Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014244.1 Corchorus olitorius cultivar O-4 contig14277, 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: 57357
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34


Found at i:8639 original size:1 final size:1

Alignment explanation


    Indices: 8633--8658  Score: 52
    Period size: 1  Copynumber: 26.0  Consensus size: 1

       8623 AGTAGTTTAT

                                      
       8633 AAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAA

       8659 GAAATGAATC


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   25  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:15673 original size:12 final size:12

Alignment explanation


    Indices: 15656--15683  Score: 56
    Period size: 12  Copynumber: 2.3  Consensus size: 12

      15646 AAAAAAACTT

                        
      15656 TATACTATACTA
          1 TATACTATACTA

                        
      15668 TATACTATACTA
          1 TATACTATACTA

                
      15680 TATA
          1 TATA

      15684 TTACTGTTAA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   16  1.00

ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43


Consensus pattern (12 bp):   
TATACTATACTA

Found at i:36864 original size:14 final size:14

Alignment explanation


    Indices: 36845--36874  Score: 51
    Period size: 14  Copynumber: 2.1  Consensus size: 14

      36835 GAGTCGGATT

                       *  
      36845 CAGATTAATCATGG
          1 CAGATTAATCAGGG

                          
      36859 CAGATTAATCAGGG
          1 CAGATTAATCAGGG

              
      36873 CA
          1 CA

      36875 AAGCCCTAGA


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23


Consensus pattern (14 bp):   
CAGATTAATCAGGG

Found at i:38014 original size:15 final size:16

Alignment explanation


    Indices: 37994--38031  Score: 53
    Period size: 15  Copynumber: 2.5  Consensus size: 16

      37984 CTTTTCTGAC

                         *  
      37994 AAAAGAAGAAG-AGAG
          1 AAAAGAAGAAGAAAAG

                            
      38009 AAAAGAA-AAGAAAAG
          1 AAAAGAAGAAGAAAAG

                    
      38024 AAAAGAAG
          1 AAAAGAAG

      38032 GAGCATTAGC


Statistics
Matches: 20,  Mismatches: 1, Indels: 3
        0.83            0.04        0.12

Matches are distributed among these distances:
  14    3  0.15
  15   17  0.85

ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00


Consensus pattern (16 bp):   
AAAAGAAGAAGAAAAG

Found at i:52987 original size:2 final size:2

Alignment explanation


    Indices: 52980--53009  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

      52970 TTTTATAATC

                                                        
      52980 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      53010 TGATAAGACA


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

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


Consensus pattern (2 bp):   
AT

Done.