Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024568.1 Corchorus olitorius cultivar O-4 contig24601, 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: 11000
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33


Found at i:1757 original size:2 final size:2

Alignment explanation


    Indices: 1750--1783  Score: 59
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       1740 AAGATCAGTC

                                                       *      
       1750 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       1784 TTAGGTAATT


Statistics
Matches: 30,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   30  1.00

ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47


Consensus pattern (2 bp):   
AT

Found at i:4370 original size:18 final size:19

Alignment explanation


    Indices: 4349--4384  Score: 56
    Period size: 18  Copynumber: 1.9  Consensus size: 19

       4339 TTACTAAATA

                               
       4349 AATAATAATTATT-TTTAG
          1 AATAATAATTATTATTTAG

                  *           
       4367 AATAATTATTATTATTTA
          1 AATAATAATTATTATTTA

       4385 ATTTAATATG


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18   12  0.75
  19    4  0.25

ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53


Consensus pattern (19 bp):   
AATAATAATTATTATTTAG

Found at i:7205 original size:55 final size:57

Alignment explanation


    Indices: 7121--7232  Score: 201
    Period size: 55  Copynumber: 2.0  Consensus size: 57

       7111 TATTCGTTTC

                                                        *            
       7121 CTTTCACACAATAAATGTTATAATAAATCCTATCCC-CC-ATCTCTACTTAATTATT
          1 CTTTCACACAATAAATGTTATAATAAATCCTATCCCTCCTATCTATACTTAATTATT

                                                                     
       7176 CTTTCACACAATAAATGTTATAATAAATCCTATCCCTCCTATCTATACTTAATTATT
          1 CTTTCACACAATAAATGTTATAATAAATCCTATCCCTCCTATCTATACTTAATTATT

       7233 TTATAAAATA


Statistics
Matches: 54,  Mismatches: 1, Indels: 2
        0.95            0.02        0.04

Matches are distributed among these distances:
  55   36  0.67
  56    2  0.04
  57   16  0.30

ACGTcount: A:0.35, C:0.24, G:0.02, T:0.39


Consensus pattern (57 bp):   
CTTTCACACAATAAATGTTATAATAAATCCTATCCCTCCTATCTATACTTAATTATT

Found at i:7358 original size:42 final size:42

Alignment explanation


    Indices: 7299--7379  Score: 144
    Period size: 42  Copynumber: 1.9  Consensus size: 42

       7289 TAAGGATCAG

                                                      
       7299 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
          1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT

                                       * *         
       7341 GATTTGAGTTGAGTATTTCTTAATTTATAGAGAATTTTC
          1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC

       7380 AAGAGTTAGC


Statistics
Matches: 37,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  42   37  1.00

ACGTcount: A:0.30, C:0.06, G:0.16, T:0.48


Consensus pattern (42 bp):   
GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
Done.