Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002445.1 Corchorus capsularis cultivar CVL-1 contig02451, 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, 708

Length: 1180
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.25


Found at i:727 original size:147 final size:146

Alignment explanation


    Indices: 459--730  Score: 341
    Period size: 147  Copynumber: 1.9  Consensus size: 146

        449 TATACTTGGA

                                                            *         *      
        459 ATTTTGGGCTGAAATTTTGCAGGGACACCAAGGAATATATAGAGATGGTCCCTGCAAATTTTCAG
          1 ATTTTGGGCTGAAATTTTGCAGGGACACCAAGGAATATATAGAGATGGACCCTGCAAAATTTCAG

            *  *  **       **          *  *                    *             
        524 GTCCAATGGATGACCGGAACTATACCGGGCCCCCCGGACCGCTCCGAAACATGGAAAATCGTAGA
         66 CTCAAAAAGATGACCCAAACTATACCGAGCACCCCGGACCGCTCCGAAACACGGAAAATCGTAGA

                            
        589 AAATAGAAAACATGGC
        131 AAATAGAAAACATGGC

                                        *                      ***           
        605 ATTTTGGGCTGAAATTTTGCAGGGACATTCAA-GAATAATATAGAGATGGAGTGTGCAAAATTTC
          1 ATTTTGGGCTGAAATTTTGCAGGGACA-CCAAGGAAT-ATATAGAGATGGACCCTGCAAAATTTC

                                              *              **            
        669 AGCTCAAAAAGATGACCCAAACTATAACCGAG-ATCCCGGACCGCTCCGGTACACGGAAAATC
         64 AGCTCAAAAAGATGACCCAAACTAT-ACCGAGCACCCCGGACCGCTCCGAAACACGGAAAATC

        731 ATGAAAAATG


Statistics
Matches: 105,  Mismatches: 18, Indels: 5
        0.82            0.14        0.04

Matches are distributed among these distances:
 146   31  0.30
 147   69  0.66
 148    5  0.05

ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21


Consensus pattern (146 bp):   
ATTTTGGGCTGAAATTTTGCAGGGACACCAAGGAATATATAGAGATGGACCCTGCAAAATTTCAG
CTCAAAAAGATGACCCAAACTATACCGAGCACCCCGGACCGCTCCGAAACACGGAAAATCGTAGA
AAATAGAAAACATGGC

Found at i:903 original size:48 final size:48

Alignment explanation


    Indices: 827--939  Score: 183
    Period size: 48  Copynumber: 2.4  Consensus size: 48

        817 TGGATTTCTA

                         *                                  
        827 ATTTTGGCCAATTATTGGGTCCGGAACTCATGATGGTTAACCTACGGC
          1 ATTTTGGCCAATTTTTGGGTCCGGAACTCATGATGGTTAACCTACGGC

                                          *              *   
        875 -TTTTCGGCCAATTTTTGGGTCCGGAACTCTTGATGGTTAACCTATGGC
          1 ATTTT-GGCCAATTTTTGGGTCCGGAACTCATGATGGTTAACCTACGGC

                             
        923 ATTTTGGCCAATTTTTG
          1 ATTTTGGCCAATTTTTG

        940 CCCCCGAAGC


Statistics
Matches: 60,  Mismatches: 3, Indels: 4
        0.90            0.04        0.06

Matches are distributed among these distances:
  47    4  0.07
  48   52  0.87
  49    4  0.07

ACGTcount: A:0.19, C:0.19, G:0.24, T:0.37


Consensus pattern (48 bp):   
ATTTTGGCCAATTTTTGGGTCCGGAACTCATGATGGTTAACCTACGGC

Found at i:1003 original size:77 final size:77

Alignment explanation


    Indices: 876--1029  Score: 202
    Period size: 77  Copynumber: 2.0  Consensus size: 77

        866 ACCTACGGCT

                                        *    ****                            
        876 TTTCGGCCAATTTTTGGGTCCGGAACTCTTGATGGTTAACCTATGGCATTTTGGCCAATTTTTGC
          1 TTTCGGCCAATTTTTGGGTCCGGAACTCATGATACAAAACCTATGGCATTTTGGCCAATTTTTGC

                   *    
        941 CCCCGAAGCTCA
         66 CCCCGAAACTCA

                     *          *          *                          *      
        953 TTTCGGCCATTTTTTGGGTCTGGAACTCATGGTACAAAACCTAAT-GCATTTTGGCCATTTTTTG
          1 TTTCGGCCAATTTTTGGGTCCGGAACTCATGATACAAAACCT-ATGGCATTTTGGCCAATTTTTG

                         
       1017 CCCCCGAAACTCA
         65 CCCCCGAAACTCA

       1030 GCGAACACCT


Statistics
Matches: 66,  Mismatches: 10, Indels: 2
        0.85            0.13        0.03

Matches are distributed among these distances:
  77   64  0.97
  78    2  0.03

ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35


Consensus pattern (77 bp):   
TTTCGGCCAATTTTTGGGTCCGGAACTCATGATACAAAACCTATGGCATTTTGGCCAATTTTTGC
CCCCGAAACTCA
Done.