Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000142.1 Corchorus olitorius cultivar O-4 contig00142, 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, 920

Length: 1534
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22


Found at i:841 original size:74 final size:74

Alignment explanation


    Indices: 714--903  Score: 276
    Period size: 74  Copynumber: 2.6  Consensus size: 74

        704 TAGCCAAATC

                                   *                    *              *     
        714 GCCGCA-CAACCCAAAATTGCCACAATTGCCACAACTAGCCAAATATGCCGCATCAACCTAAAAT
          1 GCCGCAGCAACCCAAAATTGCCAAAATTGCCACAACTAGCCAAAGATGCCGCATCAACCCAAAAT

            **       
        778 TGCAAAGTT
         66 CACAAAGTT

              *               *       *                                      
        787 GCTGCAGCAACCCAAAATAGCCAAAACTGCCACAACTAGCCAAAGATGCCGCATCAACCCAAAAT
          1 GCCGCAGCAACCCAAAATTGCCAAAATTGCCACAACTAGCCAAAGATGCCGCATCAACCCAAAAT

                     
        852 CACAAAGTT
         66 CACAAAGTT

                                    *      *            
        861 GCCGCAGCAACCCAAAATTG-CAAGATTGCCGCAACTAGCCAAA
          1 GCCGCAGCAACCCAAAATTGCCAAAATTGCCACAACTAGCCAAA

        904 ATTGCTGCAA


Statistics
Matches: 103,  Mismatches: 13, Indels: 2
        0.87            0.11        0.02

Matches are distributed among these distances:
  73   25  0.24
  74   78  0.76

ACGTcount: A:0.39, C:0.32, G:0.14, T:0.14


Consensus pattern (74 bp):   
GCCGCAGCAACCCAAAATTGCCAAAATTGCCACAACTAGCCAAAGATGCCGCATCAACCCAAAAT
CACAAAGTT

Found at i:865 original size:27 final size:27

Alignment explanation


    Indices: 827--878  Score: 86
    Period size: 27  Copynumber: 1.9  Consensus size: 27

        817 CACAACTAGC

                         *             
        827 CAAAGATGCCGCATCAACCCAAAATCA
          1 CAAAGATGCCGCAGCAACCCAAAATCA

                 *                   
        854 CAAAGTTGCCGCAGCAACCCAAAAT
          1 CAAAGATGCCGCAGCAACCCAAAAT

        879 TGCAAGATTG


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  27   23  1.00

ACGTcount: A:0.42, C:0.33, G:0.13, T:0.12


Consensus pattern (27 bp):   
CAAAGATGCCGCAGCAACCCAAAATCA

Found at i:889 original size:27 final size:27

Alignment explanation


    Indices: 829--908  Score: 83
    Period size: 27  Copynumber: 3.0  Consensus size: 27

        819 CAACTAGCCA

                        *           ** 
        829 AAGA-TGCCGCATCAACCCAAAATCAC
          1 AAGATTGCCGCAACAACCCAAAATTGC

                         *              
        855 AA-AGTTGCCGCAGCAACCCAAAATTGC
          1 AAGA-TTGCCGCAACAACCCAAAATTGC

                          * *          
        882 AAGATTGCCGCAACTAGCCAAAATTGC
          1 AAGATTGCCGCAACAACCCAAAATTGC

        909 TGCAACAAGA


Statistics
Matches: 45,  Mismatches: 6, Indels: 5
        0.80            0.11        0.09

Matches are distributed among these distances:
  25    1  0.02
  26    2  0.04
  27   41  0.91
  28    1  0.02

ACGTcount: A:0.39, C:0.30, G:0.16, T:0.15


Consensus pattern (27 bp):   
AAGATTGCCGCAACAACCCAAAATTGC

Found at i:913 original size:19 final size:19

Alignment explanation


    Indices: 885--924  Score: 53
    Period size: 19  Copynumber: 2.1  Consensus size: 19

        875 AAATTGCAAG

                       *  *    
        885 ATTGCCGCAACTAGCCAAA
          1 ATTGCCGCAACAAGACAAA

                 *             
        904 ATTGCTGCAACAAGACAAA
          1 ATTGCCGCAACAAGACAAA

              
        923 AT
          1 AT

        925 CACCAAGGCA


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  19   18  1.00

ACGTcount: A:0.42, C:0.25, G:0.15, T:0.17


Consensus pattern (19 bp):   
ATTGCCGCAACAAGACAAA
Done.