Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011189.1 Corchorus capsularis cultivar CVL-1 contig11210, 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: 32037
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:3752 original size:2 final size:2

Alignment explanation


    Indices: 3733--3771  Score: 53
    Period size: 2  Copynumber: 20.0  Consensus size: 2

       3723 AGTTTAAACT

                              *  *                                     
       3733 TA TA TA -A TA TA AA GA 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 TA TA

       3772 GAAATTATCT


Statistics
Matches: 33,  Mismatches: 3, Indels: 2
        0.87            0.08        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   32  0.97

ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44


Consensus pattern (2 bp):   
TA

Found at i:18448 original size:63 final size:63

Alignment explanation


    Indices: 18376--18507  Score: 246
    Period size: 63  Copynumber: 2.1  Consensus size: 63

      18366 TTGTACATGA

                      *               *                                    
      18376 AGGAGGATGAGGAGGAAGAAGAAGGCGAGCCACCTAGTGTTCCAAATCAAGGAAATGATGTGG
          1 AGGAGGATGAAGAGGAAGAAGAAGGCAAGCCACCTAGTGTTCCAAATCAAGGAAATGATGTGG

                                                                           
      18439 AGGAGGATGAAGAGGAAGAAGAAGGCAAGCCACCTAGTGTTCCAAATCAAGGAAATGATGTGG
          1 AGGAGGATGAAGAGGAAGAAGAAGGCAAGCCACCTAGTGTTCCAAATCAAGGAAATGATGTGG

                  
      18502 AGGAGG
          1 AGGAGG

      18508 GAGAAATAGA


Statistics
Matches: 67,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  63   67  1.00

ACGTcount: A:0.38, C:0.12, G:0.36, T:0.14


Consensus pattern (63 bp):   
AGGAGGATGAAGAGGAAGAAGAAGGCAAGCCACCTAGTGTTCCAAATCAAGGAAATGATGTGG

Found at i:20610 original size:165 final size:165

Alignment explanation


    Indices: 20338--20667  Score: 660
    Period size: 165  Copynumber: 2.0  Consensus size: 165

      20328 AAGCTGATAA

                                                                             
      20338 TGTGATCCCTAGATGGGTTTGGGTTTCTTGGATGTGTGTTGTTGTTACAGCTATTGCTGTTAGTA
          1 TGTGATCCCTAGATGGGTTTGGGTTTCTTGGATGTGTGTTGTTGTTACAGCTATTGCTGTTAGTA

                                                                             
      20403 TTTTGTGGATTTATAATTTGTGGGTTGAGTTGTTTAAAGAGAAAAAGGCTAAATTGGAGAAGAAA
         66 TTTTGTGGATTTATAATTTGTGGGTTGAGTTGTTTAAAGAGAAAAAGGCTAAATTGGAGAAGAAA

                                               
      20468 TTATGATAATGGAAGATACTTTTAGAAGGAGAGAG
        131 TTATGATAATGGAAGATACTTTTAGAAGGAGAGAG

                                                                             
      20503 TGTGATCCCTAGATGGGTTTGGGTTTCTTGGATGTGTGTTGTTGTTACAGCTATTGCTGTTAGTA
          1 TGTGATCCCTAGATGGGTTTGGGTTTCTTGGATGTGTGTTGTTGTTACAGCTATTGCTGTTAGTA

                                                                             
      20568 TTTTGTGGATTTATAATTTGTGGGTTGAGTTGTTTAAAGAGAAAAAGGCTAAATTGGAGAAGAAA
         66 TTTTGTGGATTTATAATTTGTGGGTTGAGTTGTTTAAAGAGAAAAAGGCTAAATTGGAGAAGAAA

                                               
      20633 TTATGATAATGGAAGATACTTTTAGAAGGAGAGAG
        131 TTATGATAATGGAAGATACTTTTAGAAGGAGAGAG

      20668 AGGGTTAGTT


Statistics
Matches: 165,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
 165  165  1.00

ACGTcount: A:0.28, C:0.05, G:0.29, T:0.38


Consensus pattern (165 bp):   
TGTGATCCCTAGATGGGTTTGGGTTTCTTGGATGTGTGTTGTTGTTACAGCTATTGCTGTTAGTA
TTTTGTGGATTTATAATTTGTGGGTTGAGTTGTTTAAAGAGAAAAAGGCTAAATTGGAGAAGAAA
TTATGATAATGGAAGATACTTTTAGAAGGAGAGAG

Found at i:28504 original size:28 final size:28

Alignment explanation


    Indices: 28461--28530  Score: 95
    Period size: 28  Copynumber: 2.5  Consensus size: 28

      28451 GAAATTTGAT

                                        
      28461 GGGGGCAAATTGTCTCTACTATAGTTTA
          1 GGGGGCAAATTGTCTCTACTATAGTTTA

                   *   *      *         
      28489 GGGGGCATATTTTCTCTATTATAGTTTA
          1 GGGGGCAAATTGTCTCTACTATAGTTTA

            *        *    
      28517 AGGGGCAAAGTGTC
          1 GGGGGCAAATTGTC

      28531 CTTAGCCCCA


Statistics
Matches: 35,  Mismatches: 7, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  28   35  1.00

ACGTcount: A:0.24, C:0.13, G:0.27, T:0.36


Consensus pattern (28 bp):   
GGGGGCAAATTGTCTCTACTATAGTTTA
Done.