Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024022.1 Corchorus olitorius cultivar O-4 contig24055, 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: 7299
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30


Found at i:194 original size:32 final size:32

Alignment explanation


    Indices: 147--292  Score: 215
    Period size: 32  Copynumber: 4.5  Consensus size: 32

        137 TAAAAGCAGT

                                   *          
        147 TAAATATAGCGGCGTTTTGTTCTAAAGACGCCGC
          1 TAAATA-AG-GGCGTTTTGTTCTTAAGACGCCGC

                                            *
        181 TAAATAAGGGCGTTTTGTTCTCT-AGACGCCGT
          1 TAAATAAGGGCGTTTTGTTCT-TAAGACGCCGC

                                  *         
        213 TAAATAAGGGCGTTTTGTTCTTTAGACGCCGC
          1 TAAATAAGGGCGTTTTGTTCTTAAGACGCCGC

                                             
        245 TAAATAAGGGCGTTTTGTTCTTTAA-ACGCCGC
          1 TAAATAAGGGCGTTTTGTTC-TTAAGACGCCGC

                            
        277 TAAATAAGGGCGTTTT
          1 TAAATAAGGGCGTTTT

        293 CTTTCCACAC


Statistics
Matches: 105,  Mismatches: 4, Indels: 8
        0.90            0.03        0.07

Matches are distributed among these distances:
  31    1  0.01
  32   93  0.89
  33    5  0.05
  34    6  0.06

ACGTcount: A:0.25, C:0.18, G:0.24, T:0.34


Consensus pattern (32 bp):   
TAAATAAGGGCGTTTTGTTCTTAAGACGCCGC

Found at i:2718 original size:27 final size:27

Alignment explanation


    Indices: 2680--2781  Score: 186
    Period size: 27  Copynumber: 3.8  Consensus size: 27

       2670 CGACCCGAGG

                                  *    
       2680 CGAAGTGGGAGGATCCACTGCTAGGGT
          1 CGAAGTGGGAGGATCCACTGCTGGGGT

                   *                   
       2707 CGAAGTGTGAGGATCCACTGCTGGGGT
          1 CGAAGTGGGAGGATCCACTGCTGGGGT

                                       
       2734 CGAAGTGGGAGGATCCACTGCTGGGGT
          1 CGAAGTGGGAGGATCCACTGCTGGGGT

                                 
       2761 CGAAGTGGGAGGATCCACTGC
          1 CGAAGTGGGAGGATCCACTGC

       2782 GGCAACAGTC


Statistics
Matches: 72,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  27   72  1.00

ACGTcount: A:0.21, C:0.20, G:0.41, T:0.19


Consensus pattern (27 bp):   
CGAAGTGGGAGGATCCACTGCTGGGGT

Found at i:5947 original size:33 final size:33

Alignment explanation


    Indices: 5910--5982  Score: 128
    Period size: 33  Copynumber: 2.2  Consensus size: 33

       5900 ACTATATATG

                          * *                
       5910 GCGGCGTCTGAGCTTTGAAACGCCACTAAAATA
          1 GCGGCGTCTGAGCTCTAAAACGCCACTAAAATA

                                             
       5943 GCGGCGTCTGAGCTCTAAAACGCCACTAAAATA
          1 GCGGCGTCTGAGCTCTAAAACGCCACTAAAATA

                   
       5976 GCGGCGT
          1 GCGGCGT

       5983 TTCACACCTC


Statistics
Matches: 38,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  33   38  1.00

ACGTcount: A:0.29, C:0.26, G:0.26, T:0.19


Consensus pattern (33 bp):   
GCGGCGTCTGAGCTCTAAAACGCCACTAAAATA

Found at i:6186 original size:32 final size:32

Alignment explanation


    Indices: 6150--6223  Score: 85
    Period size: 32  Copynumber: 2.3  Consensus size: 32

       6140 TGTTTAGTAA

                      *       *             
       6150 ACGCCGCTATGTAACGGCGTTTGCTTCAATAG
          1 ACGCCGCTATATAACGGCATTTGCTTCAATAG

                     *   **       *     *   
       6182 ACGCCGCTAAATAGGGGCATTTTCTTCAGTAG
          1 ACGCCGCTATATAACGGCATTTGCTTCAATAG

                      
       6214 ACGCCGCTAT
          1 ACGCCGCTAT

       6224 TTTCCAGCAA


Statistics
Matches: 34,  Mismatches: 8, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  32   34  1.00

ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27


Consensus pattern (32 bp):   
ACGCCGCTATATAACGGCATTTGCTTCAATAG
Done.