Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013532.1 Corchorus olitorius cultivar O-4 contig13565, 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: 14841
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.30


Found at i:139 original size:37 final size:37

Alignment explanation


    Indices: 63--223  Score: 134
    Period size: 36  Copynumber: 4.4  Consensus size: 37

         53 GGATGCCTCT

                                * *   *  *         
         63 GGGGACTTACAGCGCTCGG-TGACTGAGGATGCCTA-TG
          1 GGGGACTTACAGCGCTCGGCCGTC-GCGGCTGCC-ACTG

                         *     **                
        100 GGGGACTTACAGCACTCGGTTGTCGCGGCTGCCACTG
          1 GGGGACTTACAGCGCTCGGCCGTCGCGGCTGCCACTG

                      *    *  *               *  
        137 GGGGACTT-CGGCGCACGACCGTCGCGGCTGCCATTG
          1 GGGGACTTACAGCGCTCGGCCGTCGCGGCTGCCACTG

                      *     *                     
        173 GGGGACTT-CGGCGC-AGGACCGTCGCGGCTGCCACTG
          1 GGGGACTTACAGCGCTCGG-CCGTCGCGGCTGCCACTG

                      *    
        209 GGGGACTTACGGCGC
          1 GGGGACTTACAGCGC

        224 ACGACGCAAT


Statistics
Matches: 106,  Mismatches: 14, Indels: 8
        0.83            0.11        0.06

Matches are distributed among these distances:
  35    1  0.01
  36   61  0.58
  37   41  0.39
  38    3  0.03

ACGTcount: A:0.14, C:0.29, G:0.39, T:0.18


Consensus pattern (37 bp):   
GGGGACTTACAGCGCTCGGCCGTCGCGGCTGCCACTG

Found at i:166 original size:36 final size:36

Alignment explanation


    Indices: 121--228  Score: 189
    Period size: 36  Copynumber: 3.0  Consensus size: 36

        111 GCACTCGGTT

                                                
        121 GTCGCGGCTGCCACTGGGGGACTTCGGCGCACGACC
          1 GTCGCGGCTGCCACTGGGGGACTTCGGCGCACGACC

                         *                 *    
        157 GTCGCGGCTGCCATTGGGGGACTTCGGCGCAGGACC
          1 GTCGCGGCTGCCACTGGGGGACTTCGGCGCACGACC

                                                
        193 GTCGCGGCTGCCACTGGGGGACTTACGGCGCACGAC
          1 GTCGCGGCTGCCACTGGGGGACTT-CGGCGCACGAC

        229 GCAATGTTGT


Statistics
Matches: 67,  Mismatches: 4, Indels: 1
        0.93            0.06        0.01

Matches are distributed among these distances:
  36   57  0.85
  37   10  0.15

ACGTcount: A:0.12, C:0.33, G:0.40, T:0.15


Consensus pattern (36 bp):   
GTCGCGGCTGCCACTGGGGGACTTCGGCGCACGACC

Found at i:681 original size:56 final size:56

Alignment explanation


    Indices: 595--819  Score: 228
    Period size: 56  Copynumber: 4.0  Consensus size: 56

        585 TGCCAGTTAG

                          *                     * *               **   
        595 GGCG-TTGGTGCGCACTACTT-CTCTT-AGAGTTCTACAACATGGAGAGTGTCGTGTGA
          1 GGCGTTTGG-GCGCGCTACTTCCT-TTCAGAGTTCTGCCACATGG-GAGTGTCGCATGA

                                                          *  *   *   
        651 GGCGTTTGGGCGCGCTACTT-CTTTCAGAGTTCTGCCACATGGGGATTGCCGCCTGA
          1 GGCGTTTGGGCGCGCTACTTCCTTTCAGAGTTCTGCCACAT-GGGAGTGTCGCATGA

                             *                      *                
        707 GGCGTTTGGG-GCGCGTTCTTCCTTTCAGAGTTCTGCCACCTGGGAGTGTCGCATGA
          1 GGCGTTTGGGCGCGC-TACTTCCTTTCAGAGTTCTGCCACATGGGAGTGTCGCATGA

                        *                     *             *         
        763 GGCGTTTGGGGCACGCTA-TTCCTTTCAGAGTTCCGCCACATGGGGAGCGTCGCATGA
          1 GGCGTTT-GGGCGCGCTACTTCCTTTCAGAGTTCTGCCACAT-GGGAGTGTCGCATGA

        820 CTTCTTTTCA


Statistics
Matches: 144,  Mismatches: 17, Indels: 15
        0.82            0.10        0.09

Matches are distributed among these distances:
  55    6  0.04
  56   92  0.64
  57   43  0.30
  58    3  0.02

ACGTcount: A:0.15, C:0.24, G:0.32, T:0.28


Consensus pattern (56 bp):   
GGCGTTTGGGCGCGCTACTTCCTTTCAGAGTTCTGCCACATGGGAGTGTCGCATGA

Found at i:1030 original size:55 final size:57

Alignment explanation


    Indices: 924--1032  Score: 170
    Period size: 55  Copynumber: 1.9  Consensus size: 57

        914 GGCAGTCCCT

                                                      *              
        924 CATTGTAGAGCTTGATGGGAGCGCACGTCCCCTTTCGGGGATTTGTCGTGGTCCGTC
          1 CATTGTAGAGCTTGATGGGAGCGCACGTCCCCTTTCGGGGATATGTCGTGGTCCGTC

                            *                                      
        981 CATTG-AGAG-TTGATTGGAGCGCACGTCCCCTTTCGGGGATATG-CTGTGGTCC
          1 CATTGTAGAGCTTGATGGGAGCGCACGTCCCCTTTCGGGGATATGTC-GTGGTCC

       1033 ACCTGTTGAG


Statistics
Matches: 49,  Mismatches: 2, Indels: 4
        0.89            0.04        0.07

Matches are distributed among these distances:
  54    1  0.02
  55   39  0.80
  56    4  0.08
  57    5  0.10

ACGTcount: A:0.14, C:0.24, G:0.33, T:0.29


Consensus pattern (57 bp):   
CATTGTAGAGCTTGATGGGAGCGCACGTCCCCTTTCGGGGATATGTCGTGGTCCGTC

Done.