Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014760.1 Corchorus olitorius cultivar O-4 contig14793, 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: 14415
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.32


Found at i:8069 original size:56 final size:56

Alignment explanation


    Indices: 7983--8096  Score: 201
    Period size: 56  Copynumber: 2.0  Consensus size: 56

       7973 TATCCGTTTC

                                                                    
       7983 CTTTCACACAATAAATGTTAAAATAAATCCTATCCCCCTATCTCTACTTAATTATT
          1 CTTTCACACAATAAATGTTAAAATAAATCCTATCCCCCTATCTCTACTTAATTATT

                    *           *              *                    
       8039 CTTTCACAGAATAAATGTTATAATAAATCCTATCCTCCTATCTCTACTTAATTATT
          1 CTTTCACACAATAAATGTTAAAATAAATCCTATCCCCCTATCTCTACTTAATTATT

              
       8095 CT
          1 CT

       8097 AAAAAATAAA


Statistics
Matches: 55,  Mismatches: 3, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  56   55  1.00

ACGTcount: A:0.34, C:0.24, G:0.03, T:0.39


Consensus pattern (56 bp):   
CTTTCACACAATAAATGTTAAAATAAATCCTATCCCCCTATCTCTACTTAATTATT

Found at i:8396 original size:56 final size:56

Alignment explanation


    Indices: 8326--8438  Score: 208
    Period size: 56  Copynumber: 2.0  Consensus size: 56

       8316 TCAACTTGGG

                                                                    
       8326 AGCTATTGGGTCTCACTTTTTCAGTTTTTTTGTCTTCAAAATAGAATTATATATAT
          1 AGCTATTGGGTCTCACTTTTTCAGTTTTTTTGTCTTCAAAATAGAATTATATATAT

                                 * *                                
       8382 AGCTATTGGGTCTCACTTTTTTATTTTTTTTGTCTTCAAAATAGAATTATATATAT
          1 AGCTATTGGGTCTCACTTTTTCAGTTTTTTTGTCTTCAAAATAGAATTATATATAT

             
       8438 A
          1 A

       8439 TTTCTTTTAA


Statistics
Matches: 55,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  56   55  1.00

ACGTcount: A:0.27, C:0.12, G:0.12, T:0.50


Consensus pattern (56 bp):   
AGCTATTGGGTCTCACTTTTTCAGTTTTTTTGTCTTCAAAATAGAATTATATATAT

Found at i:8584 original size:2 final size:2

Alignment explanation


    Indices: 8577--8614  Score: 67
    Period size: 2  Copynumber: 19.0  Consensus size: 2

       8567 AGTAACATCA

                                        *                           
       8577 AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       8615 GTAATTTGCC


Statistics
Matches: 34,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   34  1.00

ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47


Consensus pattern (2 bp):   
AT

Found at i:12066 original size:22 final size:22

Alignment explanation


    Indices: 12038--12203  Score: 135
    Period size: 22  Copynumber: 7.4  Consensus size: 22

      12028 CAAGAAGTGT

                                  
      12038 TCTGCAAAGTGGAAAATAATGC
          1 TCTGCAAAGTGGAAAATAATGC

                       *           
      12060 TCTGCAAAAGTAGAAAATAATGC
          1 TCTGC-AAAGTGGAAAATAATGC

                            *     
      12083 TCTGCAAA---G-AAAGAAT-C
          1 TCTGCAAAGTGGAAAATAATGC

                          ***    *   
      12100 TCTGCAAAGATGTTTCCAATAGTGC
          1 TCTGCAAAG-TG--GAAAATAATGC

            ***                       
      12125 AAAGCTAAAGTTGAAGAAAATAATGC
          1 TCTGC-AAAG-TG--GAAAATAATGC

                                  
      12151 TCTGCAAAGTGGAAAATAATGC
          1 TCTGCAAAGTGGAAAATAATGC

                      *           
      12173 TCTGCAAAGTAGAAAATAATGC
          1 TCTGCAAAGTGGAAAATAATGC

                     
      12195 TCTGCAAAG
          1 TCTGCAAAG

      12204 AAGAAAGAAT


Statistics
Matches: 114,  Mismatches: 20, Indels: 20
        0.74            0.13        0.13

Matches are distributed among these distances:
  17    9  0.08
  18    6  0.05
  19    1  0.01
  22   49  0.43
  23   21  0.18
  24    6  0.05
  25    7  0.06
  26   15  0.13

ACGTcount: A:0.43, C:0.14, G:0.20, T:0.23


Consensus pattern (22 bp):   
TCTGCAAAGTGGAAAATAATGC

Found at i:12208 original size:22 final size:22

Alignment explanation


    Indices: 12137--12224  Score: 126
    Period size: 22  Copynumber: 4.1  Consensus size: 22

      12127 AGCTAAAGTT

                                  
      12137 GAAGAAAATAATGCTCTGCAAA
          1 GAAGAAAATAATGCTCTGCAAA

             **                   
      12159 GTGGAAAATAATGCTCTGCAAA
          1 GAAGAAAATAATGCTCTGCAAA

             *                    
      12181 GTAGAAAATAATGCTCTGCAAA
          1 GAAGAAAATAATGCTCTGCAAA

                    *             
      12203 GAAG-AAAGAAT-CTCTGCAAA
          1 GAAGAAAATAATGCTCTGCAAA

              
      12223 GA
          1 GA

      12225 TGTTTCCAAT


Statistics
Matches: 61,  Mismatches: 5, Indels: 2
        0.90            0.07        0.03

Matches are distributed among these distances:
  20   11  0.18
  21    6  0.10
  22   44  0.72

ACGTcount: A:0.47, C:0.14, G:0.20, T:0.19


Consensus pattern (22 bp):   
GAAGAAAATAATGCTCTGCAAA

Done.