Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001854.1 Corchorus olitorius cultivar O-4 contig01854, 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: 11449
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32


Found at i:2500 original size:24 final size:24

Alignment explanation


    Indices: 2462--2552  Score: 119
    Period size: 24  Copynumber: 3.8  Consensus size: 24

       2452 ATAGAAACGA

                  *               * 
       2462 CCACATAGTGGTCGTGAGATTCGG
          1 CCACATGGTGGTCGTGAGATTCAG

                      *     *       
       2486 CCACATGGTGATCGTGGGATTCAG
          1 CCACATGGTGGTCGTGAGATTCAG

                            *      *
       2510 CCACATGGTGGTCGTGCGATTCAA
          1 CCACATGGTGGTCGTGAGATTCAG

                         *     
       2534 CCACATGGTGGTCATGAGA
          1 CCACATGGTGGTCGTGAGA

       2553 AACGGCCACA


Statistics
Matches: 58,  Mismatches: 9, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  24   58  1.00

ACGTcount: A:0.22, C:0.22, G:0.32, T:0.24


Consensus pattern (24 bp):   
CCACATGGTGGTCGTGAGATTCAG

Found at i:2561 original size:24 final size:24

Alignment explanation


    Indices: 2462--2573  Score: 116
    Period size: 24  Copynumber: 4.7  Consensus size: 24

       2452 ATAGAAACGA

                  *                 
       2462 CCACATAGTGGTCGTGAGATTCGG
          1 CCACATGGTGGTCGTGAGATTCGG

                      *     *     * 
       2486 CCACATGGTGATCGTGGGATTCAG
          1 CCACATGGTGGTCGTGAGATTCGG

                            *     **
       2510 CCACATGGTGGTCGTGCGATTCAA
          1 CCACATGGTGGTCGTGAGATTCGG

                         *     **   
       2534 CCACATGGTGGTCATGAGAAACGG
          1 CCACATGGTGGTCGTGAGATTCGG

                  *   *     
       2558 CCACATAGTGATCGTG
          1 CCACATGGTGGTCGTG

       2574 GCAAAAAGCC


Statistics
Matches: 72,  Mismatches: 16, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  24   72  1.00

ACGTcount: A:0.23, C:0.22, G:0.31, T:0.23


Consensus pattern (24 bp):   
CCACATGGTGGTCGTGAGATTCGG

Found at i:2561 original size:48 final size:48

Alignment explanation


    Indices: 2454--2573  Score: 132
    Period size: 48  Copynumber: 2.5  Consensus size: 48

       2444 GGAGGAAAAT

                   *                      **             *  
       2454 AGAAACGACCACATAGTGGTCGTGAGATTCGGCCACATGGTGATCGTG
          1 AGAAACGGCCACATAGTGGTCGTGAGATTCAACCACATGGTGATCATG

            *  ** *       *         *                 *     
       2502 GGATTCAGCCACATGGTGGTCGTGCGATTCAACCACATGGTGGTCATG
          1 AGAAACGGCCACATAGTGGTCGTGAGATTCAACCACATGGTGATCATG

                              *     
       2550 AGAAACGGCCACATAGTGATCGTG
          1 AGAAACGGCCACATAGTGGTCGTG

       2574 GCAAAAAGCC


Statistics
Matches: 55,  Mismatches: 17, Indels: 0
        0.76            0.24        0.00

Matches are distributed among these distances:
  48   55  1.00

ACGTcount: A:0.26, C:0.22, G:0.31, T:0.22


Consensus pattern (48 bp):   
AGAAACGGCCACATAGTGGTCGTGAGATTCAACCACATGGTGATCATG

Found at i:2870 original size:28 final size:28

Alignment explanation


    Indices: 2827--2885  Score: 109
    Period size: 28  Copynumber: 2.1  Consensus size: 28

       2817 TTAGACCTTT

                                        
       2827 ATGTCTTCATGCGGTAAAAATTAACACC
          1 ATGTCTTCATGCGGTAAAAATTAACACC

                       *                
       2855 ATGTCTTCATGTGGTAAAAATTAACACC
          1 ATGTCTTCATGCGGTAAAAATTAACACC

               
       2883 ATG
          1 ATG

       2886 GTAGGTGGCG


Statistics
Matches: 30,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  28   30  1.00

ACGTcount: A:0.36, C:0.19, G:0.15, T:0.31


Consensus pattern (28 bp):   
ATGTCTTCATGCGGTAAAAATTAACACC

Found at i:5124 original size:15 final size:15

Alignment explanation


    Indices: 5104--5135  Score: 64
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       5094 AAAATCTCGA

                           
       5104 TGAGGAGAGAGAGAG
          1 TGAGGAGAGAGAGAG

                           
       5119 TGAGGAGAGAGAGAG
          1 TGAGGAGAGAGAGAG

              
       5134 TG
          1 TG

       5136 TTTGATAGGT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.38, C:0.00, G:0.53, T:0.09


Consensus pattern (15 bp):   
TGAGGAGAGAGAGAG
Done.