Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023395.1 Corchorus olitorius cultivar O-4 contig23428, 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: 15412
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32


Found at i:6436 original size:52 final size:52

Alignment explanation


    Indices: 6373--6477  Score: 174
    Period size: 52  Copynumber: 2.0  Consensus size: 52

       6363 AACAAGAATT

                                          *                     
       6373 GCAGGACAACTTCGGCCCAGAACTTGTTCACCTTCAGGACAAAAGTTATTGC
          1 GCAGGACAACTTCGGCCCAGAACTTGTTCAACTTCAGGACAAAAGTTATTGC

                                           *   *           *    
       6425 GCAGGACAACTTCGGCCCAGAACTTGTTCAATTTCGGGACAAAAGTTGTTGC
          1 GCAGGACAACTTCGGCCCAGAACTTGTTCAACTTCAGGACAAAAGTTATTGC

             
       6477 G
          1 G

       6478 GAAAGAAAAA


Statistics
Matches: 49,  Mismatches: 4, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  52   49  1.00

ACGTcount: A:0.28, C:0.25, G:0.24, T:0.24


Consensus pattern (52 bp):   
GCAGGACAACTTCGGCCCAGAACTTGTTCAACTTCAGGACAAAAGTTATTGC

Found at i:8705 original size:33 final size:33

Alignment explanation


    Indices: 8604--8708  Score: 106
    Period size: 33  Copynumber: 3.2  Consensus size: 33

       8594 TTGCAAAGAG

                          *  *       *      * 
       8604 TGTTTT-AGATGTTATTAGTGATGATACTAAACC
          1 TGTTTTAAG-TGTTGTTTGTGATGAAACTAAATC

             **                     *        
       8637 TAATTTAAGTGTTGTTTGTGATGACACTAAATC
          1 TGTTTTAAGTGTTGTTTGTGATGAAACTAAATC

                   *                          
       8670 TGTTTTAGGTGTTGTTTGTGATGAAAC-AAATTC
          1 TGTTTTAAGTGTTGTTTGTGATGAAACTAAA-TC

                  
       8703 TGTTTT
          1 TGTTTT

       8709 GGATGCTAAT


Statistics
Matches: 60,  Mismatches: 10, Indels: 4
        0.81            0.14        0.05

Matches are distributed among these distances:
  32    3  0.05
  33   55  0.92
  34    2  0.03

ACGTcount: A:0.27, C:0.08, G:0.20, T:0.46


Consensus pattern (33 bp):   
TGTTTTAAGTGTTGTTTGTGATGAAACTAAATC

Found at i:11672 original size:52 final size:52

Alignment explanation


    Indices: 11609--11713  Score: 183
    Period size: 52  Copynumber: 2.0  Consensus size: 52

      11599 AACAAGAATT

                               *                        *       
      11609 GCAGGACAACTTCGGCCCAGAACTTGTTCAACTTCGGGACAAAATTTGTTGC
          1 GCAGGACAACTTCGGCCCAAAACTTGTTCAACTTCGGGACAAAAGTTGTTGC

                                                     *          
      11661 GCAGGACAACTTCGGCCCAAAACTTGTTCAACTTCGGGACAGAAGTTGTTGC
          1 GCAGGACAACTTCGGCCCAAAACTTGTTCAACTTCGGGACAAAAGTTGTTGC

             
      11713 G
          1 G

      11714 GAAAGAAAAA


Statistics
Matches: 50,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  52   50  1.00

ACGTcount: A:0.27, C:0.25, G:0.25, T:0.24


Consensus pattern (52 bp):   
GCAGGACAACTTCGGCCCAAAACTTGTTCAACTTCGGGACAAAAGTTGTTGC

Found at i:14216 original size:46 final size:46

Alignment explanation


    Indices: 14149--14241  Score: 168
    Period size: 46  Copynumber: 2.0  Consensus size: 46

      14139 TAGGGAGTCT

                                                          
      14149 ACATGCATACTGATCATAATCTTAATCAATGCCATAATTTTTTCGA
          1 ACATGCATACTGATCATAATCTTAATCAATGCCATAATTTTTTCGA

                     *                     *              
      14195 ACATGCATATTGATCATAATCTTAATCAATGTCATAATTTTTTCGA
          1 ACATGCATACTGATCATAATCTTAATCAATGCCATAATTTTTTCGA

             
      14241 A
          1 A

      14242 AATTTTGAAA


Statistics
Matches: 45,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  46   45  1.00

ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39


Consensus pattern (46 bp):   
ACATGCATACTGATCATAATCTTAATCAATGCCATAATTTTTTCGA
Done.