAAGAAAGCGGA

                       **        
       2119 GGAGTTGCAGACTAAAGCGGA
          1 GGAGTTGCAGAAGAAAGCGGA

       2140 AGCAGAGGAA


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.36, C:0.10, G:0.43, T:0.12


Consensus pattern (21 bp):   
GGAGTTGCAGAAGAAAGCGGA

Found at i:6873 original size:2 final size:2

Alignment explanation


    Indices: 6866--6899  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       6856 TGGTACTAGA

                                                              
       6866 AT AT AT 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

       6900 CTTTATCTTT


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

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


Consensus pattern (2 bp):   
AT

Done.