Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024481.1 Corchorus olitorius cultivar O-4 contig24514, 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: 16114
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:281 original size:119 final size:118

Alignment explanation


    Indices: 29--380  Score: 600
    Period size: 119  Copynumber: 3.0  Consensus size: 118

         19 TATTGTTAAC

                       *                                                *    
         29 GCGTTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGT
          1 GCGTTTGGGATTTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTAAAGT

                                                              *  
         94 GGAAAATTTAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGA
         66 GGAAAATTTAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTAGA

                   *  *                                 *                    
        147 GCGTTTGAGACTTAAGAATTAAGGAGTAATTTATACTA-TTTTAATGGAAGAGTTGGTTTAAAGT
          1 GCGTTTGGGATTTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTAAAGT

                                                                   
        211 GGAAAATTTAAGGACTTGAGAAGTTCCTCAAAACAATATTCATGGTTGTGGTAGA
         66 GGAAAATTTAAGGACTTGA-AA-TTCCTCAAAACAATATTCATGGTTGTGGTAGA

                                                                             
        266 GCGTTTGGGATTTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAA-
          1 GCGTTTGGGATTTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTT-AAAG

                     *                                         
        330 TGGAAAATTGAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGT
         65 TGGAAAATTTAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGT

        381 GGATGTTCTT


Statistics
Matches: 220,  Mismatches: 10, Indels: 8
        0.92            0.04        0.03

Matches are distributed among these distances:
 117   43  0.20
 118   66  0.30
 119   69  0.31
 120   39  0.18
 121    3  0.01

ACGTcount: A:0.34, C:0.07, G:0.24, T:0.35


Consensus pattern (118 bp):   
GCGTTTGGGATTTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTAAAGT
GGAAAATTTAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTAGA

Found at i:12409 original size:7 final size:7

Alignment explanation


    Indices: 12397--12428  Score: 64
    Period size: 7  Copynumber: 4.6  Consensus size: 7

      12387 AAGGTATATT

                   
      12397 GCAAATC
          1 GCAAATC

                   
      12404 GCAAATC
          1 GCAAATC

                   
      12411 GCAAATC
          1 GCAAATC

                   
      12418 GCAAATC
          1 GCAAATC

                
      12425 GCAA
          1 GCAA

      12429 TCGAGATAGT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   25  1.00

ACGTcount: A:0.44, C:0.28, G:0.16, T:0.12


Consensus pattern (7 bp):   
GCAAATC

Found at i:13817 original size:2 final size:2

Alignment explanation


    Indices: 13810--13835  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

      13800 GGAGGTGATA

                                                  
      13810 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

      13836 TTCATGTAGA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.