Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007365.1 Corchorus olitorius cultivar O-4 contig07390, 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, 660

Length: 1101
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30


Found at i:827 original size:36 final size:37

Alignment explanation


    Indices: 785--867  Score: 93
    Period size: 36  Copynumber: 2.3  Consensus size: 37

        775 AGGCCTGGCG

                     *                            
        785 TGGCCCAAGTGCCCAGGCC-AG-GCACGGGCCAGCACA
          1 TGGCCCAAGCGCCCAGGCCTAGCGCACGGGCCAGC-CA

                       *        *    *           
        821 TGGCCC-AGCGTCCAGGCCTGGCGCGCGGGCCAGCCA
          1 TGGCCCAAGCGCCCAGGCCTAGCGCACGGGCCAGCCA

                        
        857 TGGCCC-AGCGC
          1 TGGCCCAAGCGC

        868 TCAAGCTTGG


Statistics
Matches: 40,  Mismatches: 5, Indels: 4
        0.82            0.10        0.08

Matches are distributed among these distances:
  35   10  0.25
  36   19  0.47
  37   11  0.28

ACGTcount: A:0.16, C:0.41, G:0.36, T:0.07


Consensus pattern (37 bp):   
TGGCCCAAGCGCCCAGGCCTAGCGCACGGGCCAGCCA

Found at i:860 original size:18 final size:19

Alignment explanation


    Indices: 809--866  Score: 59
    Period size: 18  Copynumber: 3.1  Consensus size: 19

        799 AGGCCAGGCA

                                
        809 CGGGCCAGCACATGGCCCAG
          1 CGGGCCAGC-CATGGCCCAG

               *            *   
        829 C-GTCCAGGCC-TGGCGC-G
          1 CGGGCCA-GCCATGGCCCAG

                               
        846 CGGGCCAGCCATGGCCCAG
          1 CGGGCCAGCCATGGCCCAG

              
        865 CG
          1 CG

        867 CTCAAGCTTG


Statistics
Matches: 30,  Mismatches: 4, Indels: 9
        0.70            0.09        0.21

Matches are distributed among these distances:
  17    5  0.17
  18   14  0.47
  19    8  0.27
  20    3  0.10

ACGTcount: A:0.14, C:0.41, G:0.38, T:0.07


Consensus pattern (19 bp):   
CGGGCCAGCCATGGCCCAG
Done.