Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024382.1 Corchorus olitorius cultivar O-4 contig24415, 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: 8016
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31


Found at i:460 original size:61 final size:61

Alignment explanation


    Indices: 365--486  Score: 226
    Period size: 61  Copynumber: 2.0  Consensus size: 61

        355 CCAACCCAAA

                               *   *                                     
        365 TGATGCGCCAAGGACTCATCATGTTCTTGAAGAGCACAATGGAGATCATGGAGAGGATGTG
          1 TGATGCGCCAAGGACTCATAATGGTCTTGAAGAGCACAATGGAGATCATGGAGAGGATGTG

                                                                         
        426 TGATGCGCCAAGGACTCATAATGGTCTTGAAGAGCACAATGGAGATCATGGAGAGGATGTG
          1 TGATGCGCCAAGGACTCATAATGGTCTTGAAGAGCACAATGGAGATCATGGAGAGGATGTG

        487 CATATGCGGC


Statistics
Matches: 59,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  61   59  1.00

ACGTcount: A:0.30, C:0.16, G:0.32, T:0.22


Consensus pattern (61 bp):   
TGATGCGCCAAGGACTCATAATGGTCTTGAAGAGCACAATGGAGATCATGGAGAGGATGTG

Found at i:3903 original size:35 final size:35

Alignment explanation


    Indices: 3864--4051  Score: 259
    Period size: 35  Copynumber: 5.3  Consensus size: 35

       3854 AACATAAATC

                *       *                      
       3864 TCATTTGAATTCCTCTTTGAAGATGCTACACCGAG
          1 TCATCTGAATTCATCTTTGAAGATGCTACACCGAG

                *       *                  *   
       3899 TCATTTGAATTCCTCTTTGAAGATGCTACACTGAG
          1 TCATCTGAATTCATCTTTGAAGATGCTACACCGAG

                         *        *     *       
       3934 TCATCTGAATTCAACTTTGAAAAATGCTTCACCGAG
          1 TCATCTGAATTCATCTTTG-AAGATGCTACACCGAG

                  *        ***                 
       3970 TCATCTAAATTCATCCACGAAGATGCTACACCGAG
          1 TCATCTGAATTCATCTTTGAAGATGCTACACCGAG

                                               
       4005 TCATCTGAATTCATCTTTGAAGATGCTACACCGAG
          1 TCATCTGAATTCATCTTTGAAGATGCTACACCGAG

                        
       4040 TCATCTGAATTC
          1 TCATCTGAATTC

       4052 CTGAAAAATT


Statistics
Matches: 134,  Mismatches: 18, Indels: 2
        0.87            0.12        0.01

Matches are distributed among these distances:
  35  107  0.80
  36   27  0.20

ACGTcount: A:0.29, C:0.23, G:0.15, T:0.32


Consensus pattern (35 bp):   
TCATCTGAATTCATCTTTGAAGATGCTACACCGAG

Found at i:3992 original size:71 final size:70

Alignment explanation


    Indices: 3864--4051  Score: 259
    Period size: 71  Copynumber: 2.7  Consensus size: 70

       3854 AACATAAATC

                *       *                          *       *  ***            
       3864 TCATTTGAATTCCTCTTTGAAGATGCTACACCGAGTCATTTGAATTCCTCTTTGAAGATGCTACA
          1 TCATCTGAATTCATCTTTGAAGATGCTACACCGAGTCATCTGAATTCATCCACGAAGATGCTACA

             *   
       3929 CTGAG
         66 CCGAG

                         *        *     *             *                      
       3934 TCATCTGAATTCAACTTTGAAAAATGCTTCACCGAGTCATCTAAATTCATCCACGAAGATGCTAC
          1 TCATCTGAATTCATCTTTG-AAGATGCTACACCGAGTCATCTGAATTCATCCACGAAGATGCTAC

                  
       3999 ACCGAG
         65 ACCGAG

                                                           
       4005 TCATCTGAATTCATCTTTGAAGATGCTACACCGAGTCATCTGAATTC
          1 TCATCTGAATTCATCTTTGAAGATGCTACACCGAGTCATCTGAATTC

       4052 CTGAAAAATT


Statistics
Matches: 101,  Mismatches: 16, Indels: 2
        0.85            0.13        0.02

Matches are distributed among these distances:
  70   41  0.41
  71   60  0.59

ACGTcount: A:0.29, C:0.23, G:0.15, T:0.32


Consensus pattern (70 bp):   
TCATCTGAATTCATCTTTGAAGATGCTACACCGAGTCATCTGAATTCATCCACGAAGATGCTACA
CCGAG

Found at i:5748 original size:21 final size:21

Alignment explanation


    Indices: 5722--5763  Score: 75
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       5712 GCATCTTAGG

                                 
       5722 CAACTCCGATGAGCTTGAAAC
          1 CAACTCCGATGAGCTTGAAAC

                  *              
       5743 CAACTCTGATGAGCTTGAAAC
          1 CAACTCCGATGAGCTTGAAAC

       5764 TTCTTCCTTA


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21


Consensus pattern (21 bp):   
CAACTCCGATGAGCTTGAAAC

Found at i:7596 original size:21 final size:21

Alignment explanation


    Indices: 7572--7663  Score: 159
    Period size: 21  Copynumber: 4.4  Consensus size: 21

       7562 CTTAGGCAAT

                         *       
       7572 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                 
       7593 TCCAATGAGCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                 
       7614 TCCAATGAGCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                  
       7635 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                    
       7656 TCCAATGA
          1 TCCAATGA

       7664 TCTCCTAGCA


Statistics
Matches: 69,  Mismatches: 1, Indels: 2
        0.96            0.01        0.03

Matches are distributed among these distances:
  20    3  0.04
  21   66  0.96

ACGTcount: A:0.26, C:0.27, G:0.18, T:0.28


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC

Done.