Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000266.1 Corchorus olitorius cultivar O-4 contig00266, 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, 604

Length: 1008
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.25


Found at i:133 original size:33 final size:32

Alignment explanation


    Indices: 96--202  Score: 108
    Period size: 33  Copynumber: 3.2  Consensus size: 32

         86 CCGCCCTGCT

                  *                          
         96 AGGGCGGCGTGGCTATGACCATGCCGCCCAAGG
          1 AGGGCGCCGTGGC-ATGACCATGCCGCCCAAGG

                    *                        *
        129 AGGGCGCCATGGACAT-AGCCATGCCGCCCAAGA
          1 AGGGCGCCGTGG-CATGA-CCATGCCGCCCAAGG

                           * *            ** 
        162 AGGGCGCCGTGGCCAAGTCCATGCCGCCCACCG
          1 AGGGCGCCGTGG-CATGACCATGCCGCCCAAGG

                    
        195 AGGGCGCC
          1 AGGGCGCC

        203 ATGACTTGGC


Statistics
Matches: 61,  Mismatches: 10, Indels: 6
        0.79            0.13        0.08

Matches are distributed among these distances:
  32    1  0.02
  33   59  0.97
  34    1  0.02

ACGTcount: A:0.20, C:0.36, G:0.36, T:0.09


Consensus pattern (32 bp):   
AGGGCGCCGTGGCATGACCATGCCGCCCAAGG

Found at i:191 original size:66 final size:65

Alignment explanation


    Indices: 96--232  Score: 166
    Period size: 66  Copynumber: 2.1  Consensus size: 65

         86 CCGCCCTGCT

                  *      * *               *                      *          
         96 AGGGCGGCGTGGCTATGACCATGCCGCCCAAGGAGGGCGCCATGGACATAGCCATGCCGCCCAAG
          1 AGGGCGCCGTGGCCAAGACCATGCCGCCCAACGAGGGCGCCAT-GACATAGCCACGCCGCCCAAG

             
        161 A
         65 A

                             *            *               * *            *  *
        162 AGGGCGCCGTGGCCAAGTCCATGCCGCCCACCGAGGGCGCCATGACTTGGCCACGCCGCCCTAGC
          1 AGGGCGCCGTGGCCAAGACCATGCCGCCCAACGAGGGCGCCATGACATAGCCACGCCGCCCAAGA

                  
        227 AGGGCG
          1 AGGGCG

        233 GCACCGACCA


Statistics
Matches: 60,  Mismatches: 11, Indels: 1
        0.83            0.15        0.01

Matches are distributed among these distances:
  65   23  0.38
  66   37  0.62

ACGTcount: A:0.19, C:0.36, G:0.35, T:0.10


Consensus pattern (65 bp):   
AGGGCGCCGTGGCCAAGACCATGCCGCCCAACGAGGGCGCCATGACATAGCCACGCCGCCCAAGA
Done.