Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007654.1 Corchorus capsularis cultivar CVL-1 contig07675, 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: 16514
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32


Found at i:14404 original size:27 final size:27

Alignment explanation


    Indices: 14366--14422  Score: 114
    Period size: 27  Copynumber: 2.1  Consensus size: 27

      14356 ATTATTAGGA

                                       
      14366 GACATAACAGACCTGATCACGCTTGGG
          1 GACATAACAGACCTGATCACGCTTGGG

                                       
      14393 GACATAACAGACCTGATCACGCTTGGG
          1 GACATAACAGACCTGATCACGCTTGGG

               
      14420 GAC
          1 GAC

      14423 TACATCTCTC


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   30  1.00

ACGTcount: A:0.30, C:0.26, G:0.26, T:0.18


Consensus pattern (27 bp):   
GACATAACAGACCTGATCACGCTTGGG

Found at i:15212 original size:15 final size:15

Alignment explanation


    Indices: 15174--15217  Score: 61
    Period size: 15  Copynumber: 2.9  Consensus size: 15

      15164 CTCATCATCA

                    *  *   
      15174 TCTTCCTCTTCATCT
          1 TCTTCCTCCTCCTCT

            *              
      15189 ACTTCCTCCTCCTCT
          1 TCTTCCTCCTCCTCT

                          
      15204 TCTTCCTCCTCCTC
          1 TCTTCCTCCTCCTC

      15218 CACATAATCT


Statistics
Matches: 25,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  15   25  1.00

ACGTcount: A:0.05, C:0.50, G:0.00, T:0.45


Consensus pattern (15 bp):   
TCTTCCTCCTCCTCT

Found at i:15324 original size:102 final size:102

Alignment explanation


    Indices: 15212--15521  Score: 530
    Period size: 102  Copynumber: 3.0  Consensus size: 102

      15202 CTTCTTCCTC

                                                                             
      15212 CTCCTCCACATAATCTTCATCTTCCTCTTCTTCATCTGATGCACTTTTCTGCTTTCGGGATTTTC
          1 CTCCTCCACATAATCTTCATCTTCCTCTTCTTCATCTGATGCACTTTTCTGCTTTCGGGATTTTC

                                                 
      15277 TACCCACAATCTTCATCTCCTTTGGTGAAGGCATCTT
         66 TACCCACAATCTTCATCTCCTTTGGTGAAGGCATCTT

                                                                             
      15314 CTCCTCCACATAATCTTCATCTTCCTCTTCTTCATCTGATGCACTTTTCTGCTTTCGGGATTTTC
          1 CTCCTCCACATAATCTTCATCTTCCTCTTCTTCATCTGATGCACTTTTCTGCTTTCGGGATTTTC

                                                 
      15379 TACCCACAATCTTCATCTCCTTTGGTGAAGGCATCTT
         66 TACCCACAATCTTCATCTCCTTTGGTGAAGGCATCTT

                                                         *         *         
      15416 CTCCTCCACATAATCTTCATCTACCTCTTCCTCTTCTTCATCTGAAGCACTTTTCCGCTTTCGGG
          1 CTCCTCCACATAATC-T--TC-A--TCTTCCTCTTCTTCATCTGATGCACTTTTCTGCTTTCGGG

                         *      *                    
      15481 ATTTTCTACCCACGATCTTCCTCTCCTTTGGTGAAGGCATC
         60 ATTTTCTACCCACAATCTTCATCTCCTTTGGTGAAGGCATC

      15522 CGTCTAGCTT


Statistics
Matches: 198,  Mismatches: 4, Indels: 6
        0.95            0.02        0.03

Matches are distributed among these distances:
 102  117  0.59
 103    1  0.01
 105    2  0.01
 106    1  0.01
 108   77  0.39

ACGTcount: A:0.16, C:0.33, G:0.11, T:0.40


Consensus pattern (102 bp):   
CTCCTCCACATAATCTTCATCTTCCTCTTCTTCATCTGATGCACTTTTCTGCTTTCGGGATTTTC
TACCCACAATCTTCATCTCCTTTGGTGAAGGCATCTT

Found at i:16485 original size:2 final size:2

Alignment explanation


    Indices: 16480--16514  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

      16470 GTGTGTGTGT

                                                                
      16480 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
          1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G


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


Consensus pattern (2 bp):   
GA

Done.