Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021121.1 Corchorus olitorius cultivar O-4 contig21154, 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: 4835
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.34


Found at i:255 original size:14 final size:13

Alignment explanation


    Indices: 236--274  Score: 51
    Period size: 14  Copynumber: 2.9  Consensus size: 13

        226 AAATTGTAAA

                         
        236 ATTTAAAAAATTT
          1 ATTTAAAAAATTT

                   *    * 
        249 CATTTAAGAAATAT
          1 -ATTTAAAAAATTT

                        
        263 ATTTAAAAAATT
          1 ATTTAAAAAATT

        275 CTAATATATA


Statistics
Matches: 21,  Mismatches: 4, Indels: 1
        0.81            0.15        0.04

Matches are distributed among these distances:
  13   10  0.48
  14   11  0.52

ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41


Consensus pattern (13 bp):   
ATTTAAAAAATTT

Found at i:3700 original size:19 final size:18

Alignment explanation


    Indices: 3676--3724  Score: 62
    Period size: 19  Copynumber: 2.6  Consensus size: 18

       3666 TAAGATTTTT

                               
       3676 AATAATAATTATTCAATAA
          1 AATAATAATTATTCAAT-A

                  *          *
       3695 AATAATTATTATTCAATT
          1 AATAATAATTATTCAATA

                        
       3713 AATAATTAATTA
          1 AATAA-TAATTA

       3725 ATTTCAGCCT


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  18    5  0.19
  19   21  0.81

ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43


Consensus pattern (18 bp):   
AATAATAATTATTCAATA

Found at i:4162 original size:132 final size:134

Alignment explanation


    Indices: 4021--4281  Score: 382
    Period size: 132  Copynumber: 1.9  Consensus size: 134

       4011 AAATATTTTT

                            *             *   *                           *  
       4021 AAAAATTCTAATATATCTAAGTTTTTTAATTAAATTACTAAAATGGTAAAAATAAAATAGGTGTA
          1 AAAAATTCTAATATATATAAGTTTTTTAATCAAAATACTAAAATGGTAAAAATAAAATAGGTATA

                                          *                                  
       4086 AGGACATTAGATTTAATTAAA-T-AAAAAATAGAATTTTTAGTTAAGTAAAACTATAAAAGTATA
         66 AGGACATTAGATTTAATTAAATTAAAAAAAAAGAATTTTTAGTTAAGTAAAACTATAAAAGTATA

                
       4149 TTTA
        131 TTTA

                                *                *               *      *    
       4153 AAAAATTCTAATATATATAATTTTTTTAATCAAAATAGTAAAATGGTAAAAATTAAATAGTTATA
          1 AAAAATTCTAATATATATAAGTTTTTTAATCAAAATACTAAAATGGTAAAAATAAAATAGGTATA

                *                               *         *                 
       4218 AGGATATTAGATTTAATTAAATTTAAAAAAAAAAGAGTTTTTAGTTGAGTAAAACTATAAAAGT
         66 AGGACATTAGATTTAATTAAA-TT-AAAAAAAAAGAATTTTTAGTTAAGTAAAACTATAAAAGT

       4282 TTAAACAATG


Statistics
Matches: 113,  Mismatches: 12, Indels: 4
        0.88            0.09        0.03

Matches are distributed among these distances:
 132   77  0.68
 134    1  0.01
 136   35  0.31

ACGTcount: A:0.51, C:0.03, G:0.10, T:0.36


Consensus pattern (134 bp):   
AAAAATTCTAATATATATAAGTTTTTTAATCAAAATACTAAAATGGTAAAAATAAAATAGGTATA
AGGACATTAGATTTAATTAAATTAAAAAAAAAGAATTTTTAGTTAAGTAAAACTATAAAAGTATA
TTTA

Found at i:4816 original size:78 final size:75

Alignment explanation


    Indices: 4686--4832  Score: 222
    Period size: 78  Copynumber: 1.9  Consensus size: 75

       4676 ATTTTATTTT

                                       *       *                         *   
       4686 ACTAAAAATCTATTTTATTTAATAAATCTAATATCTTTATAACTATTCTATTTTACCATTTTACT
          1 ACTAAAAATCTATTTTATTTAATAAATATAATATCCTTATAACTATTCTATTTTACCATTTCACT

                      
       4751 ATTTTACTCA
         66 ATTTTACTCA

                                        *                     *              
       4761 ACTAAAAACTCTATTTTTATTTAACTAAGTATAATATCCTTATAACTATTTTATTTTACCATTTC
          1 ACTAAAAA-TCTA-TTTTATTTAA-TAAATATAATATCCTTATAACTATTCTATTTTACCATTTC

                   
       4826 ACTATTT
         63 ACTATTT

       4833 AAA


Statistics
Matches: 64,  Mismatches: 5, Indels: 3
        0.89            0.07        0.04

Matches are distributed among these distances:
  75    8  0.12
  76    4  0.06
  77   10  0.16
  78   42  0.66

ACGTcount: A:0.35, C:0.15, G:0.01, T:0.49


Consensus pattern (75 bp):   
ACTAAAAATCTATTTTATTTAATAAATATAATATCCTTATAACTATTCTATTTTACCATTTCACT
ATTTTACTCA
Done.