Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012136.1 Corchorus olitorius cultivar O-4 contig12169, 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: 20433
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33


Found at i:5885 original size:31 final size:31

Alignment explanation


    Indices: 5848--6033  Score: 182
    Period size: 31  Copynumber: 6.1  Consensus size: 31

       5838 ACGGTGTCCG

                    *    *             *   
       5848 ACGTGGCATGCCATGTGTACCAAAAAGCGAC
          1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC

             *                             
       5879 ATGTGGCACGCCACGTGTA-CAAAAAGTGAC
          1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC

                          *              * 
       5909 ACGTGGCACGCCACATGTACCAAAAAGTGGC
          1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC

                 * *  *   *    *           
       5940 ACGTGACCCGTCACATGTATCAAAAAGTGAC
          1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC

                 *       *     *           
       5971 ACGTGTCACGCCATGTGTATCAAAAAGTGAC
          1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC

             *      *   *       *          
       6002 ATGTGGCATGCCTCGTG--CAAAAAAG-GAC
          1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC

                
       6030 ACGT
          1 ACGT

       6034 ACCACGTGTC


Statistics
Matches: 129,  Mismatches: 25, Indels: 5
        0.81            0.16        0.03

Matches are distributed among these distances:
  28    6  0.05
  29    6  0.05
  30   27  0.21
  31   90  0.70

ACGTcount: A:0.33, C:0.25, G:0.25, T:0.18


Consensus pattern (31 bp):   
ACGTGGCACGCCACGTGTACCAAAAAGTGAC

Found at i:6383 original size:31 final size:31

Alignment explanation


    Indices: 6333--6474  Score: 160
    Period size: 31  Copynumber: 4.5  Consensus size: 31

       6323 GCTTGCTACA

                         **                 
       6333 TGTACCAAAAAAGCAACATGTAGCACGCCACG
          1 TGTACC-AAAAAGTGACATGTAGCACGCCACG

                        *                   
       6365 TGTACCAAAAAGCGACATG-AGGCACGCCACG
          1 TGTACCAAAAAGTGACATGTA-GCACGCCACG

                                 *       * 
       6396 TGTACCAAAAAGTGACATGTATCACGCCATG
          1 TGTACCAAAAAGTGACATGTAGCACGCCACG

                  *             *   *    * 
       6427 TGTACCCAAAAGTGACATGTGGCATGCCATG
          1 TGTACCAAAAAGTGACATGTAGCACGCCACG

               **            
       6458 TGTTTCAAAAAGTGACA
          1 TGTACCAAAAAGTGACA

       6475 CATGGCATGC


Statistics
Matches: 97,  Mismatches: 11, Indels: 5
        0.86            0.10        0.04

Matches are distributed among these distances:
  30    1  0.01
  31   89  0.92
  32    7  0.07

ACGTcount: A:0.36, C:0.24, G:0.22, T:0.18


Consensus pattern (31 bp):   
TGTACCAAAAAGTGACATGTAGCACGCCACG

Found at i:6738 original size:68 final size:68

Alignment explanation


    Indices: 6629--6762  Score: 232
    Period size: 68  Copynumber: 2.0  Consensus size: 68

       6619 GCGTTTTGGT

                                      *                            *   *     
       6629 CAAAATAAAAAAGTTGGGTGCAAAGTGGCAGTCCGTATAAACTTAAGGGTGCAAAGTGGTATTTA
          1 CAAAATAAAAAAGTTGGGTGCAAAGTAGCAGTCCGTATAAACTTAAGGGTGCAAAATGGCATTTA

               
       6694 TGC
         66 TGC

                                *                                            
       6697 CAAAATAAAAAAGTTGGGTGTAAAGTAGCAGTCCGTATAAACTTAAGGGTGCAAAATGGCATTTA
          1 CAAAATAAAAAAGTTGGGTGCAAAGTAGCAGTCCGTATAAACTTAAGGGTGCAAAATGGCATTTA

             
       6762 T
         66 T

       6763 ACCTTAAAGA


Statistics
Matches: 62,  Mismatches: 4, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  68   62  1.00

ACGTcount: A:0.39, C:0.11, G:0.25, T:0.25


Consensus pattern (68 bp):   
CAAAATAAAAAAGTTGGGTGCAAAGTAGCAGTCCGTATAAACTTAAGGGTGCAAAATGGCATTTA
TGC

Found at i:15117 original size:19 final size:20

Alignment explanation


    Indices: 15093--15150  Score: 73
    Period size: 19  Copynumber: 2.9  Consensus size: 20

      15083 CTGTTTAACA

                                
      15093 ACTGTACAGATGAGATTA-C
          1 ACTGTACAGATGAGATTAGC

                    *  *        *
      15112 ACTGTACATATTAGATTAGGT
          1 ACTGTACAGATGAGATTA-GC

                              
      15133 ACTGTACAGATGAGATTA
          1 ACTGTACAGATGAGATTA

      15151 TTAGAGTAAC


Statistics
Matches: 32,  Mismatches: 5, Indels: 2
        0.82            0.13        0.05

Matches are distributed among these distances:
  19   16  0.50
  21   16  0.50

ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31


Consensus pattern (20 bp):   
ACTGTACAGATGAGATTAGC
Done.