Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024588.1 Corchorus olitorius cultivar O-4 contig24621, 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: 6442
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35


Found at i:1881 original size:2 final size:2

Alignment explanation


    Indices: 1874--1903  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       1864 ACATTTACTA

                                                        
       1874 AT AT 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 AT AT

       1904 GGACCCGGCC


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:5703 original size:19 final size:19

Alignment explanation


    Indices: 5679--5717  Score: 69
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       5669 TTCATTTTCT

                               
       5679 AACTCTCAAAACTTCTTCA
          1 AACTCTCAAAACTTCTTCA

                   *           
       5698 AACTCTCTAAACTTCTTCA
          1 AACTCTCAAAACTTCTTCA

             
       5717 A
          1 A

       5718 GAACATCATG


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  19   19  1.00

ACGTcount: A:0.36, C:0.31, G:0.00, T:0.33


Consensus pattern (19 bp):   
AACTCTCAAAACTTCTTCA

Found at i:6315 original size:45 final size:45

Alignment explanation


    Indices: 6251--6340  Score: 137
    Period size: 45  Copynumber: 2.0  Consensus size: 45

       6241 GCAGTTGCAA

                                *                         
       6251 AGGGAGAGAGAGGCTGAGGCTGCTCGAATGTATA-GGAAGAGGGAG
          1 AGGGAGAGAGAGGCTGAGGCAGCTCGAATGTATAGGGAA-AGGGAG

                    *                 *                  
       6296 AGGGAGAGGGAGGCTGAGGCAGCTCGGATGTATAGGGAAAGGGAG
          1 AGGGAGAGAGAGGCTGAGGCAGCTCGAATGTATAGGGAAAGGGAG

       6341 GCTGCTGCTG


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

Matches are distributed among these distances:
  45   37  0.90
  46    4  0.10

ACGTcount: A:0.30, C:0.09, G:0.49, T:0.12


Consensus pattern (45 bp):   
AGGGAGAGAGAGGCTGAGGCAGCTCGAATGTATAGGGAAAGGGAG
Done.