Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015712.1 Corchorus olitorius cultivar O-4 contig15745, 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: 11105
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36


Found at i:5844 original size:107 final size:108

Alignment explanation


    Indices: 5644--5908  Score: 378
    Period size: 107  Copynumber: 2.5  Consensus size: 108

       5634 AATTTTCCTA

                           * **                                              
       5644 ACCCTTAAAATAAAATTTTAATTTTAATTT-GGGCTAAACTTAGTG-AATTAGTTATATATTTTA
          1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA

                *              *                 *     
       5707 TTATTTCTAAAGCCATATATCAATATTATTAATTATGGAATTT
         66 TTATATCTAAAGCCATATAACAATATTATTAATTATGAAATTT

                                                                   * *       
       5750 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
          1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA

                          *                     *        
       5815 TT-TAT-TAAA-CCCTATAACAATAAATTATTAATTTTGAAATTT
         66 TTATATCTAAAGCCATATAACAAT--ATTATTAATTATGAAATTT

                         *                                      
       5857 ACCCTTAAAATAATAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
          1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA

       5909 AGGCTAAACT


Statistics
Matches: 144,  Mismatches: 11, Indels: 7
        0.89            0.07        0.04

Matches are distributed among these distances:
 105   10  0.07
 106   31  0.22
 107   85  0.59
 108   18  0.12

ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42


Consensus pattern (108 bp):   
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
TTATATCTAAAGCCATATAACAATATTATTAATTATGAAATTT

Found at i:5913 original size:21 final size:21

Alignment explanation


    Indices: 5889--5941  Score: 97
    Period size: 21  Copynumber: 2.5  Consensus size: 21

       5879 TTTAATTTGG

                                 
       5889 GGCTAAACTTAGTGAAATTAA
          1 GGCTAAACTTAGTGAAATTAA

                                 
       5910 GGCTAAACTTAGTGAAATTAA
          1 GGCTAAACTTAGTGAAATTAA

              *        
       5931 GGGTAAACTTA
          1 GGCTAAACTTA

       5942 ATAAAAAGAA


Statistics
Matches: 31,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  21   31  1.00

ACGTcount: A:0.42, C:0.09, G:0.21, T:0.28


Consensus pattern (21 bp):   
GGCTAAACTTAGTGAAATTAA

Found at i:7522 original size:11 final size:12

Alignment explanation


    Indices: 7492--7524  Score: 50
    Period size: 12  Copynumber: 2.8  Consensus size: 12

       7482 TATATAATTA

                     *  
       7492 ATTTTAATTATT
          1 ATTTTAATTTTT

                        
       7504 ATTTTAATTTTT
          1 ATTTTAATTTTT

                      
       7516 A-TTTAATTT
          1 ATTTTAATTT

       7525 AAACACGAGT


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  11    8  0.40
  12   12  0.60

ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70


Consensus pattern (12 bp):   
ATTTTAATTTTT

Found at i:7610 original size:12 final size:12

Alignment explanation


    Indices: 7591--7626  Score: 54
    Period size: 12  Copynumber: 3.0  Consensus size: 12

       7581 ATGACACGTC

                        
       7591 AGGAGGGAGACT
          1 AGGAGGGAGACT

             *          
       7603 ATGAGGGAGACT
          1 AGGAGGGAGACT

                  *     
       7615 AGGAGGAAGACT
          1 AGGAGGGAGACT

       7627 TTGGAAGAGC


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  12   21  1.00

ACGTcount: A:0.36, C:0.08, G:0.44, T:0.11


Consensus pattern (12 bp):   
AGGAGGGAGACT

Found at i:10504 original size:25 final size:24

Alignment explanation


    Indices: 10479--10558  Score: 80
    Period size: 22  Copynumber: 3.5  Consensus size: 24

      10469 TTAGTAATTA

                                    
      10479 AATATATATTATTTATTTATTTTT
          1 AATATATATTATTTATTTATTTTT

               *  *               **
      10503 AA-CT-CATTATTTA-TTATTTAA
          1 AATATATATTATTTATTTATTTTT

                                     
      10524 AATATAT-TTA-TTATTTATTTATT
          1 AATATATATTATTTATTTATTT-TT

                        
      10547 AATATATATTAT
          1 AATATATATTAT

      10559 ATCTAAGATA


Statistics
Matches: 42,  Mismatches: 8, Indels: 11
        0.69            0.13        0.18

Matches are distributed among these distances:
  21   11  0.26
  22   18  0.43
  23    8  0.19
  24    5  0.12

ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60


Consensus pattern (24 bp):   
AATATATATTATTTATTTATTTTT

Found at i:11060 original size:16 final size:16

Alignment explanation


    Indices: 11039--11070  Score: 64
    Period size: 16  Copynumber: 2.0  Consensus size: 16

      11029 TTTTCATTTT

                            
      11039 CACATTTACGATTAAA
          1 CACATTTACGATTAAA

                            
      11055 CACATTTACGATTAAA
          1 CACATTTACGATTAAA

      11071 AATGTAAGCG


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31


Consensus pattern (16 bp):   
CACATTTACGATTAAA
Done.