Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013879.1 Corchorus olitorius cultivar O-4 contig13912, 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: 2653
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34


Found at i:1920 original size:14 final size:14

Alignment explanation


    Indices: 1901--1935  Score: 70
    Period size: 14  Copynumber: 2.5  Consensus size: 14

       1891 AGATTGGACA

                          
       1901 AAGACAAACTTAAT
          1 AAGACAAACTTAAT

                          
       1915 AAGACAAACTTAAT
          1 AAGACAAACTTAAT

                   
       1929 AAGACAA
          1 AAGACAA

       1936 GGGACATGAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   21  1.00

ACGTcount: A:0.60, C:0.14, G:0.09, T:0.17


Consensus pattern (14 bp):   
AAGACAAACTTAAT

Found at i:2178 original size:28 final size:28

Alignment explanation


    Indices: 2146--2245  Score: 166
    Period size: 28  Copynumber: 3.6  Consensus size: 28

       2136 GCACTTGAAG

                                        
       2146 TGACCAAAATGCCCCTGGATATGCAAAA
          1 TGACCAAAATGCCCCTGGATATGCAAAA

                        *               
       2174 TGACCAAAATGCTCCTGGATATGCAAAA
          1 TGACCAAAATGCCCCTGGATATGCAAAA

                                         
       2202 TGACCAAAATGCCCCTGG-TCATGCAAAA
          1 TGACCAAAATGCCCCTGGAT-ATGCAAAA

               *            
       2230 TGATCAAAATGCCCCT
          1 TGACCAAAATGCCCCT

       2246 TTAAGTGACC


Statistics
Matches: 68,  Mismatches: 3, Indels: 2
        0.93            0.04        0.03

Matches are distributed among these distances:
  27    1  0.01
  28   67  0.99

ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20


Consensus pattern (28 bp):   
TGACCAAAATGCCCCTGGATATGCAAAA

Found at i:2540 original size:35 final size:35

Alignment explanation


    Indices: 2501--2653  Score: 207
    Period size: 35  Copynumber: 4.4  Consensus size: 35

       2491 TGAGTTCATA

                            *     *  *     * * 
       2501 TTGAAGATGCTACACCAAGTCATCTAAATTCGTTT
          1 TTGAAGATGCTACACCGAGTCACCTGAATTCATCT

                                           * * 
       2536 TTGAAGATGCTACACCGAGTCACCTGAATTCGTTT
          1 TTGAAGATGCTACACCGAGTCACCTGAATTCATCT

                           *                   
       2571 TTGAAGATGCTACACTGAGTCACCTGAATTCATCT
          1 TTGAAGATGCTACACCGAGTCACCTGAATTCATCT

                                  *   *   *    
       2606 TTGAAGATGCTACACCGAGTCATCTGGATTTATCT
          1 TTGAAGATGCTACACCGAGTCACCTGAATTCATCT

                         
       2641 TTGAAGATGCTAC
          1 TTGAAGATGCTAC


Statistics
Matches: 108,  Mismatches: 10, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  35  108  1.00

ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33


Consensus pattern (35 bp):   
TTGAAGATGCTACACCGAGTCACCTGAATTCATCT

Done.