Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013559.1 Corchorus capsularis cultivar CVL-1 contig13580, 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: 48012
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:5413 original size:17 final size:17

Alignment explanation


    Indices: 5391--5423  Score: 57
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       5381 GAAATCAATT

                             
       5391 TATTCTCTTCAAGTTTC
          1 TATTCTCTTCAAGTTTC

                     *      
       5408 TATTCTCTTTAAGTTT
          1 TATTCTCTTCAAGTTT

       5424 GTGCCCATGG


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.18, C:0.18, G:0.06, T:0.58


Consensus pattern (17 bp):   
TATTCTCTTCAAGTTTC

Found at i:18864 original size:29 final size:30

Alignment explanation


    Indices: 18809--18874  Score: 98
    Period size: 30  Copynumber: 2.2  Consensus size: 30

      18799 GCTCAATTAT

                     *     *              
      18809 GGGCAAAACGTTTCAGTTCGGCTTAATTTG
          1 GGGCAAAACCTTTCAATTCGGCTTAATTTG

                         *                
      18839 GGGCAAAACCTTTTAATTCGG-TTAATTTG
          1 GGGCAAAACCTTTCAATTCGGCTTAATTTG

                   
      18868 GGGCAAA
          1 GGGCAAA

      18875 GAGTGACTTA


Statistics
Matches: 33,  Mismatches: 3, Indels: 1
        0.89            0.08        0.03

Matches are distributed among these distances:
  29   15  0.45
  30   18  0.55

ACGTcount: A:0.27, C:0.15, G:0.26, T:0.32


Consensus pattern (30 bp):   
GGGCAAAACCTTTCAATTCGGCTTAATTTG

Found at i:19983 original size:71 final size:71

Alignment explanation


    Indices: 19899--20040  Score: 266
    Period size: 71  Copynumber: 2.0  Consensus size: 71

      19889 GCGATTTCGA

                                                                             
      19899 GACGTTTTGCCCTAAATCAACCAAATTAAAAGGTTTTGCCCCAAATTAAATCGAACCCAAAACGT
          1 GACGTTTTGCCCTAAATCAACCAAATTAAAAGGTTTTGCCCCAAATTAAATCGAACCCAAAACGT

                  
      19964 TTTGCC
         66 TTTGCC

                                 *                *                          
      19970 GACGTTTTGCCCTAAATCAACTAAATTAAAAGGTTTTGTCCCAAATTAAATCGAACCCAAAACGT
          1 GACGTTTTGCCCTAAATCAACCAAATTAAAAGGTTTTGCCCCAAATTAAATCGAACCCAAAACGT

                  
      20035 TTTGCC
         66 TTTGCC

      20041 CTTAATTGAG


Statistics
Matches: 69,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  71   69  1.00

ACGTcount: A:0.35, C:0.24, G:0.13, T:0.28


Consensus pattern (71 bp):   
GACGTTTTGCCCTAAATCAACCAAATTAAAAGGTTTTGCCCCAAATTAAATCGAACCCAAAACGT
TTTGCC

Found at i:22193 original size:21 final size:22

Alignment explanation


    Indices: 22162--22210  Score: 75
    Period size: 22  Copynumber: 2.3  Consensus size: 22

      22152 ATGGGGACAC

                                  
      22162 TGATG-TTTTTCC-ATACATTG
          1 TGATGTTTTTTCCTATACATTG

                                  
      22182 TGATGTTTTTTCCTATACATTG
          1 TGATGTTTTTTCCTATACATTG

            *      
      22204 AGATGTT
          1 TGATGTT

      22211 CCTTTCAGCT


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  20    5  0.19
  21    7  0.27
  22   14  0.54

ACGTcount: A:0.20, C:0.12, G:0.16, T:0.51


Consensus pattern (22 bp):   
TGATGTTTTTTCCTATACATTG

Found at i:23811 original size:39 final size:39

Alignment explanation


    Indices: 23757--23876  Score: 143
    Period size: 39  Copynumber: 3.1  Consensus size: 39

      23747 AGATAAAAAA

                              *                    
      23757 GTAGCTTTCCACCACAAATGCAATACCAAATAATTTATG
          1 GTAGCTTTCCACCACAAACGCAATACCAAATAATTTATG

                                      *            
      23796 GTAGCTTTCCACCACAAACGCAATACTAAATAATTTATG
          1 GTAGCTTTCCACCACAAACGCAATACCAAATAATTTATG

               *   *   * **                 *        
      23835 GTTTG-TGTCAAAAGACAAACGCAATACCAAACAATTTATG
          1 G-TAGCTTTC-CACCACAAACGCAATACCAAATAATTTATG

              
      23875 GT
          1 GT

      23877 TTGTGTTAAA


Statistics
Matches: 70,  Mismatches: 9, Indels: 4
        0.84            0.11        0.05

Matches are distributed among these distances:
  39   42  0.60
  40   28  0.40

ACGTcount: A:0.39, C:0.21, G:0.12, T:0.28


Consensus pattern (39 bp):   
GTAGCTTTCCACCACAAACGCAATACCAAATAATTTATG

Found at i:23871 original size:40 final size:40

Alignment explanation


    Indices: 23809--23888  Score: 133
    Period size: 40  Copynumber: 2.0  Consensus size: 40

      23799 GCTTTCCACC

                         *   *                      
      23809 ACAAACGCAATACTAAATAATTTATGGTTTGTGTCAAAAG
          1 ACAAACGCAATACCAAACAATTTATGGTTTGTGTCAAAAG

                                              *     
      23849 ACAAACGCAATACCAAACAATTTATGGTTTGTGTTAAAAG
          1 ACAAACGCAATACCAAACAATTTATGGTTTGTGTCAAAAG

      23889 CTAGTTTTGA


Statistics
Matches: 37,  Mismatches: 3, Indels: 0
        0.93            0.08        0.00

Matches are distributed among these distances:
  40   37  1.00

ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29


Consensus pattern (40 bp):   
ACAAACGCAATACCAAACAATTTATGGTTTGTGTCAAAAG
Done.