Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008108.1 Corchorus olitorius cultivar O-4 contig08135, 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, 665

Length: 1109
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.29


Found at i:683 original size:9 final size:9

Alignment explanation


    Indices: 658--697  Score: 53
    Period size: 9  Copynumber: 4.3  Consensus size: 9

        648 CCCTTTTTCT

                     
        658 CAAGAACAC
          1 CAAGAACAC

             *        
        667 TAAAGAACAC
          1 -CAAGAACAC

                     
        677 CAAGAACAC
          1 CAAGAACAC

                   * 
        686 CAAGAACCC
          1 CAAGAACAC

               
        695 CAA
          1 CAA

        698 CCACCACCGG


Statistics
Matches: 27,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
   9   19  0.70
  10    8  0.30

ACGTcount: A:0.55, C:0.33, G:0.10, T:0.03


Consensus pattern (9 bp):   
CAAGAACAC

Found at i:713 original size:10 final size:10

Alignment explanation


    Indices: 698--735  Score: 67
    Period size: 10  Copynumber: 3.8  Consensus size: 10

        688 AGAACCCCAA

                      
        698 CCACCACCGG
          1 CCACCACCGG

                     *
        708 CCACCACCGA
          1 CCACCACCGG

                      
        718 CCACCACCGG
          1 CCACCACCGG

                    
        728 CCACCACC
          1 CCACCACC

        736 CCAAAACACC


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  10   26  1.00

ACGTcount: A:0.24, C:0.63, G:0.13, T:0.00


Consensus pattern (10 bp):   
CCACCACCGG

Found at i:722 original size:20 final size:20

Alignment explanation


    Indices: 697--735  Score: 78
    Period size: 20  Copynumber: 1.9  Consensus size: 20

        687 AAGAACCCCA

                                
        697 ACCACCACCGGCCACCACCG
          1 ACCACCACCGGCCACCACCG

                               
        717 ACCACCACCGGCCACCACC
          1 ACCACCACCGGCCACCACC

        736 CCAAAACACC


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.26, C:0.62, G:0.13, T:0.00


Consensus pattern (20 bp):   
ACCACCACCGGCCACCACCG

Done.