Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005269.1 Corchorus capsularis cultivar CVL-1 contig05287, 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: 3048
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.27


Found at i:486 original size:27 final size:27

Alignment explanation


    Indices: 446--616  Score: 279
    Period size: 27  Copynumber: 6.3  Consensus size: 27

        436 CGACCCGAGG

                                *      
        446 CGAAGTGGGAGGATCCACTGATGGGGT
          1 CGAAGTGGGAGGATCCACTGCTGGGGT

             *                  *      
        473 CAAAGTGGGAGGATCCACTGTTGGGGT
          1 CGAAGTGGGAGGATCCACTGCTGGGGT

                               *       
        500 CGAAGTGGGAGGATCCACTTCTGGGGT
          1 CGAAGTGGGAGGATCCACTGCTGGGGT

                                       
        527 CGAAGTGGGAGGATCCACTGCTGGGGT
          1 CGAAGTGGGAGGATCCACTGCTGGGGT

             *                         
        554 CAAAGTGGGAGGATCCACTGCTGGGGT
          1 CGAAGTGGGAGGATCCACTGCTGGGGT

                  *            *       
        581 CGAAGTAGGAGGATCCACTTCTGGGGT
          1 CGAAGTGGGAGGATCCACTGCTGGGGT

                     
        608 CGAAGTGGG
          1 CGAAGTGGG

        617 GAGAGCCGTA


Statistics
Matches: 133,  Mismatches: 11, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  27  133  1.00

ACGTcount: A:0.21, C:0.17, G:0.42, T:0.20


Consensus pattern (27 bp):   
CGAAGTGGGAGGATCCACTGCTGGGGT

Found at i:581 original size:81 final size:81

Alignment explanation


    Indices: 446--616  Score: 315
    Period size: 81  Copynumber: 2.1  Consensus size: 81

        436 CGACCCGAGG

                                                           *            *    
        446 CGAAGTGGGAGGATCCACTGATGGGGTCAAAGTGGGAGGATCCACTGTTGGGGTCGAAGTGGGAG
          1 CGAAGTGGGAGGATCCACTGATGGGGTCAAAGTGGGAGGATCCACTGCTGGGGTCGAAGTAGGAG

                            
        511 GATCCACTTCTGGGGT
         66 GATCCACTTCTGGGGT

                                *                                            
        527 CGAAGTGGGAGGATCCACTGCTGGGGTCAAAGTGGGAGGATCCACTGCTGGGGTCGAAGTAGGAG
          1 CGAAGTGGGAGGATCCACTGATGGGGTCAAAGTGGGAGGATCCACTGCTGGGGTCGAAGTAGGAG

                            
        592 GATCCACTTCTGGGGT
         66 GATCCACTTCTGGGGT

                     
        608 CGAAGTGGG
          1 CGAAGTGGG

        617 GAGAGCCGTA


Statistics
Matches: 87,  Mismatches: 3, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  81   87  1.00

ACGTcount: A:0.21, C:0.17, G:0.42, T:0.20


Consensus pattern (81 bp):   
CGAAGTGGGAGGATCCACTGATGGGGTCAAAGTGGGAGGATCCACTGCTGGGGTCGAAGTAGGAG
GATCCACTTCTGGGGT

Found at i:2314 original size:11 final size:11

Alignment explanation


    Indices: 2298--2324  Score: 54
    Period size: 11  Copynumber: 2.5  Consensus size: 11

       2288 CGCTGCGAAT

                       
       2298 GAGAAGGAAAG
          1 GAGAAGGAAAG

                       
       2309 GAGAAGGAAAG
          1 GAGAAGGAAAG

                 
       2320 GAGAA
          1 GAGAA

       2325 AAGTAAATCA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   16  1.00

ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00


Consensus pattern (11 bp):   
GAGAAGGAAAG
Done.