Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020723.1 Corchorus olitorius cultivar O-4 contig20756, 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: 59274
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31


Found at i:10722 original size:262 final size:260

Alignment explanation


    Indices: 10259--10780  Score: 918
    Period size: 262  Copynumber: 2.0  Consensus size: 260

      10249 AAGCAAGAGA

                                                                  *          
      10259 AAACTGAGAGACCCATGGCGATCGACCGAGAGAGAAATTATTCTAATCCCGCTCCAAAATAAAGG
          1 AAACTGAGAGACCCATGGCGATCGACCGAGAGAGAAATTATTCTAATCCCGCTCAAAAATAAAGG

                              *              *                               
      10324 GAAAAAGAAAGCATCACAGAAGTTATAAAGCCAGAGATTTTGCATAAAAACACAAATTAGGGTTT
         66 GAAAAAGAAAGCATCACAAAAGTTATAAAGCCAAAGATTTTGCATAAAAACACAAATTAGGGTTT

                                                                    *        
      10389 CTGAAAACGTATTAAATACCAAGTCCCAACAAGAACGAAAACAGAAGCATAAAAAGGGAAATTTT
        131 CTGAAAACGTATTAAATACCAAGTCCCAACAAGAACGAAAACAGAAGCATAAAAAGAGAAATTTT

                                                                      *      
      10454 GAAGGAAGATCAAAGTAACAAATTTGTAGAACACTAAACTAGTATAAAAGATTTTCGAGAAGAAT
        196 GAAGGAAGATCAAAGTAACAAATTTGTAGAACACTAAACTAGTATAAAAGATTTTCGAAAAGAAT

                                     *               *                       
      10519 AAACTGAGAGACCCATGGCGATCGATCGAGAGAGAAAAATTTTTCTAATCCCGCTCAAAAATAAA
          1 AAACTGAGAGACCCATGGCGATCGACCGAGAGAG--AAATTATTCTAATCCCGCTCAAAAATAAA

                                                                             
      10584 GGGAAAAAGAAAGCATCACAAAAGTTATAAAGCCAAAGATTTTGCATAAAAACACAAATTAGGGT
         64 GGGAAAAAGAAAGCATCACAAAAGTTATAAAGCCAAAGATTTTGCATAAAAACACAAATTAGGGT

                        *      *                      *       *              
      10649 TTCTGAAAACGTTTTAAATCCCAAGTCCCAACAAGAACGAAAGCAGAAGCGTAAAAAGAGAAATT
        129 TTCTGAAAACGTATTAAATACCAAGTCCCAACAAGAACGAAAACAGAAGCATAAAAAGAGAAATT

                                               *                             
      10714 TTGAAGGAAGATCAAAGTAACAAATTTGTAGAACATTAAACTAGTATAAAAGATTTTCGAAAAGA
        194 TTGAAGGAAGATCAAAGTAACAAATTTGTAGAACACTAAACTAGTATAAAAGATTTTCGAAAAGA

              
      10779 AT
        259 AT

      10781 CTAACAGAAA


Statistics
Matches: 248,  Mismatches: 12, Indels: 2
        0.95            0.05        0.01

Matches are distributed among these distances:
 260   33  0.13
 262  215  0.87

ACGTcount: A:0.47, C:0.15, G:0.18, T:0.20


Consensus pattern (260 bp):   
AAACTGAGAGACCCATGGCGATCGACCGAGAGAGAAATTATTCTAATCCCGCTCAAAAATAAAGG
GAAAAAGAAAGCATCACAAAAGTTATAAAGCCAAAGATTTTGCATAAAAACACAAATTAGGGTTT
CTGAAAACGTATTAAATACCAAGTCCCAACAAGAACGAAAACAGAAGCATAAAAAGAGAAATTTT
GAAGGAAGATCAAAGTAACAAATTTGTAGAACACTAAACTAGTATAAAAGATTTTCGAAAAGAAT

Found at i:13928 original size:15 final size:15

Alignment explanation


    Indices: 13908--13937  Score: 60
    Period size: 15  Copynumber: 2.0  Consensus size: 15

      13898 TGTTCAACTG

                           
      13908 ACACCTTTTCTTAAT
          1 ACACCTTTTCTTAAT

                           
      13923 ACACCTTTTCTTAAT
          1 ACACCTTTTCTTAAT

      13938 TATTCTCGTT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.27, C:0.27, G:0.00, T:0.47


Consensus pattern (15 bp):   
ACACCTTTTCTTAAT

Found at i:14071 original size:6 final size:6

Alignment explanation


    Indices: 14060--14084  Score: 50
    Period size: 6  Copynumber: 4.2  Consensus size: 6

      14050 TTTCTTTGCA

                                         
      14060 TTGTTC TTGTTC TTGTTC TTGTTC T
          1 TTGTTC TTGTTC TTGTTC TTGTTC T

      14085 GCTTAGAGCT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   19  1.00

ACGTcount: A:0.00, C:0.16, G:0.16, T:0.68


Consensus pattern (6 bp):   
TTGTTC

Found at i:35487 original size:36 final size:36

Alignment explanation


    Indices: 35437--35550  Score: 210
    Period size: 36  Copynumber: 3.1  Consensus size: 36

      35427 AGTTTGTCTA

                     *                          
      35437 AACTCCAAAAGGTACATAGGGTAAGTCCTAAGTCGT
          1 AACTCCAAAGGGTACATAGGGTAAGTCCTAAGTCGT

                                                
      35473 AACTCCAAAGGGTACATAGGGTAAGTCCTAAGTCGT
          1 AACTCCAAAGGGTACATAGGGTAAGTCCTAAGTCGT

                                                
      35509 AACTCCAAAGGGTACATAGGGTAAGTCCTAAGTCGT
          1 AACTCCAAAGGGTACATAGGGTAAGTCCTAAGTCGT

                  
      35545 CAACTC
          1 -AACTC

      35551 TTACGAGGAT


Statistics
Matches: 76,  Mismatches: 1, Indels: 1
        0.97            0.01        0.01

Matches are distributed among these distances:
  36   71  0.93
  37    5  0.07

ACGTcount: A:0.34, C:0.21, G:0.23, T:0.22


Consensus pattern (36 bp):   
AACTCCAAAGGGTACATAGGGTAAGTCCTAAGTCGT

Found at i:50228 original size:63 final size:63

Alignment explanation


    Indices: 50129--50254  Score: 243
    Period size: 63  Copynumber: 2.0  Consensus size: 63

      50119 TTTCCTTGCA

                                                                           
      50129 CTGACAGTCACTTTTGCTGCAGTTTCATCTTTCTGTTGAGGTTGATCATTTACCGGAACTTTG
          1 CTGACAGTCACTTTTGCTGCAGTTTCATCTTTCTGTTGAGGTTGATCATTTACCGGAACTTTG

                              *                                            
      50192 CTGACAGTCACTTTTGCTTCAGTTTCATCTTTCTGTTGAGGTTGATCATTTACCGGAACTTTG
          1 CTGACAGTCACTTTTGCTGCAGTTTCATCTTTCTGTTGAGGTTGATCATTTACCGGAACTTTG

      50255 GATGAATTTA


Statistics
Matches: 62,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  63   62  1.00

ACGTcount: A:0.17, C:0.21, G:0.20, T:0.42


Consensus pattern (63 bp):   
CTGACAGTCACTTTTGCTGCAGTTTCATCTTTCTGTTGAGGTTGATCATTTACCGGAACTTTG
Done.