Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015271.1 Corchorus olitorius cultivar O-4 contig15304, 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: 6838
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34


Found at i:2900 original size:39 final size:38

Alignment explanation


    Indices: 2857--3059  Score: 116
    Period size: 39  Copynumber: 5.3  Consensus size: 38

       2847 CGAAGCTCTG

                             *                     
       2857 AGCAGGTTTACTTAAATGGAAATTCTAAACGAGGACCTA
          1 AGCAGGTTTACTTAAA-CGAAATTCTAAACGAGGACCTA

                                ***     *           
       2896 AGCAGGTTTGA-TTAAACGATGCTCTAAGC-AGAGACCTA
          1 AGCAGGTTT-ACTTAAACGAAATTCTAAACGAG-GACCTA

            *              **         *  *        
       2934 TGCAGG----CTT-ATGGAAATTCTACACAAGGACCTA
          1 AGCAGGTTTACTTAAACGAAATTCTAAACGAGGACCTA

                *    * *                  *         
       2967 AGCAAGTTCGATTTAAACGAAACTTCTAAATGAGGACCTA
          1 AGCAGGTT-TACTTAAACGAAA-TTCTAAACGAGGACCTA

                         *       *        *    *    
       3007 AGCAGGTTTACTTGAACGAGAGTTCTAGAAAG-GGGCCTA
          1 AGCAGGTTTACTTAAACGA-AATTCTA-AACGAGGACCTA

                          
       3046 AGCAGGTTTTACTT
          1 AGCAGG-TTTACTT

       3060 GAATGGAACA


Statistics
Matches: 122,  Mismatches: 28, Indels: 27
        0.69            0.16        0.15

Matches are distributed among these distances:
  33   18  0.15
  34    4  0.03
  37    2  0.02
  38   21  0.17
  39   44  0.36
  40   33  0.27

ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26


Consensus pattern (38 bp):   
AGCAGGTTTACTTAAACGAAATTCTAAACGAGGACCTA

Found at i:5232 original size:19 final size:18

Alignment explanation


    Indices: 5208--5243  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       5198 TGAAGACTTA

                    *          
       5208 TTGAAGACTATTTGAAGAT
          1 TTGAAGACCA-TTGAAGAT

                             
       5227 TTGAAGACCATTGAAGA
          1 TTGAAGACCATTGAAGA

       5244 ATAATTTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31


Consensus pattern (18 bp):   
TTGAAGACCATTGAAGAT

Found at i:6604 original size:19 final size:18

Alignment explanation


    Indices: 6580--6615  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       6570 TGAAGACTTA

                    *          
       6580 TTGAAGACTATTTGAAGAT
          1 TTGAAGACCA-TTGAAGAT

                             
       6599 TTGAAGACCATTGAAGA
          1 TTGAAGACCATTGAAGA

       6616 ATAATTTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31


Consensus pattern (18 bp):   
TTGAAGACCATTGAAGAT
Done.