Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020033.1 Corchorus olitorius cultivar O-4 contig20066, 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: 15694
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32


Found at i:6240 original size:26 final size:26

Alignment explanation


    Indices: 6192--6243  Score: 77
    Period size: 26  Copynumber: 2.0  Consensus size: 26

       6182 TAGTGGATTT

                         *  * *       
       6192 ATTTTGCAAATTGTAATGGTTTTTGC
          1 ATTTTGCAAATTGCAACGATTTTTGC

                                      
       6218 ATTTTGCAAATTGCAACGATTTTTGC
          1 ATTTTGCAAATTGCAACGATTTTTGC

       6244 GTCGGATTAT


Statistics
Matches: 23,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  26   23  1.00

ACGTcount: A:0.25, C:0.12, G:0.17, T:0.46


Consensus pattern (26 bp):   
ATTTTGCAAATTGCAACGATTTTTGC

Found at i:10724 original size:18 final size:18

Alignment explanation


    Indices: 10701--10740  Score: 64
    Period size: 18  Copynumber: 2.2  Consensus size: 18

      10691 GCGGATCAAA

                               
      10701 ATAATGGATACAA-CAGCC
          1 ATAATGGATACAATCA-CC

                              
      10719 ATAATGGATACAATCACC
          1 ATAATGGATACAATCACC

                
      10737 ATAA
          1 ATAA

      10741 ATTTTGGCCA


Statistics
Matches: 21,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  18   19  0.90
  19    2  0.10

ACGTcount: A:0.47, C:0.20, G:0.12, T:0.20


Consensus pattern (18 bp):   
ATAATGGATACAATCACC

Found at i:11816 original size:31 final size:31

Alignment explanation


    Indices: 11778--11853  Score: 109
    Period size: 31  Copynumber: 2.5  Consensus size: 31

      11768 TTTAGCTAGT

                                            
      11778 AATTTGAGGCTAAACCTTTCAAAAGTTG-CTC
          1 AATTTGAGGCTAAACCTTTCAAAAGTTGAC-C

                          *                
      11809 AATTTGAGGCTAAATCTTTCAAAAGTTGACC
          1 AATTTGAGGCTAAACCTTTCAAAAGTTGACC

                 *  *     
      11840 AATTTAAGCCTAAA
          1 AATTTGAGGCTAAA

      11854 AACAGAAACG


Statistics
Matches: 41,  Mismatches: 3, Indels: 2
        0.89            0.07        0.04

Matches are distributed among these distances:
  31   40  0.98
  32    1  0.02

ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32


Consensus pattern (31 bp):   
AATTTGAGGCTAAACCTTTCAAAAGTTGACC
Done.