Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01004174.1 Corchorus olitorius cultivar O-4 contig04187, 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, 774

Length: 1291
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.27


Found at i:702 original size:27 final size:26

Alignment explanation


    Indices: 669--723  Score: 101
    Period size: 27  Copynumber: 2.1  Consensus size: 26

        659 ATACTAATCT

                                       
        669 AATACTAATCTAATACTAATAGAATAG
          1 AATACTAATCTAATACT-ATAGAATAG

                                      
        696 AATACTAATCTAATACTATAGAATAG
          1 AATACTAATCTAATACTATAGAATAG

              
        722 AA
          1 AA

        724 AAAATAGAAT


Statistics
Matches: 28,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  26   11  0.39
  27   17  0.61

ACGTcount: A:0.53, C:0.11, G:0.07, T:0.29


Consensus pattern (26 bp):   
AATACTAATCTAATACTATAGAATAG

Found at i:710 original size:21 final size:21

Alignment explanation


    Indices: 678--759  Score: 71
    Period size: 21  Copynumber: 3.9  Consensus size: 21

        668 TAATACTAAT

                                  
        678 CTAATACTAATAGAATAGAATA
          1 CTAATA-TAATAGAATAGAATA

                 *     **        
        700 CTAATCTAATACTATAGAATA
          1 CTAATATAATAGAATAGAATA

             *    *                
        721 -GAA-AAAATAGAATAGAAAATA
          1 CTAATATAATAGAATAG--AATA

                               
        742 CTAATATAATAGAA-AGAA
          1 CTAATATAATAGAATAGAA

        760 AAGAACTGTC


Statistics
Matches: 46,  Mismatches: 10, Indels: 10
        0.70            0.15        0.15

Matches are distributed among these distances:
  19    8  0.17
  20    4  0.09
  21   17  0.37
  22    9  0.20
  23    8  0.17

ACGTcount: A:0.59, C:0.07, G:0.10, T:0.24


Consensus pattern (21 bp):   
CTAATATAATAGAATAGAATA

Found at i:713 original size:11 final size:11

Alignment explanation


    Indices: 651--688  Score: 69
    Period size: 11  Copynumber: 3.5  Consensus size: 11

        641 AGCCGGGATC

                       
        651 ACTAA-CTAAT
          1 ACTAATCTAAT

                       
        661 ACTAATCTAAT
          1 ACTAATCTAAT

                       
        672 ACTAATCTAAT
          1 ACTAATCTAAT

                  
        683 ACTAAT
          1 ACTAAT

        689 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:732 original size:14 final size:14

Alignment explanation


    Indices: 713--739  Score: 54
    Period size: 14  Copynumber: 1.9  Consensus size: 14

        703 ATCTAATACT

                          
        713 ATAGAATAGAAAAA
          1 ATAGAATAGAAAAA

                         
        727 ATAGAATAGAAAA
          1 ATAGAATAGAAAA

        740 TACTAATATA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   13  1.00

ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15


Consensus pattern (14 bp):   
ATAGAATAGAAAAA
Done.