Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01003966.1 Corchorus olitorius cultivar O-4 contig03977, 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:0.28, C:0.26, G:0.17, T:0.30


Found at i:129 original size:3 final size:3

Alignment explanation


    Indices: 114--201  Score: 59
    Period size: 3  Copynumber: 29.3  Consensus size: 3

        104 CAACGCACAC

                      *               *   *       *   * * *       *       *
        114 CAG CAG CAA CAG CAG CAG CAA CAT CAG CAT CAA TAT CAG CAT CAG CAT
          1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG

                  *       *   *               *                  
        162 CAG CAT CAG CAT CAA CAG CAG CAG CAT CAG CAG CAG CAG C
          1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG C

        202 GTCTAATTTA


Statistics
Matches: 63,  Mismatches: 22, Indels: 0
        0.74            0.26        0.00

Matches are distributed among these distances:
   3   63  1.00

ACGTcount: A:0.38, C:0.33, G:0.19, T:0.10


Consensus pattern (3 bp):   
CAG

Found at i:198 original size:18 final size:18

Alignment explanation


    Indices: 123--201  Score: 74
    Period size: 18  Copynumber: 4.6  Consensus size: 18

        113 CCAGCAGCAA

                       *      
        123 CAGCAGCAGCAACATCAG
          1 CAGCAGCAGCAGCATCAG

              *  ** *         
        141 CATCAATATCAGCATCAG
          1 CAGCAGCAGCAGCATCAG

              *     *         
        159 CATCAGCATCAGCATCA-
          1 CAGCAGCAGCAGCATCAG

                              
        176 -A-CAGCAGCAGCATCAG
          1 CAGCAGCAGCAGCATCAG

                      
        192 CAGCAGCAGC
          1 CAGCAGCAGC

        202 GTCTAATTTA


Statistics
Matches: 50,  Mismatches: 8, Indels: 6
        0.78            0.12        0.09

Matches are distributed among these distances:
  15   13  0.26
  16    1  0.02
  17    1  0.02
  18   35  0.70

ACGTcount: A:0.37, C:0.33, G:0.19, T:0.11


Consensus pattern (18 bp):   
CAGCAGCAGCAGCATCAG
Done.