Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024794.1 Corchorus olitorius cultivar O-4 contig24827, 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: 23827
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32


Found at i:3732 original size:25 final size:25

Alignment explanation


    Indices: 3694--3741  Score: 62
    Period size: 25  Copynumber: 1.9  Consensus size: 25

       3684 TTATTTATTA

                          **         
       3694 TAAAAATATAATTTTTAAATTTTTT
          1 TAAAAATATAATTTGAAAATTTTTT

                                    
       3719 TAAAAATA-AGATTTGAAAATTTT
          1 TAAAAATATA-ATTTGAAAATTTT

       3742 AAAACTTAAT


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  24    1  0.05
  25   19  0.95

ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48


Consensus pattern (25 bp):   
TAAAAATATAATTTGAAAATTTTTT

Found at i:5572 original size:30 final size:30

Alignment explanation


    Indices: 5538--5598  Score: 72
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       5528 TGGAAGAAGT

                               *            
       5538 AATGGAAGATAT-AA-GAATGATGCAAGATCA
          1 AATGGAAGAT-TCAATGAAAGATG-AAGATCA

                 *                        
       5568 AATGGTAGATTCAATGAAAGATGAAGATCA
          1 AATGGAAGATTCAATGAAAGATGAAGATCA

             
       5598 A
          1 A

       5599 GTTCGAGGCC


Statistics
Matches: 27,  Mismatches: 2, Indels: 4
        0.82            0.06        0.12

Matches are distributed among these distances:
  29    1  0.04
  30   19  0.70
  31    7  0.26

ACGTcount: A:0.49, C:0.07, G:0.23, T:0.21


Consensus pattern (30 bp):   
AATGGAAGATTCAATGAAAGATGAAGATCA

Found at i:13126 original size:36 final size:36

Alignment explanation


    Indices: 13072--13149  Score: 104
    Period size: 36  Copynumber: 2.2  Consensus size: 36

      13062 TCTATTTGGG

                 *                              
      13072 CCCAATACATAATGCCCACCACTCCCTTAATTCGGC
          1 CCCAAAACATAATGCCCACCACTCCCTTAATTCGGC

                                         **     *
      13108 CCCAAAACATGAAT-CCCACCACTCCCTTGGTTCGGG
          1 CCCAAAACAT-AATGCCCACCACTCCCTTAATTCGGC

                  
      13144 CCCAAA
          1 CCCAAA

      13150 GAAAAAACTC


Statistics
Matches: 37,  Mismatches: 4, Indels: 2
        0.86            0.09        0.05

Matches are distributed among these distances:
  36   34  0.92
  37    3  0.08

ACGTcount: A:0.28, C:0.41, G:0.12, T:0.19


Consensus pattern (36 bp):   
CCCAAAACATAATGCCCACCACTCCCTTAATTCGGC
Done.