Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011219.1 Corchorus olitorius cultivar O-4 contig11252, 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: 3614
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31


Found at i:656 original size:20 final size:21

Alignment explanation


    Indices: 614--656  Score: 61
    Period size: 21  Copynumber: 2.1  Consensus size: 21

        604 TCCTTTGTTG

                                 
        614 ATGATCTCCAATGGGCTTCAA
          1 ATGATCTCCAATGGGCTTCAA

                     *        *  
        635 ATGATCTCCGAT-GGCTTTAA
          1 ATGATCTCCAATGGGCTTCAA

              
        655 AT
          1 AT

        657 TCTTCAAGAT


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  20    9  0.45
  21   11  0.55

ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33


Consensus pattern (21 bp):   
ATGATCTCCAATGGGCTTCAA

Found at i:793 original size:21 final size:20

Alignment explanation


    Indices: 769--862  Score: 125
    Period size: 21  Copynumber: 4.5  Consensus size: 20

        759 ATCTTAGGCA

                      *          
        769 TCTCCAATGATCTTGGAAACT
          1 TCTCCAATGAGCTTGG-AACT

                      *          
        790 TCTCCAATGAACTTGGAACCT
          1 TCTCCAATGAGCTTGGAA-CT

            *                   
        811 GCTCCAATGAGCTTGGAACT
          1 TCTCCAATGAGCTTGGAACT

                                 
        831 TGCTCCAATGAGCTTGGAACT
          1 T-CTCCAATGAGCTTGGAACT

                       
        852 TGCTCCAATGA
          1 T-CTCCAATGA

        863 ACTTCTAGCA


Statistics
Matches: 67,  Mismatches: 4, Indels: 4
        0.89            0.05        0.05

Matches are distributed among these distances:
  20    4  0.06
  21   63  0.94

ACGTcount: A:0.27, C:0.26, G:0.19, T:0.29


Consensus pattern (20 bp):   
TCTCCAATGAGCTTGGAACT

Found at i:817 original size:42 final size:42

Alignment explanation


    Indices: 770--862  Score: 143
    Period size: 42  Copynumber: 2.2  Consensus size: 42

        760 TCTTAGGCAT

                     *                                 
        770 CTCCAATGATCTTGGAAACTT-CTCCAATGAACTTGGAACCTG
          1 CTCCAATGAGCTTGG-AACTTGCTCCAATGAACTTGGAACCTG

                                          *        *  
        812 CTCCAATGAGCTTGGAACTTGCTCCAATGAGCTTGGAACTTG
          1 CTCCAATGAGCTTGGAACTTGCTCCAATGAACTTGGAACCTG

                     
        854 CTCCAATGA
          1 CTCCAATGA

        863 ACTTCTAGCA


Statistics
Matches: 47,  Mismatches: 3, Indels: 2
        0.90            0.06        0.04

Matches are distributed among these distances:
  41    5  0.11
  42   42  0.89

ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28


Consensus pattern (42 bp):   
CTCCAATGAGCTTGGAACTTGCTCCAATGAACTTGGAACCTG
Done.