Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017033.1 Corchorus olitorius cultivar O-4 contig17066, 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: 10502
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31


Found at i:293 original size:30 final size:31

Alignment explanation


    Indices: 233--291  Score: 118
    Period size: 31  Copynumber: 1.9  Consensus size: 31

        223 ACCTACTCAC

                                           
        233 ATATATCATAAGAACCGAGAAAAAAAAAACT
          1 ATATATCATAAGAACCGAGAAAAAAAAAACT

                                        
        264 ATATATCATAAGAACCGAGAAAAAAAAA
          1 ATATATCATAAGAACCGAGAAAAAAAAA

        292 CTCTATAACT


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

Matches are distributed among these distances:
  31   28  1.00

ACGTcount: A:0.63, C:0.12, G:0.10, T:0.15


Consensus pattern (31 bp):   
ATATATCATAAGAACCGAGAAAAAAAAAACT

Found at i:2107 original size:13 final size:13

Alignment explanation


    Indices: 2089--2116  Score: 56
    Period size: 13  Copynumber: 2.2  Consensus size: 13

       2079 ACATGCAAGA

                         
       2089 AAATGGAATGCAG
          1 AAATGGAATGCAG

                         
       2102 AAATGGAATGCAG
          1 AAATGGAATGCAG

              
       2115 AA
          1 AA

       2117 GATATTACAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   15  1.00

ACGTcount: A:0.50, C:0.07, G:0.29, T:0.14


Consensus pattern (13 bp):   
AAATGGAATGCAG

Found at i:5026 original size:26 final size:26

Alignment explanation


    Indices: 4985--5037  Score: 88
    Period size: 26  Copynumber: 2.0  Consensus size: 26

       4975 CATTTGCACA

                      **              
       4985 TTCAGGGGCATTTTGGTCATTTTAAG
          1 TTCAGGGGCACGTTGGTCATTTTAAG

                                      
       5011 TTCAGGGGCACGTTGGTCATTTTAAG
          1 TTCAGGGGCACGTTGGTCATTTTAAG

             
       5037 T
          1 T

       5038 ACATTCTTAA


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  26   25  1.00

ACGTcount: A:0.19, C:0.13, G:0.28, T:0.40


Consensus pattern (26 bp):   
TTCAGGGGCACGTTGGTCATTTTAAG

Found at i:7594 original size:14 final size:14

Alignment explanation


    Indices: 7575--7616  Score: 66
    Period size: 14  Copynumber: 3.0  Consensus size: 14

       7565 AAATAGAGAG

                     **   
       7575 GAAGAAGAAGGAAA
          1 GAAGAAGAAAAAAA

                          
       7589 GAAGAAGAAAAAAA
          1 GAAGAAGAAAAAAA

                          
       7603 GAAGAAGAAAAAAA
          1 GAAGAAGAAAAAAA

       7617 TCTGAAAGAA


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

Matches are distributed among these distances:
  14   26  1.00

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


Consensus pattern (14 bp):   
GAAGAAGAAAAAAA

Found at i:9767 original size:31 final size:31

Alignment explanation


    Indices: 9729--9790  Score: 99
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       9719 CTTTTTTTTG

                                *           
       9729 TTTTTTTTGGC-CAAAGCAACAGATCTACTTT
          1 TTTTTTTTGGCAC-AAGCAAAAGATCTACTTT

                                           
       9760 TTTTTTTTGGCACAAGCAAAAGATCTACTTT
          1 TTTTTTTTGGCACAAGCAAAAGATCTACTTT

       9791 AGTTTTGCCT


Statistics
Matches: 29,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
  31   28  0.97
  32    1  0.03

ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42


Consensus pattern (31 bp):   
TTTTTTTTGGCACAAGCAAAAGATCTACTTT
Done.