Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001061.1 Corchorus capsularis cultivar CVL-1 contig01061, 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: 15806
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34


Found at i:14 original size:2 final size:2

Alignment explanation


    Indices: 8--43  Score: 72
    Period size: 2  Copynumber: 18.0  Consensus size: 2

          1 ATACTAC

                                                                 
          8 TA TA 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 TA TA

         44 GTATGATGCT


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   34  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:5830 original size:3 final size:3

Alignment explanation


    Indices: 5822--5855  Score: 68
    Period size: 3  Copynumber: 11.3  Consensus size: 3

       5812 TGTACATTAC

                                                         
       5822 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A

       5856 CACTTTCACA


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   31  1.00

ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65


Consensus pattern (3 bp):   
ATT

Found at i:12427 original size:11 final size:11

Alignment explanation


    Indices: 12411--12446  Score: 72
    Period size: 11  Copynumber: 3.3  Consensus size: 11

      12401 TACCTCTACC

                       
      12411 AAATAGACATT
          1 AAATAGACATT

                       
      12422 AAATAGACATT
          1 AAATAGACATT

                       
      12433 AAATAGACATT
          1 AAATAGACATT

               
      12444 AAA
          1 AAA

      12447 GGTAAAGAGT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   25  1.00

ACGTcount: A:0.58, C:0.08, G:0.08, T:0.25


Consensus pattern (11 bp):   
AAATAGACATT

Found at i:13866 original size:8 final size:8

Alignment explanation


    Indices: 13853--13895  Score: 86
    Period size: 8  Copynumber: 5.4  Consensus size: 8

      13843 AAGAATAGCC

                    
      13853 ATAGGAGT
          1 ATAGGAGT

                    
      13861 ATAGGAGT
          1 ATAGGAGT

                    
      13869 ATAGGAGT
          1 ATAGGAGT

                    
      13877 ATAGGAGT
          1 ATAGGAGT

                    
      13885 ATAGGAGT
          1 ATAGGAGT

               
      13893 ATA
          1 ATA

      13896 TATATTATAT


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   8   35  1.00

ACGTcount: A:0.40, C:0.00, G:0.35, T:0.26


Consensus pattern (8 bp):   
ATAGGAGT

Found at i:15766 original size:33 final size:33

Alignment explanation


    Indices: 15724--15798  Score: 107
    Period size: 33  Copynumber: 2.3  Consensus size: 33

      15714 TACACTGAAA

                                 *            
      15724 CTCCCCACTA-GGACGGCTCAGCCACGGCGGAGC
          1 CTCCCCACTAGGGA-GGCTCAACCACGGCGGAGC

                            *       *        
      15757 CTCCCCACTAGGGAGGTTCAACCATGGCGGAGC
          1 CTCCCCACTAGGGAGGCTCAACCACGGCGGAGC

                     
      15790 CTCCCCACT
          1 CTCCCCACT

      15799 GGGGCGGC


Statistics
Matches: 38,  Mismatches: 3, Indels: 2
        0.88            0.07        0.05

Matches are distributed among these distances:
  33   35  0.92
  34    3  0.08

ACGTcount: A:0.19, C:0.41, G:0.27, T:0.13


Consensus pattern (33 bp):   
CTCCCCACTAGGGAGGCTCAACCACGGCGGAGC
Done.