Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021812.1 Corchorus olitorius cultivar O-4 contig21845, 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: 13113
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36


Found at i:5886 original size:109 final size:109

Alignment explanation


    Indices: 5767--5979  Score: 372
    Period size: 109  Copynumber: 2.0  Consensus size: 109

       5757 ATTATATATA

                                                                             
       5767 TATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATA
          1 TATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATA

                   *      *  *                          
       5832 CAAAATGTAATGAATTATTGGATTTAAAGAAAAATACAAGCACC
         66 CAAAATGCAATGAACTACTGGATTTAAAGAAAAATACAAGCACC

                              *               *                              
       5876 TATTATTATTAATTGTGTTGTTTATTCAATTGAATCTATTAAATAAGCACACATACCAAACAATA
          1 TATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATA

                *                                  
       5941 CAAAGTGCAATGAACTACTGGATTTAAAGAAAAATACAA
         66 CAAAATGCAATGAACTACTGGATTTAAAGAAAAATACAA

       5980 ATACCAAAAT


Statistics
Matches: 98,  Mismatches: 6, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
 109   98  1.00

ACGTcount: A:0.44, C:0.13, G:0.11, T:0.32


Consensus pattern (109 bp):   
TATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATA
CAAAATGCAATGAACTACTGGATTTAAAGAAAAATACAAGCACC

Found at i:7140 original size:109 final size:109

Alignment explanation


    Indices: 6949--7161  Score: 372
    Period size: 109  Copynumber: 2.0  Consensus size: 109

       6939 ATTTTGGTGC

                                                       *                     
       6949 TTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGGTATGTGTGCTTATCTA
          1 TTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTATTTGGTATGTGTGCTTATCTA

                                   *      *             
       7014 ATAGGTTCAATTGAATAAACAACGCAATTATTAATAATAGGTTA
         66 ATAGGTTCAATTGAATAAACAACACAATTAATAATAATAGGTTA

                                              *                           *  
       7058 TTGTATTTTTCTTTAAATCCAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTA
          1 TTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTATTTGGTATGTGTGCTTATCTA

                                *                  
       7123 ATAGGTTCAATTGAATAAACCACACAATTAATAATAATA
         66 ATAGGTTCAATTGAATAAACAACACAATTAATAATAATA

       7162 TATATAATAG


Statistics
Matches: 98,  Mismatches: 6, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
 109   98  1.00

ACGTcount: A:0.31, C:0.11, G:0.13, T:0.45


Consensus pattern (109 bp):   
TTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTATTTGGTATGTGTGCTTATCTA
ATAGGTTCAATTGAATAAACAACACAATTAATAATAATAGGTTA

Found at i:8366 original size:22 final size:20

Alignment explanation


    Indices: 8333--8374  Score: 57
    Period size: 22  Copynumber: 2.0  Consensus size: 20

       8323 CCGTCATATT

                        *       
       8333 AAAAAAAGGAAAGAAAAACA
          1 AAAAAAAGGAAAAAAAAACA

                                  
       8353 AAAAAAAGCAGAAAAAAAAACA
          1 AAAAAAAG--GAAAAAAAAACA

       8375 TGGTATTAGA


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  20    8  0.42
  22   11  0.58

ACGTcount: A:0.81, C:0.07, G:0.12, T:0.00


Consensus pattern (20 bp):   
AAAAAAAGGAAAAAAAAACA
Done.