Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015119.1 Corchorus olitorius cultivar O-4 contig15152, 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: 10782
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32


Found at i:6605 original size:32 final size:32

Alignment explanation


    Indices: 6569--6641  Score: 85
    Period size: 32  Copynumber: 2.3  Consensus size: 32

       6559 ATTTTCGGGT

                               *           * 
       6569 TCAGGCTTGAATC-AGACCGGGTTAAATTTGGG
          1 TCAGG-TTGAATCGAGACCAGGTTAAATTTGAG

                     *     **               
       6601 TCAGGTTGATTCGAGTTCAGGTTAAATTTGAG
          1 TCAGGTTGAATCGAGACCAGGTTAAATTTGAG

                     
       6633 TCAGGTTGA
          1 TCAGGTTGA

       6642 TTCGGGTTCG


Statistics
Matches: 35,  Mismatches: 5, Indels: 2
        0.83            0.12        0.05

Matches are distributed among these distances:
  31    6  0.17
  32   29  0.83

ACGTcount: A:0.25, C:0.12, G:0.30, T:0.33


Consensus pattern (32 bp):   
TCAGGTTGAATCGAGACCAGGTTAAATTTGAG

Found at i:6620 original size:16 final size:16

Alignment explanation


    Indices: 6601--6650  Score: 57
    Period size: 16  Copynumber: 3.1  Consensus size: 16

       6591 TAAATTTGGG

                            
       6601 TCAGGTTGATTCGAGT
          1 TCAGGTTGATTCGAGT

                    *   *    
       6617 TCAGGTTAAATTTGAG-
          1 TCAGGTT-GATTCGAGT

                         *  
       6633 TCAGGTTGATTCGGGT
          1 TCAGGTTGATTCGAGT

              
       6649 TC
          1 TC

       6651 GGGTCAATTT


Statistics
Matches: 27,  Mismatches: 5, Indels: 4
        0.75            0.14        0.11

Matches are distributed among these distances:
  15    5  0.19
  16   16  0.59
  17    6  0.22

ACGTcount: A:0.20, C:0.12, G:0.30, T:0.38


Consensus pattern (16 bp):   
TCAGGTTGATTCGAGT

Found at i:6642 original size:32 final size:31

Alignment explanation


    Indices: 6586--6687  Score: 132
    Period size: 32  Copynumber: 3.2  Consensus size: 31

       6576 TGAATCAGAC

                                        *   
       6586 CGGGTTAAATTTGGGTCAGGTTGATTCGAGTT
          1 CGGGTTAAATTT-GGTCAGGTTGATTCGGGTT

             *                              
       6618 CAGGTTAAATTTGAGTCAGGTTGATTCGGGTT
          1 CGGGTTAAATTTG-GTCAGGTTGATTCGGGTT

                 *  *             *         
       6650 CGGGTCAATTTTGGATCAGGTTAATTCGGGTT
          1 CGGGTTAAATTTGG-TCAGGTTGATTCGGGTT

                  
       6682 CGGGTT
          1 CGGGTT

       6688 TGATGAACCA


Statistics
Matches: 61,  Mismatches: 7, Indels: 4
        0.85            0.10        0.06

Matches are distributed among these distances:
  31    2  0.03
  32   59  0.97

ACGTcount: A:0.19, C:0.11, G:0.33, T:0.37


Consensus pattern (31 bp):   
CGGGTTAAATTTGGTCAGGTTGATTCGGGTT

Found at i:6687 original size:16 final size:16

Alignment explanation


    Indices: 6636--6687  Score: 50
    Period size: 16  Copynumber: 3.2  Consensus size: 16

       6626 ATTTGAGTCA

                *           
       6636 GGTTGATTCGGGTTCG
          1 GGTTAATTCGGGTTCG

               *    **  *  *
       6652 GGTCAATTTTGGATCA
          1 GGTTAATTCGGGTTCG

                            
       6668 GGTTAATTCGGGTTCG
          1 GGTTAATTCGGGTTCG

                
       6684 GGTT
          1 GGTT

       6688 TGATGAACCA


Statistics
Matches: 25,  Mismatches: 11, Indels: 0
        0.69            0.31        0.00

Matches are distributed among these distances:
  16   25  1.00

ACGTcount: A:0.13, C:0.12, G:0.37, T:0.38


Consensus pattern (16 bp):   
GGTTAATTCGGGTTCG
Done.