Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014463.1 Corchorus capsularis cultivar CVL-1 contig14484, 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: 28987
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32


Found at i:26735 original size:31 final size:31

Alignment explanation


    Indices: 26665--26865  Score: 231
    Period size: 31  Copynumber: 6.5  Consensus size: 31

      26655 TCCTTTTATG

                          *              ** 
      26665 CACGTGGCATGCCACGTGTCACTTTTTTGAAA
          1 CACGTGGCATGCCATGTGTCAC-TTTTTGGTA

              *                            
      26697 CATGTGGCATGCCATGTGTCACTTTTTGGTA
          1 CACGTGGCATGCCATGTGTCACTTTTTGGTA

                       *                   
      26728 CACGTGGCATGACATGTGTCACTTTTTGGTA
          1 CACGTGGCATGCCATGTGTCACTTTTTGGTA

                  * *  *    *              
      26759 CACGTGACGTGACATGCGTCACTTTTTGGTA
          1 CACGTGGCATGCCATGTGTCACTTTTTGGTA

                 *  *  *       *       *   
      26790 CACGTAGCGTGACATGTGTTACTTTTTTGTA
          1 CACGTGGCATGCCATGTGTCACTTTTTGGTA

              *     *     **               
      26821 CATGTGGCGTGCCACATGTCACTTTTTGGTA
          1 CACGTGGCATGCCATGTGTCACTTTTTGGTA

                          
      26852 CACGTGGCATGCCA
          1 CACGTGGCATGCCA

      26866 CGTCGGACAC


Statistics
Matches: 146,  Mismatches: 23, Indels: 1
        0.86            0.14        0.01

Matches are distributed among these distances:
  31  126  0.86
  32   20  0.14

ACGTcount: A:0.19, C:0.22, G:0.25, T:0.34


Consensus pattern (31 bp):   
CACGTGGCATGCCATGTGTCACTTTTTGGTA

Found at i:27746 original size:32 final size:32

Alignment explanation


    Indices: 27710--27838  Score: 177
    Period size: 32  Copynumber: 4.0  Consensus size: 32

      27700 ATTTGGTGAC

                         *    *  **        *
      27710 CTCACCAGGTGAGCATTGTACTGGGTGAGTAG
          1 CTCACCAGGTGAGTATTGCACCAGGTGAGTAT

                                            
      27742 CTCACCAGGTGAGTATTGCACCAGGTGAGTAT
          1 CTCACCAGGTGAGTATTGCACCAGGTGAGTAT

                                            
      27774 CTCACCAGGTGAGTATTGCACCAGGTGAGTAT
          1 CTCACCAGGTGAGTATTGCACCAGGTGAGTAT

             *     *           *             
      27806 CGCACCATGTGAGTATTTGTACCAGGTGAGTAT
          1 CTCACCAGGTGAGTA-TTGCACCAGGTGAGTAT

      27839 TTGTATTGGG


Statistics
Matches: 88,  Mismatches: 8, Indels: 1
        0.91            0.08        0.01

Matches are distributed among these distances:
  32   72  0.82
  33   16  0.18

ACGTcount: A:0.24, C:0.20, G:0.29, T:0.26


Consensus pattern (32 bp):   
CTCACCAGGTGAGTATTGCACCAGGTGAGTAT

Found at i:27821 original size:16 final size:16

Alignment explanation


    Indices: 27733--27838  Score: 131
    Period size: 16  Copynumber: 6.6  Consensus size: 16

      27723 CATTGTACTG

                    * *     
      27733 GGTGAGTAGCTCACCA
          1 GGTGAGTATCGCACCA

                     *      
      27749 GGTGAGTATTGCACCA
          1 GGTGAGTATCGCACCA

                      *     
      27765 GGTGAGTATCTCACCA
          1 GGTGAGTATCGCACCA

                     *      
      27781 GGTGAGTATTGCACCA
          1 GGTGAGTATCGCACCA

                            
      27797 GGTGAGTATCGCACCA
          1 GGTGAGTATCGCACCA

            *         * *    
      27813 TGTGAGTATTTGTACCA
          1 GGTGAGTA-TCGCACCA

                     
      27830 GGTGAGTAT
          1 GGTGAGTAT

      27839 TTGTATTGGG


Statistics
Matches: 77,  Mismatches: 12, Indels: 2
        0.85            0.13        0.02

Matches are distributed among these distances:
  16   64  0.83
  17   13  0.17

ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26


Consensus pattern (16 bp):   
GGTGAGTATCGCACCA

Found at i:28044 original size:2 final size:2

Alignment explanation


    Indices: 28037--28071  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

      28027 ACATACATAC

                                                                
      28037 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      28072 CTAGTTAATG


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Done.