Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000772.1 Corchorus olitorius cultivar O-4 contig00772, 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: 17962
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:5058 original size:32 final size:32

Alignment explanation


    Indices: 5017--5090  Score: 132
    Period size: 32  Copynumber: 2.3  Consensus size: 32

       5007 TAAGATCAAA

                          *                 
       5017 AGGGATTTTAGGCAGAAATTGAGAAGTAGACG
          1 AGGGATTTTAGGCAAAAATTGAGAAGTAGACG

                                            
       5049 AGGGATTTTAGGCAAAAATTGAGAAGTAGACG
          1 AGGGATTTTAGGCAAAAATTGAGAAGTAGACG

                       
       5081 AGGG-TTTTAG
          1 AGGGATTTTAG

       5091 ACTGCAAGAA


Statistics
Matches: 41,  Mismatches: 1, Indels: 1
        0.95            0.02        0.02

Matches are distributed among these distances:
  31    6  0.15
  32   35  0.85

ACGTcount: A:0.36, C:0.05, G:0.34, T:0.24


Consensus pattern (32 bp):   
AGGGATTTTAGGCAAAAATTGAGAAGTAGACG

Found at i:5631 original size:27 final size:27

Alignment explanation


    Indices: 5601--5670  Score: 113
    Period size: 27  Copynumber: 2.6  Consensus size: 27

       5591 GAGAGGGATG

                                       
       5601 AGGGAAGTCACTGAGAGGAAGGAACCA
          1 AGGGAAGTCACTGAGAGGAAGGAACCA

                   *   *              *
       5628 AGGGAAGCCACCGAGAGGAAGGAACCG
          1 AGGGAAGTCACTGAGAGGAAGGAACCA

                            
       5655 AGGGAAGTCACTGAGA
          1 AGGGAAGTCACTGAGA

       5671 TAGAAGAAGC


Statistics
Matches: 38,  Mismatches: 5, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  27   38  1.00

ACGTcount: A:0.39, C:0.17, G:0.39, T:0.06


Consensus pattern (27 bp):   
AGGGAAGTCACTGAGAGGAAGGAACCA

Found at i:5654 original size:14 final size:13

Alignment explanation


    Indices: 5617--5661  Score: 54
    Period size: 13  Copynumber: 3.4  Consensus size: 13

       5607 GTCACTGAGA

                      *  
       5617 GGAAGGAACCAAG
          1 GGAAGGAACCGAG

                 **      
       5630 GGAAGCCACCGAG
          1 GGAAGGAACCGAG

                          
       5643 AGGAAGGAACCGAG
          1 -GGAAGGAACCGAG

                 
       5657 GGAAG
          1 GGAAG

       5662 TCACTGAGAT


Statistics
Matches: 26,  Mismatches: 5, Indels: 2
        0.79            0.15        0.06

Matches are distributed among these distances:
  13   15  0.58
  14   11  0.42

ACGTcount: A:0.40, C:0.18, G:0.42, T:0.00


Consensus pattern (13 bp):   
GGAAGGAACCGAG

Found at i:6919 original size:177 final size:178

Alignment explanation


    Indices: 6532--7012  Score: 477
    Period size: 177  Copynumber: 2.7  Consensus size: 178

       6522 TTAAAATTGT

                    * *   *   *      **               *                      
       6532 ATAATTTTCGTTCCGGATATCCGATCAAGGTGATTCAAGTGTTTATTAAAAGGTTGTTTCATGAT
          1 ATAATTTTTGATCCAGATGTCCGATTGAGGTGATTCAAGTGTCTATTAAAAGGTTGTTTCATGAT

                               *         *                   *               
       6597 CTACAACTTTCATGAAGGACTCAAAAACTGAATTTAATGTTTAAAGTATCAAAAATACTTCCGAA
         66 CTACAACTTTCATGAAGGAATCAAAAACTAAATTTAATGTTTAAAGTATAAAAAATACTTCCGAA

                                ***         *    *          
       6662 AAATTAGTTGTTTCGGTTAATGGGAATGGACGTTCCATTTAATATTAC
        131 AAATTAGTTGTTTCGGTTAACAAGAATGGACGGTCCACTTAATATTAC

                *  *       *     *            *   *     *              *  *  
       6710 ATAACTTCTGATCCAAATGTCTGATTGAGGTGATGCAACTGTCTCTTAAAAGGTTGTTTTATTAT
          1 ATAATTTTTGATCCAGATGTCCGATTGAGGTGATTCAAGTGTCTATTAAAAGGTTGTTTCATGAT

                                  *     *               **            *      
       6775 CTACAACTTTCAT-ACA-GAATTATAAAGCTAAATTTAATGTTTCGAGTATAAAAAATGCTT-C-
         66 CTACAACTTTCATGA-AGGAATCA-AAAACTAAATTTAATGTTTAAAGTATAAAAAATACTTCCG

                                  *          *                 
       6836 AAAAATTTAGTTGTTTCGGTTAGCAAGAATGGATGGTCCACTTAATATTAC
        129 AAAAA-TTAGTTGTTTCGGTTAACAAGAATGGACGGTCCACTTAATATTAC

                      *                             **  *                    
       6887 ATAATTTTTGCTCCAGATGTCCGATTGAGGTGATTCAAGTACCTGTTAAAAGGTTGTTTCATGAT
          1 ATAATTTTTGATCCAGATGTCCGATTGAGGTGATTCAAGTGTCTATTAAAAGGTTGTTTCATGAT

            * ***              *  *   *        *  *           *      *    
       6952 ATGTGACTTTCATGAAGGACTCGAAATCTAAATTTGATTTTTCAAA-TATCAAAAATTCTTC
         66 CTACAACTTTCATGAAGGAATCAAAAACTAAATTTAATGTTT-AAAGTATAAAAAATACTTC

       7013 TAAAAAAATT


Statistics
Matches: 239,  Mismatches: 57, Indels: 14
        0.77            0.18        0.05

Matches are distributed among these distances:
 176    5  0.02
 177  135  0.56
 178   99  0.41

ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37


Consensus pattern (178 bp):   
ATAATTTTTGATCCAGATGTCCGATTGAGGTGATTCAAGTGTCTATTAAAAGGTTGTTTCATGAT
CTACAACTTTCATGAAGGAATCAAAAACTAAATTTAATGTTTAAAGTATAAAAAATACTTCCGAA
AAATTAGTTGTTTCGGTTAACAAGAATGGACGGTCCACTTAATATTAC

Found at i:16682 original size:52 final size:52

Alignment explanation


    Indices: 16601--16705  Score: 165
    Period size: 52  Copynumber: 2.0  Consensus size: 52

      16591 TCACACTTTT

                       *         *                              
      16601 TCTCTTATTCATACATTCTTATTCCACGCATGTAACAACCACTTCAGTTAAA
          1 TCTCTTATTCACACATTCTTACTCCACGCATGTAACAACCACTTCAGTTAAA

                        *           *                *          
      16653 TCTCTTATTCACGCATTCTTACTCTACGCATGTAACAACCATTTCAGTTAAA
          1 TCTCTTATTCACACATTCTTACTCCACGCATGTAACAACCACTTCAGTTAAA

             
      16705 T
          1 T

      16706 GTTCATGTAC


Statistics
Matches: 48,  Mismatches: 5, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  52   48  1.00

ACGTcount: A:0.30, C:0.27, G:0.07, T:0.37


Consensus pattern (52 bp):   
TCTCTTATTCACACATTCTTACTCCACGCATGTAACAACCACTTCAGTTAAA
Done.