Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024425.1 Corchorus olitorius cultivar O-4 contig24458, 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: 8109
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.28


Found at i:1382 original size:21 final size:21

Alignment explanation


    Indices: 1358--1414  Score: 60
    Period size: 21  Copynumber: 2.7  Consensus size: 21

       1348 ATCCAACATC

                                 
       1358 TGAGGCAGGCACAAGAAGAAA
          1 TGAGGCAGGCACAAGAAGAAA

                *  ** *        * 
       1379 TGAGACATTCGCAAGAAGAGA
          1 TGAGGCAGGCACAAGAAGAAA

                     *     
       1400 TGAGGCAGGAACAAG
          1 TGAGGCAGGCACAAG

       1415 GTGTTATAAA


Statistics
Matches: 26,  Mismatches: 10, Indels: 0
        0.72            0.28        0.00

Matches are distributed among these distances:
  21   26  1.00

ACGTcount: A:0.44, C:0.14, G:0.33, T:0.09


Consensus pattern (21 bp):   
TGAGGCAGGCACAAGAAGAAA

Found at i:4724 original size:29 final size:29

Alignment explanation


    Indices: 4691--4891  Score: 244
    Period size: 29  Copynumber: 6.9  Consensus size: 29

       4681 GCTCGAGGGA

                                   *     
       4691 ATTTTGGTCATTTTTGCATATCTGGGGGC
          1 ATTTTGGTCATTTTTGCATATCTAGGGGC

                              *          
       4720 ATTTTGGTCATTTTTGCACATCTAGGGGC
          1 ATTTTGGTCATTTTTGCATATCTAGGGGC

                            *      **     
       4749 ATTTTGGTC-TTTTTCACATATCCGGGGGC
          1 ATTTTGGTCATTTTT-GCATATCTAGGGGC

                              *          
       4778 ATTTTGGTCATTTTTGCACATCTAGGGGC
          1 ATTTTGGTCATTTTTGCATATCTAGGGGC

             *                    *      
       4807 AGTTTGGTCATTTTTGCATATCCAGGGGC
          1 ATTTTGGTCATTTTTGCATATCTAGGGGC

                       *   *  *           
       4836 ATTTTGGTCATCTTTACACATTCT-GGGGC
          1 ATTTTGGTCATTTTTGCATA-TCTAGGGGC

             *      *                  
       4865 AGTTTGGTTATTTTTGCATACTCTAGG
          1 ATTTTGGTCATTTTTGCATA-TCTAGG

       4892 TTCTCCTTGG


Statistics
Matches: 144,  Mismatches: 24, Indels: 7
        0.82            0.14        0.04

Matches are distributed among these distances:
  28    5  0.03
  29  130  0.90
  30    9  0.06

ACGTcount: A:0.16, C:0.17, G:0.24, T:0.42


Consensus pattern (29 bp):   
ATTTTGGTCATTTTTGCATATCTAGGGGC

Found at i:4781 original size:58 final size:58

Alignment explanation


    Indices: 4693--4884  Score: 289
    Period size: 58  Copynumber: 3.3  Consensus size: 58

       4683 TCGAGGGAAT

                                *                                    *
       4693 TTTGGTCATTTTTGCATATCTGGGGGCATTTTGGTCATTTTTGCACATCTAGGGGCAT
          1 TTTGGTCATTTTTGCATATCCGGGGGCATTTTGGTCATTTTTGCACATCTAGGGGCAG

                          *                                            
       4751 TTTGGTC-TTTTTCACATATCCGGGGGCATTTTGGTCATTTTTGCACATCTAGGGGCAG
          1 TTTGGTCATTTTT-GCATATCCGGGGGCATTTTGGTCATTTTTGCACATCTAGGGGCAG

                                 *                *   *                
       4809 TTTGGTCATTTTTGCATATCCAGGGGCATTTTGGTCATCTTTACACATTCT-GGGGCAG
          1 TTTGGTCATTTTTGCATATCCGGGGGCATTTTGGTCATTTTTGCACA-TCTAGGGGCAG

                  *           
       4867 TTTGGTTATTTTTGCATA
          1 TTTGGTCATTTTTGCATA

       4885 CTCTAGGTTC


Statistics
Matches: 123,  Mismatches: 8, Indels: 6
        0.90            0.06        0.04

Matches are distributed among these distances:
  57    5  0.04
  58  110  0.89
  59    8  0.07

ACGTcount: A:0.16, C:0.17, G:0.24, T:0.43


Consensus pattern (58 bp):   
TTTGGTCATTTTTGCATATCCGGGGGCATTTTGGTCATTTTTGCACATCTAGGGGCAG

Found at i:4837 original size:87 final size:87

Alignment explanation


    Indices: 4691--4891  Score: 280
    Period size: 87  Copynumber: 2.3  Consensus size: 87

       4681 GCTCGAGGGA

                                   *      *                    *             
       4691 ATTTTGGTCATTTTTGCATATCTGGGGGCATTTTGGTCATTTTTGCACATCTAGGGGCATTTTGG
          1 ATTTTGGTCATTTTTGCATATCTAGGGGCAGTTTGGTCATTTTTGCACATCCAGGGGCATTTTGG

                    *               
       4756 TC-T-TTTTCACATATCCGGGGGC
         66 TCATCTTTACACAT-T-CGGGGGC

                              *                            *                 
       4778 ATTTTGGTCATTTTTGCACATCTAGGGGCAGTTTGGTCATTTTTGCATATCCAGGGGCATTTTGG
          1 ATTTTGGTCATTTTTGCATATCTAGGGGCAGTTTGGTCATTTTTGCACATCCAGGGGCATTTTGG

                            *     
       4843 TCATCTTTACACATTCTGGGGC
         66 TCATCTTTACACATTCGGGGGC

             *      *                  
       4865 AGTTTGGTTATTTTTGCATACTCTAGG
          1 ATTTTGGTCATTTTTGCATA-TCTAGG

       4892 TTCTCCTTGG


Statistics
Matches: 101,  Mismatches: 10, Indels: 5
        0.87            0.09        0.04

Matches are distributed among these distances:
  87   85  0.84
  88    8  0.08
  89    8  0.08

ACGTcount: A:0.16, C:0.17, G:0.24, T:0.42


Consensus pattern (87 bp):   
ATTTTGGTCATTTTTGCATATCTAGGGGCAGTTTGGTCATTTTTGCACATCCAGGGGCATTTTGG
TCATCTTTACACATTCGGGGGC
Done.