Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024201.1 Corchorus olitorius cultivar O-4 contig24234, 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: 11298
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:5634 original size:21 final size:22

Alignment explanation


    Indices: 5609--5651  Score: 61
    Period size: 21  Copynumber: 2.0  Consensus size: 22

       5599 TTTCCCTCAT

                                  
       5609 GCATTCATTCAT-CATGCCATG
          1 GCATTCATTCATGCATGCCATG

                  *         *     
       5630 GCATTCGTTCATGCATTCCATG
          1 GCATTCATTCATGCATGCCATG

       5652 AAGTCTTAGC


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  21   11  0.58
  22    8  0.42

ACGTcount: A:0.21, C:0.28, G:0.16, T:0.35


Consensus pattern (22 bp):   
GCATTCATTCATGCATGCCATG

Found at i:9554 original size:50 final size:50

Alignment explanation


    Indices: 9479--9863  Score: 644
    Period size: 50  Copynumber: 7.7  Consensus size: 50

       9469 AATGCTTTGA

                    *   *                 *                   
       9479 CTTTTCCATAAGTCAAACTCGTTTCCATACAAGTCAATTATCAACATAGG
          1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATAGG

                        *                                     
       9529 CTTTTCCACAAGTCAAACTCGTTTCCATACGAGTCAATTATCAACATAGG
          1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATAGG

                                *               *             
       9579 CTTTTCCACAAGCCAAACTCATTTCCATACGAGTCAGTTATCAACATAGG
          1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATAGG

                                *                             
       9629 CTTTTCCACAAGCCAAACTCATTTCCATACGAGTCAATTATCAACATAGG
          1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATAGG

                                                *             
       9679 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTATCAACATAGG
          1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATAGG

                                    *                        *
       9729 CTTTTCCACAAGCCAAACTCGTTTTCATACGAGTCAATTATCAACATAGA
          1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATAGG

                                         *          *   *  *  
       9779 CTTTTCCACAAGCCAAACTCGTTTCCATATGAGTCAATTAGCAATATGGG
          1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATAGG

                                               
       9829 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTC
          1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTC

       9864 GGTTCAAGCC


Statistics
Matches: 317,  Mismatches: 18, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  50  317  1.00

ACGTcount: A:0.32, C:0.27, G:0.12, T:0.29


Consensus pattern (50 bp):   
CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATAGG

Found at i:9920 original size:69 final size:69

Alignment explanation


    Indices: 9829--10162  Score: 506
    Period size: 69  Copynumber: 4.8  Consensus size: 69

       9819 GCAATATGGG

                    *   *                                   *          *     
       9829 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGGTTCAAGCCTTGTTTCCATCCAAACCATA
          1 CTTTTCCATAAGTCAAACTCGTTTCCATACGAGTCGGTTCAAGCCTTGGTTCCATCCAAGCCATA

                
       9894 TAGA
         66 TAGA

                                                                             
       9898 CTTTTCCATAAGTCAAACTCGTTTCCATACGAGTCGGTTCAAGCCTTGGTTCCATCCAAGCCATA
          1 CTTTTCCATAAGTCAAACTCGTTTCCATACGAGTCGGTTCAAGCCTTGGTTCCATCCAAGCCATA

                
       9963 TAGA
         66 TAGA

                                         *      *                          **
       9967 CTTTTCCATAAGTCAAACTCGTTTCCATAAGAGTCGTTTCAAGCCTTGGTTCCATCCAAGCCACG
          1 CTTTTCCATAAGTCAAACTCGTTTCCATACGAGTCGGTTCAAGCCTTGGTTCCATCCAAGCCATA

               *
      10032 TAGG
         66 TAGA

                    *   *                      **                            
      10036 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTCAAGCCTTGGTTCCATCCAAGCCATA
          1 CTTTTCCATAAGTCAAACTCGTTTCCATACGAGTCGGTTCAAGCCTTGGTTCCATCCAAGCCATA

                
      10101 TAGA
         66 TAGA

               *                        *      *      * *             
      10105 CTTGTCCATAAGTCAAACTCGTTTCCATGCGAGTCAGTTCAAACATTGGTTCCATCCA
          1 CTTTTCCATAAGTCAAACTCGTTTCCATACGAGTCGGTTCAAGCCTTGGTTCCATCCA

      10163 TACTGCAGAG


Statistics
Matches: 241,  Mismatches: 24, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  69  241  1.00

ACGTcount: A:0.27, C:0.29, G:0.15, T:0.30


Consensus pattern (69 bp):   
CTTTTCCATAAGTCAAACTCGTTTCCATACGAGTCGGTTCAAGCCTTGGTTCCATCCAAGCCATA
TAGA

Done.