Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002309.1 Corchorus olitorius cultivar O-4 contig02309, 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, 643

Length: 1073
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33


Found at i:584 original size:21 final size:21

Alignment explanation


    Indices: 558--647  Score: 180
    Period size: 21  Copynumber: 4.3  Consensus size: 21

        548 GGAATTACTG

                                 
        558 ATAAAAGTTGTATATATCTAT
          1 ATAAAAGTTGTATATATCTAT

                                 
        579 ATAAAAGTTGTATATATCTAT
          1 ATAAAAGTTGTATATATCTAT

                                 
        600 ATAAAAGTTGTATATATCTAT
          1 ATAAAAGTTGTATATATCTAT

                                 
        621 ATAAAAGTTGTATATATCTAT
          1 ATAAAAGTTGTATATATCTAT

                  
        642 ATAAAA
          1 ATAAAA

        648 AAATTTTTAA


Statistics
Matches: 69,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   69  1.00

ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41


Consensus pattern (21 bp):   
ATAAAAGTTGTATATATCTAT

Found at i:712 original size:19 final size:20

Alignment explanation


    Indices: 688--734  Score: 87
    Period size: 19  Copynumber: 2.4  Consensus size: 20

        678 ACTAATACTC

                                
        688 TATATAAATTAATAATAA-T
          1 TATATAAATTAATAATAATT

                                
        707 TATATAAATTAATAATAATT
          1 TATATAAATTAATAATAATT

                    
        727 TATATAAA
          1 TATATAAA

        735 AAATTATATA


Statistics
Matches: 27,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  19   18  0.67
  20    9  0.33

ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43


Consensus pattern (20 bp):   
TATATAAATTAATAATAATT

Found at i:741 original size:12 final size:12

Alignment explanation


    Indices: 712--750  Score: 53
    Period size: 12  Copynumber: 3.3  Consensus size: 12

        702 ATAATTATAT

                       *
        712 AAATTA-ATAAT
          1 AAATTATATAAA

              *         
        723 AATTTATATAAA
          1 AAATTATATAAA

                        
        735 AAATTATATAAA
          1 AAATTATATAAA

                
        747 AAAT
          1 AAAT

        751 CAAAATAAAG


Statistics
Matches: 24,  Mismatches: 3, Indels: 1
        0.86            0.11        0.04

Matches are distributed among these distances:
  11    5  0.21
  12   19  0.79

ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36


Consensus pattern (12 bp):   
AAATTATATAAA
Done.