Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008142.1 Corchorus olitorius cultivar O-4 contig08169, 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, 789

Length: 1315
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34


Found at i:113 original size:53 final size:54

Alignment explanation


    Indices: 50--524  Score: 484
    Period size: 54  Copynumber: 8.9  Consensus size: 54

         40 ACCATATTGA

                               *             *    *               
         50 AGATCAACTCTGATCATCGGAAACTTCTT-GAACGACCACACTGGATCATCTGG
          1 AGATCAACTCTGATCATCGAAAACTTCTTGGAATGACCGCACTGGATCATCTGG

                           *              *  *    **              *
        103 AGATCAACTCTGATCTTCGAAAACTTCTTGAAACGACCATA-TCGGATCATCTGA
          1 AGATCAACTCTGATCATCGAAAACTTCTTGGAATGACCGCACT-GGATCATCTGG

                     *     *       *      *  *   *                 
        157 AGATCAACTATGATCTTCG-AAATTTCTTGAAACGACAGCACCT-GATCATCTGG
          1 AGATCAACTCTGATCATCGAAAACTTCTTGGAATGACCGCA-CTGGATCATCTGG

                     *     * *          *                          
        210 AGATCAACTTTGATCTTTGAAAACTTCTAGGAA-GAACCGCACTGGATCATCTGG
          1 AGATCAACTCTGATCATCGAAAACTTCTTGGAATG-ACCGCACTGGATCATCTGG

             *           * *                  *                    
        264 ACATCAACTCTGAACTTCGAAAACGTT-TTGGAAGGACCGCACTGGATCATCTGG
          1 AGATCAACTCTGATCATCGAAAAC-TTCTTGGAATGACCGCACTGGATCATCTGG

                            * *                       *           
        318 AGATCAACTCTGATCACCAAAAACTTCTTGGAATGACCGCACAGGATCATCT-G
          1 AGATCAACTCTGATCATCGAAAACTTCTTGGAATGACCGCACTGGATCATCTGG

                    *                             *            *   
        371 AGGATCAATTCTGATCAT--AAAACTTCTTGGAATGACAGCACTGGATC-TTTGG
          1 A-GATCAACTCTGATCATCGAAAACTTCTTGGAATGACCGCACTGGATCATCTGG

            *      *     *   *                            * * *   
        423 CGATCAATTCTGACCATTGAAAACTTCTTGGAATGACCGCACTGGACCTTTTGG
          1 AGATCAACTCTGATCATCGAAAACTTCTTGGAATGACCGCACTGGATCATCTGG

            *            *   *                              
        477 GGATCAACTCTGACCATTGAAAACTTCTTGGAATGACCGCACTGGATC
          1 AGATCAACTCTGATCATCGAAAACTTCTTGGAATGACCGCACTGGATC

        525 TTTTCTTTTT


Statistics
Matches: 366,  Mismatches: 41, Indels: 29
        0.84            0.09        0.07

Matches are distributed among these distances:
  51   17  0.05
  52   28  0.08
  53  105  0.29
  54  212  0.58
  55    4  0.01

ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27


Consensus pattern (54 bp):   
AGATCAACTCTGATCATCGAAAACTTCTTGGAATGACCGCACTGGATCATCTGG

Found at i:233 original size:107 final size:106

Alignment explanation


    Indices: 47--450  Score: 344
    Period size: 107  Copynumber: 3.8  Consensus size: 106

         37 GTAACCATAT

                              *                                              
         47 TGAAGATCAACTCTGATCATCGGAAACTTCTTGAACGAC-CACACTGGATCATCTGGAGATCAAC
          1 TGAAGATCAACTCTGATCTTC-GAAACTTCTTGAACGACGCAC-CTGGATCATCTGGAGATCAAC

                                *           *            
        111 TCTGATCTTCGAAAACTTCTTGAAACG-ACCATA-TCGGATCATC
         64 TCTGATCTTCGAAAACTTCTAGAAA-GAACCACACT-GGATCATC

                        *            *                                       
        154 TGAAGATCAACTATGATCTTCGAAATTTCTTGAAACGACAGCACCT-GATCATCTGGAGATCAAC
          1 TGAAGATCAACTCTGATCTTCGAAACTTCTTG-AACGAC-GCACCTGGATCATCTGGAGATCAAC

             *       *            *       *            
        218 TTTGATCTTTGAAAACTTCTAGGAAGAACCGCACTGGATCATC
         64 TCTGATCTTCGAAAACTTCTAGAAAGAACCACACTGGATCATC

              * *           *                    *                           
        261 TGGACATCAACTCTGAACTTCGAAAACGTT-TTGGAAGGACCGCA-CTGGATCATCTGGAGATCA
          1 TGAAGATCAACTCTGATCTTCG-AAAC-TTCTT-GAACGA-CGCACCTGGATCATCTGGAGATCA

                     ** *          *   *     *   *        
        324 ACTCTGATCACCAAAAACTTCTTGGAATG-ACCGCACAGGATCATC
         62 ACTCTGATCTTCGAAAACTTC-TAGAAAGAACCACACTGGATCATC

               *      *       *  *             *                 *   *      *
        369 TGAGGATCAATTCTGATCAT-AAAACTTCTTGGAATGACAGCA-CTGGATC-TTTGGCGATCAAT
          1 TGAAGATCAACTCTGATCTTCGAAACTTCTT-GAACGAC-GCACCTGGATCATCTGGAGATCAAC

                 *               
        431 TCTGACCATT-GAAAACTTCT
         64 TCTGATC-TTCGAAAACTTCT

        451 TGGAATGACC


Statistics
Matches: 244,  Mismatches: 39, Indels: 31
        0.78            0.12        0.10

Matches are distributed among these distances:
 104    1  0.00
 105   27  0.11
 106   33  0.14
 107   96  0.39
 108   76  0.31
 109   11  0.05

ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27


Consensus pattern (106 bp):   
TGAAGATCAACTCTGATCTTCGAAACTTCTTGAACGACGCACCTGGATCATCTGGAGATCAACTC
TGATCTTCGAAAACTTCTAGAAAGAACCACACTGGATCATC

Done.