Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012817.1 Corchorus capsularis cultivar CVL-1 contig12838, 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: 29936
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29


Found at i:50 original size:33 final size:33

Alignment explanation


    Indices: 13--77  Score: 96
    Period size: 33  Copynumber: 2.0  Consensus size: 33

          3 GGGGCGGCCT

                                              
         13 GCCGTGGC-GAAGCCGCCCCAGTGGGGAGGCTCC
          1 GCCGTGGCTGAA-CCGCCCCAGTGGGGAGGCTCC

                           *  *             
         46 GCCGTGGCTGAACCGTCCTAGTGGGGAGGCTC
          1 GCCGTGGCTGAACCGCCCCAGTGGGGAGGCTC

         78 AGTGTAAAAG


Statistics
Matches: 29,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  33   26  0.90
  34    3  0.10

ACGTcount: A:0.12, C:0.32, G:0.42, T:0.14


Consensus pattern (33 bp):   
GCCGTGGCTGAACCGCCCCAGTGGGGAGGCTCC

Found at i:8853 original size:14 final size:15

Alignment explanation


    Indices: 8821--8862  Score: 50
    Period size: 14  Copynumber: 2.7  Consensus size: 15

       8811 GGCTCAGTGT

                          *  
       8821 AAAAGTGTAAAAAGTGC
          1 AAAAGTGT--AAAGGGC

                           
       8838 AAAAG-GTAAAGGGC
          1 AAAAGTGTAAAGGGC

                       
       8852 AAAAGTGTAAA
          1 AAAAGTGTAAA

       8863 AAATGGGACG


Statistics
Matches: 23,  Mismatches: 1, Indels: 4
        0.82            0.04        0.14

Matches are distributed among these distances:
  14   11  0.48
  15    5  0.22
  16    2  0.09
  17    5  0.22

ACGTcount: A:0.55, C:0.05, G:0.26, T:0.14


Consensus pattern (15 bp):   
AAAAGTGTAAAGGGC

Found at i:8885 original size:21 final size:21

Alignment explanation


    Indices: 8861--8904  Score: 63
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       8851 CAAAAGTGTA

                                  
       8861 AAAAAT-GGGACGGTATTTAGC
          1 AAAAATAGGG-CGGTATTTAGC

                *                
       8882 AAAACTAGGGCGGTATTTAGC
          1 AAAAATAGGGCGGTATTTAGC

              
       8903 AA
          1 AA

       8905 CACCCTTTCA


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  21   18  0.86
  22    3  0.14

ACGTcount: A:0.39, C:0.11, G:0.27, T:0.23


Consensus pattern (21 bp):   
AAAAATAGGGCGGTATTTAGC

Found at i:15801 original size:2 final size:2

Alignment explanation


    Indices: 15794--15822  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

      15784 TGTTTAATCT

                                                       
      15794 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      15823 GTTTTATTTG


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:29849 original size:2 final size:2

Alignment explanation


    Indices: 29842--29936  Score: 181
    Period size: 2  Copynumber: 47.5  Consensus size: 2

      29832 CATAGAGTAA

                        *                                                 
      29842 AG AG AG AG CG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG

                                                                          
      29884 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG

                            
      29926 AG AG AG AG AG A
          1 AG AG AG AG AG A


Statistics
Matches: 91,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
   2   91  1.00

ACGTcount: A:0.49, C:0.01, G:0.49, T:0.00


Consensus pattern (2 bp):   
AG

Done.