Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024902.1 Corchorus olitorius cultivar O-4 contig24935, 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: 8825
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33


Found at i:43 original size:33 final size:33

Alignment explanation


    Indices: 1--63  Score: 117
    Period size: 33  Copynumber: 1.9  Consensus size: 33

                                             
          1 GGGCGGCATGCCATGGAGAGTGCCGCCCTCCTA
          1 GGGCGGCATGCCATGGAGAGTGCCGCCCTCCTA

                            *             
         34 GGGCGGCATGCCATGGCGAGTGCCGCCCTC
          1 GGGCGGCATGCCATGGAGAGTGCCGCCCTC

         64 GGAGGACGGC


Statistics
Matches: 29,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  33   29  1.00

ACGTcount: A:0.13, C:0.35, G:0.38, T:0.14


Consensus pattern (33 bp):   
GGGCGGCATGCCATGGAGAGTGCCGCCCTCCTA

Found at i:74 original size:33 final size:33

Alignment explanation


    Indices: 4--74  Score: 106
    Period size: 33  Copynumber: 2.2  Consensus size: 33

          1 GGG

                                        *   *
          4 CGGCATGCCATGGAGAGTGCCGCCCTCCTAGGG
          1 CGGCATGCCATGGAGAGTGCCGCCCTCCGAGGA

                         *             *     
         37 CGGCATGCCATGGCGAGTGCCGCCCTCGGAGGA
          1 CGGCATGCCATGGAGAGTGCCGCCCTCCGAGGA

                 
         70 CGGCA
          1 CGGCA

         75 CCGCGCCTAG


Statistics
Matches: 34,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  33   34  1.00

ACGTcount: A:0.15, C:0.34, G:0.38, T:0.13


Consensus pattern (33 bp):   
CGGCATGCCATGGAGAGTGCCGCCCTCCGAGGA

Found at i:5158 original size:17 final size:17

Alignment explanation


    Indices: 5128--5160  Score: 50
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       5118 GAGTGCGAGC

                             
       5128 GATTTCAAATTAATTAA
          1 GATTTCAAATTAATTAA

                             
       5145 GATTT-AAATGTAATTA
          1 GATTTCAAAT-TAATTA

       5161 CTAAATAAGT


Statistics
Matches: 15,  Mismatches: 0, Indels: 2
        0.88            0.00        0.12

Matches are distributed among these distances:
  16    4  0.27
  17   11  0.73

ACGTcount: A:0.45, C:0.03, G:0.09, T:0.42


Consensus pattern (17 bp):   
GATTTCAAATTAATTAA

Found at i:6872 original size:22 final size:22

Alignment explanation


    Indices: 6842--6883  Score: 66
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       6832 GTTTATAATA

                *                 
       6842 TTCTTGGGTCATCCGGGTTAAC
          1 TTCTCGGGTCATCCGGGTTAAC

                        *       
       6864 TTCTCGGGTCATTCGGGTTA
          1 TTCTCGGGTCATCCGGGTTA

       6884 CGGGTTTGTC


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  22   18  1.00

ACGTcount: A:0.12, C:0.21, G:0.29, T:0.38


Consensus pattern (22 bp):   
TTCTCGGGTCATCCGGGTTAAC
Done.