Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01005271.1 Corchorus olitorius cultivar O-4 contig05294, 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, 605

Length: 1009
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28


Found at i:719 original size:11 final size:11

Alignment explanation


    Indices: 698--735  Score: 69
    Period size: 11  Copynumber: 3.5  Consensus size: 11

        688 AGCCGGGATC

                       
        698 ACTAA-CTAAT
          1 ACTAATCTAAT

                       
        708 ACTAATCTAAT
          1 ACTAATCTAAT

                       
        719 ACTAATCTAAT
          1 ACTAATCTAAT

                  
        730 ACTAAT
          1 ACTAAT

        736 AGAATAGAAT


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

Matches are distributed among these distances:
  10    5  0.19
  11   22  0.81

ACGTcount: A:0.47, C:0.18, G:0.00, T:0.34


Consensus pattern (11 bp):   
ACTAATCTAAT

Found at i:749 original size:27 final size:27

Alignment explanation


    Indices: 716--771  Score: 112
    Period size: 27  Copynumber: 2.1  Consensus size: 27

        706 ATACTAATCT

                                       
        716 AATACTAATCTAATACTAATAGAATAG
          1 AATACTAATCTAATACTAATAGAATAG

                                       
        743 AATACTAATCTAATACTAATAGAATAG
          1 AATACTAATCTAATACTAATAGAATAG

              
        770 AA
          1 AA

        772 AAAATAGAAT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   29  1.00

ACGTcount: A:0.54, C:0.11, G:0.07, T:0.29


Consensus pattern (27 bp):   
AATACTAATCTAATACTAATAGAATAG

Found at i:756 original size:5 final size:6

Alignment explanation


    Indices: 702--763  Score: 71
    Period size: 6  Copynumber: 11.2  Consensus size: 6

        692 GGGATCACTA

                                                        *      *   
        702 ACTAAT ACTAAT -CTAAT ACTAAT -CTAAT ACTAAT A-GAAT A-GAAT
          1 ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT

                                  
        746 ACTAAT -CTAAT ACTAAT A
          1 ACTAAT ACTAAT ACTAAT A

        764 GAATAGAAAA


Statistics
Matches: 50,  Mismatches: 2, Indels: 8
        0.83            0.03        0.13

Matches are distributed among these distances:
   5   24  0.48
   6   26  0.52

ACGTcount: A:0.50, C:0.15, G:0.03, T:0.32


Consensus pattern (6 bp):   
ACTAAT

Found at i:763 original size:22 final size:22

Alignment explanation


    Indices: 698--768  Score: 72
    Period size: 27  Copynumber: 3.0  Consensus size: 22

        688 AGCCGGGATC

                             **   
        698 ACTAA-CTAATACTAATCTAAT
          1 ACTAATCTAATACTAATAGAAT

                                       
        719 ACTAATCTAATACTAATAGAATAGAAT
          1 ACTAATCTAATAC---T--AATAGAAT

                                  
        746 ACTAATCTAATACTAATAGAAT
          1 ACTAATCTAATACTAATAGAAT

             
        768 A
          1 A

        769 GAAAAAATAG


Statistics
Matches: 42,  Mismatches: 2, Indels: 11
        0.76            0.04        0.20

Matches are distributed among these distances:
  21    5  0.12
  22   16  0.38
  24    1  0.02
  25    1  0.02
  27   19  0.45

ACGTcount: A:0.51, C:0.14, G:0.04, T:0.31


Consensus pattern (22 bp):   
ACTAATCTAATACTAATAGAAT

Found at i:779 original size:14 final size:14

Alignment explanation


    Indices: 760--787  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

        750 ATCTAATACT

                          
        760 AATAGAATAGAAAA
          1 AATAGAATAGAAAA

                          
        774 AATAGAATAGAAAA
          1 AATAGAATAGAAAA

        788 TACTAATATA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14


Consensus pattern (14 bp):   
AATAGAATAGAAAA
Done.