Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012775.1 Corchorus olitorius cultivar O-4 contig12808, 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: 2326
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.30


Found at i:2143 original size:6 final size:6

Alignment explanation


    Indices: 2087--2142  Score: 94
    Period size: 6  Copynumber: 9.3  Consensus size: 6

       2077 CAGGCTGCAC

                                                               *   
       2087 CACAAT CACAAT CACAAT CACAAT CACAAT CACAAT CACAAT CATAAT
          1 CACAAT CACAAT CACAAT CACAAT CACAAT CACAAT CACAAT CACAAT

              *      
       2135 CATAAT CA
          1 CACAAT CA

       2143 TCCGTTAACG


Statistics
Matches: 49,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
   6   49  1.00

ACGTcount: A:0.50, C:0.30, G:0.00, T:0.20


Consensus pattern (6 bp):   
CACAAT

Found at i:2298 original size:39 final size:38

Alignment explanation


    Indices: 2172--2320  Score: 219
    Period size: 38  Copynumber: 3.9  Consensus size: 38

       2162 TCAAGTCTAG

                                       *          
       2172 CCAACAG-TTAACCCCCTGAGGCACGGATCCACTCTTA
          1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA

                                                  
       2209 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
          1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA

                               *  * *              
       2247 CCAACAGTTTAACCCCCTGTGGTATGGGTCCACTCTTTA
          1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTC-TTA

               *                   *           
       2286 CCATCAGTTTAACCCCCCTGAGGTACGGGTCCACT
          1 CCAACAGTTTAA-CCCCCTGAGGCACGGGTCCACT

       2321 ATGCAC


Statistics
Matches: 102,  Mismatches: 7, Indels: 3
        0.91            0.06        0.03

Matches are distributed among these distances:
  37    7  0.07
  38   61  0.60
  39   14  0.14
  40   20  0.20

ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23


Consensus pattern (38 bp):   
CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA

Done.