Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008995.1 Corchorus olitorius cultivar O-4 contig09023, 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: 1694
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.28


Found at i:732 original size:21 final size:21

Alignment explanation


    Indices: 702--741  Score: 71
    Period size: 21  Copynumber: 1.9  Consensus size: 21

        692 CTAAAAACAG

                 *               
        702 GACAAGTCCTGCCCAGGACTT
          1 GACAACTCCTGCCCAGGACTT

                               
        723 GACAACTCCTGCCCAGGAC
          1 GACAACTCCTGCCCAGGAC

        742 CTGGTCTGTT


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.25, C:0.38, G:0.23, T:0.15


Consensus pattern (21 bp):   
GACAACTCCTGCCCAGGACTT

Found at i:800 original size:21 final size:21

Alignment explanation


    Indices: 774--815  Score: 84
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        764 AAAATTCAGA

                                 
        774 ACAACTCCTGCCCAGGACTTG
          1 ACAACTCCTGCCCAGGACTTG

                                 
        795 ACAACTCCTGCCCAGGACTTG
          1 ACAACTCCTGCCCAGGACTTG

        816 GTCTGTTGAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.24, C:0.38, G:0.19, T:0.19


Consensus pattern (21 bp):   
ACAACTCCTGCCCAGGACTTG

Found at i:824 original size:71 final size:71

Alignment explanation


    Indices: 703--887  Score: 325
    Period size: 71  Copynumber: 2.6  Consensus size: 71

        693 TAAAAACAGG

                                                   *             *           
        703 ACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACCTGGTCTGTTGAAAGACGGAAGAAAA
          1 ACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACTTGGTCTGTTGAAAAACGGAAGAAAA

                  
        768 TTCAGA
         66 TTCAGA

                *                                                            
        774 ACAACTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACTTGGTCTGTTGAAAAACGGAAGAAAA
          1 ACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACTTGGTCTGTTGAAAAACGGAAGAAAA

                  
        839 TTCAGA
         66 TTCAGA

                      *                                
        845 ACAAGTCCTGTCCAGGACTTGGACAACTCCTGCCCAGGACTTG
          1 ACAAGTCCTGCCCAGGACTT-GACAACTCCTGCCCAGGACTTG

        888 TTGCGGAAAA


Statistics
Matches: 108,  Mismatches: 5, Indels: 1
        0.95            0.04        0.01

Matches are distributed among these distances:
  71   86  0.80
  72   22  0.20

ACGTcount: A:0.30, C:0.28, G:0.23, T:0.19


Consensus pattern (71 bp):   
ACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACTTGGTCTGTTGAAAAACGGAAGAAAA
TTCAGA

Found at i:875 original size:22 final size:22

Alignment explanation


    Indices: 845--887  Score: 68
    Period size: 22  Copynumber: 2.0  Consensus size: 22

        835 AAAATTCAGA

                *     *           
        845 ACAAGTCCTGTCCAGGACTTGG
          1 ACAACTCCTGCCCAGGACTTGG

                                 
        867 ACAACTCCTGCCCAGGACTTG
          1 ACAACTCCTGCCCAGGACTTG

        888 TTGCGGAAAA


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.23, C:0.33, G:0.23, T:0.21


Consensus pattern (22 bp):   
ACAACTCCTGCCCAGGACTTGG

Done.