Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024580.1 Corchorus olitorius cultivar O-4 contig24613, 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: 6945
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29


Found at i:568 original size:33 final size:33

Alignment explanation


    Indices: 528--624  Score: 151
    Period size: 33  Copynumber: 2.9  Consensus size: 33

        518 GACTGCCCAA

                          *                  
        528 GGCTAGTCGCGACCAGATCGCGACTTGCCCGTG
          1 GGCTAGTCGCGACCGGATCGCGACTTGCCCGTG

                                       *      
        561 GGCTAGTCGCGACCGGATCGCGA-TATTCCCGTG
          1 GGCTAGTCGCGACCGGATCGCGACT-TGCCCGTG

                                    *      
        594 GGCTAGTCGCGACCGGATCGCGACATGCCCG
          1 GGCTAGTCGCGACCGGATCGCGACTTGCCCG

        625 CCGGCTTATT


Statistics
Matches: 58,  Mismatches: 4, Indels: 4
        0.88            0.06        0.06

Matches are distributed among these distances:
  32    1  0.02
  33   57  0.98

ACGTcount: A:0.15, C:0.33, G:0.34, T:0.18


Consensus pattern (33 bp):   
GGCTAGTCGCGACCGGATCGCGACTTGCCCGTG

Found at i:723 original size:32 final size:32

Alignment explanation


    Indices: 662--723  Score: 79
    Period size: 32  Copynumber: 1.9  Consensus size: 32

        652 TACCCCCATT

                    *       *    * **       
        662 GGCCGGTCGCGATCCGGTCGCGATTGGCCACG
          1 GGCCGGTCACGATCCGCTCGCAACCGGCCACG

                                          
        694 GGCCGGTCACGATCCGCTCGCAACCGGCCA
          1 GGCCGGTCACGATCCGCTCGCAACCGGCCA

        724 TATTTTCGAA


Statistics
Matches: 25,  Mismatches: 5, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  32   25  1.00

ACGTcount: A:0.13, C:0.39, G:0.35, T:0.13


Consensus pattern (32 bp):   
GGCCGGTCACGATCCGCTCGCAACCGGCCACG

Found at i:805 original size:21 final size:21

Alignment explanation


    Indices: 775--815  Score: 64
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        765 ATTTACCCCG

                          *      
        775 TCTGGCGTCGATGGCTCGTTT
          1 TCTGGCGTCGATGGATCGTTT

                 *              
        796 TCTGGGGTCGATGGATCGTT
          1 TCTGGCGTCGATGGATCGTT

        816 ATTGTCCATA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.07, C:0.20, G:0.37, T:0.37


Consensus pattern (21 bp):   
TCTGGCGTCGATGGATCGTTT

Found at i:6851 original size:34 final size:36

Alignment explanation


    Indices: 6777--6864  Score: 135
    Period size: 34  Copynumber: 2.5  Consensus size: 36

       6767 AAAAACCGAA

                              *             *  *
       6777 TGGGAACTTTCCCAATTTTAAAACTTAAAAACTTGT
          1 TGGGAACTTTCCCAATTTAAAAACTTAAAAACCTGG

                                                
       6813 TGGGAACTTTCCCAATTTAAAAAC-T-AAAACCTGG
          1 TGGGAACTTTCCCAATTTAAAAACTTAAAAACCTGG

                              
       6847 TGGGAACTTTCCCAATTT
          1 TGGGAACTTTCCCAATTT

       6865 GGAAACTTCG


Statistics
Matches: 49,  Mismatches: 3, Indels: 2
        0.91            0.06        0.04

Matches are distributed among these distances:
  34   25  0.51
  35    1  0.02
  36   23  0.47

ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33


Consensus pattern (36 bp):   
TGGGAACTTTCCCAATTTAAAAACTTAAAAACCTGG

Done.