Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024828.1 Corchorus olitorius cultivar O-4 contig24861, 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: 29897
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:3838 original size:11 final size:11

Alignment explanation


    Indices: 3798--3831  Score: 68
    Period size: 11  Copynumber: 3.1  Consensus size: 11

       3788 AGGAGTAGGA

                       
       3798 TCCTTCCTAGC
          1 TCCTTCCTAGC

                       
       3809 TCCTTCCTAGC
          1 TCCTTCCTAGC

                       
       3820 TCCTTCCTAGC
          1 TCCTTCCTAGC

             
       3831 T
          1 T

       3832 TTTTCCTTTA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   23  1.00

ACGTcount: A:0.09, C:0.44, G:0.09, T:0.38


Consensus pattern (11 bp):   
TCCTTCCTAGC

Found at i:7442 original size:21 final size:21

Alignment explanation


    Indices: 7416--7507  Score: 150
    Period size: 21  Copynumber: 4.4  Consensus size: 21

       7406 TGCTAGGAGA

                                  
       7416 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                        *        
       7437 TCATTGGAGAAGTTTCCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                                 
       7458 TCATTGGAGAAGGTTCCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                           *     
       7479 TCATTGGAGAAGGTTTCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                    
       7500 TCATTGGA
          1 TCATTGGA

       7508 ATTGCCTAAG


Statistics
Matches: 67,  Mismatches: 3, Indels: 2
        0.93            0.04        0.03

Matches are distributed among these distances:
  20    2  0.03
  21   65  0.97

ACGTcount: A:0.28, C:0.18, G:0.26, T:0.27


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTCCAAGC

Found at i:10704 original size:112 final size:109

Alignment explanation


    Indices: 10517--10733  Score: 301
    Period size: 112  Copynumber: 2.0  Consensus size: 109

      10507 GAACTTGAAC

                        **      *                                            
      10517 TTAGGTCCTCACGGTCTAGGTATCATGCACCTAAATCTACGTGCAATGGCATTGGAATTAAAAAG
          1 TTAGGTCCTCACAATCTAGGCATCATGCACCTAAATCTACGTGCAATGGCATTGG-A--AAAAAG

              *          *                    *            
      10582 TATGACTTTTTTTTTCCAAATGCTAGAAGATTTTTTTAAAGAGTAGT
         63 TAGGACTTTTTTTATCCAAATGCTAGAAGATTTTATTAAAGAGTAGT

                                                   *   *                     
      10629 TTAGGTCCTCACAATCTAGGCATCATGCACCTAAATCTATGTGTAATGGCATTGG-AAAAAGTAG
          1 TTAGGTCCTCACAATCTAGGCATCATGCACCTAAATCTACGTGCAATGGCATTGGAAAAAAGTAG

                              *                      
      10693 GACTTTTTTTTTATCCAACTGCTAGAAGATTTTATTAAAGA
         66 GAC--TTTTTTTATCCAAATGCTAGAAGATTTTATTAAAGA

      10734 CAAGTTCAAT


Statistics
Matches: 94,  Mismatches: 9, Indels: 6
        0.86            0.08        0.06

Matches are distributed among these distances:
 108   11  0.12
 110   33  0.35
 112   50  0.53

ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35


Consensus pattern (109 bp):   
TTAGGTCCTCACAATCTAGGCATCATGCACCTAAATCTACGTGCAATGGCATTGGAAAAAAGTAG
GACTTTTTTTATCCAAATGCTAGAAGATTTTATTAAAGAGTAGT

Found at i:28451 original size:21 final size:21

Alignment explanation


    Indices: 28425--28558  Score: 189
    Period size: 21  Copynumber: 6.4  Consensus size: 21

      28415 TGCTAGAAGT

                                  
      28425 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                     * *         
      28446 TCATTGGAGGATGTTCCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                     *           
      28467 TCATTGGAGTAGGTTCCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                                *
      28488 TCATTGGAGAAGGTTCCAAGT
          1 TCATTGGAGAAGGTTCCAAGC

                                *
      28509 TCATTGGAGAAGGTTCCAAGA
          1 TCATTGGAGAAGGTTCCAAGC

            *              *     
      28530 ACATTGGAGAAGGTTTCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                    
      28551 TCATTGGA
          1 TCATTGGA

      28559 ATTGCTTAAG


Statistics
Matches: 102,  Mismatches: 10, Indels: 2
        0.89            0.09        0.02

Matches are distributed among these distances:
  20    1  0.01
  21  101  0.99

ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTCCAAGC

Done.