Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024498.1 Corchorus olitorius cultivar O-4 contig24531, 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: 5010
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28


Found at i:2592 original size:313 final size:322

Alignment explanation


    Indices: 2007--2798  Score: 974
    Period size: 333  Copynumber: 2.4  Consensus size: 322

       1997 ATTGAGTGGA

                *        *                                                   
       2007 AGCATAACAATTCCAGTATCAATGGTTGTCTTGGTATATTGTGTTCATGTACTAAATAAATATGA
          1 AGCAGAACAATTCTAGTATCAATGGTTGTCTTGGTATATTGTGTTCATGTACTAAATAAATATGA

                  *               *         *           *                    
       2072 ATTCATAAATTAGAAAGAAAATGCAGATTATTGTTACC-TCCTTGTTTGATTCCATAGAAAGAGG
         66 ATTCATGAATTAGAAAGAAAATACAGATTATTATTACCTTCC-TATTTGATTCCATAGAAAGA-G

                                        *                       *   *     *  
       2136 AAGAGCCGCTAGAGTCATCTCAATATCAGTGATAAATAAATACTCAGGCATTGAAGGTGCTGGAG
        129 --GA------AGAGTCA-CTCAATATCAATGATAAATAAATACTCAGGCATTAAAGATGCTGAAG

                          *                            **        *           
       2201 TTATTTCAGGACTTGGTGCAGTCTGAGGATCACTTGGGACAATTTCCAACTGCGAAAGGAAATCA
        185 TTATTTCAGGACTTAGTGCAGTCTGAGGATCACTTGGGACAATCACCAACTGCAAAAGGAAATCA

            *                      *                                      * *
       2266 TTGGCCCAC-TTTT-T-ATC-AATA-AAAAAAGAA-AAGAAAAGAAGAATAAGTTG-TTGCATAG
        250 CTGGCCCACTTTTTGTAATCAAAAAGAAAAAAGAAGAAGAAAAGAAGAATAAGTTGTTTGCACAA

                    
       2324 TAATGTGC
        315 TAATGTGC

                               *                    *                        
       2332 AGCAGAACAATTCTAGTATTAATGGTTGTCTTGGTATATTTTGTTCATGTACTAAATAAATATGA
          1 AGCAGAACAATTCTAGTATCAATGGTTGTCTTGGTATATTGTGTTCATGTACTAAATAAATATGA

                        *     **     *                                   *   
       2397 ATTCATGAATTAAAAAGATGATACATATTATTATTACCTTCCTATTTGATTCCATAGAAAGCGGA
         66 ATTCATGAATTAGAAAGAAAATACAGATTATTATTACCTTCCTATTTGATTCCATAGAAAGAGGA

                                    *     *    *                             
       2462 AGAG-C-CTCAATATCAATGATAACTAAATGCTCATGCATTAAAGATGCTGAAGTTATTTCAGGA
        131 AGAGTCACTCAATATCAATGATAAATAAATACTCAGGCATTAAAGATGCTGAAGTTATTTCAGGA

                                                                             
       2525 CTTAGTGCAGTCTGAGGATCACTTGGGACAATCACCAACTGCAAAAGGAAATCACTGGCCCACTT
        196 CTTAGTGCAGTCTGAGGATCACTTGGGACAATCACCAACTGCAAAAGGAAATCACTGGCCCACTT

                                                                          *  
       2590 TTTGTCAATCAAAAAAAAAAGAAAAAGAAAAAAGAAGGAAGAAAAGAAGAATAAGTTGTTTGTAC
        261 TTTGT-AATC-----------AAAAAGAAAAAAGAA-GAAGAAAAGAAGAATAAGTTGTTTGCAC

                *     
       2655 AATATTGTGC
        313 AATAATGTGC

                                                                           * 
       2665 AGCAGAACAATTCTAGTATCAATGGTTGTCTTGGTATATTGTGTTCATGTACTAAATAAATATTA
          1 AGCAGAACAATTCTAGTATCAATGGTTGTCTTGGTATATTGTGTTCATGTACTAAATAAATATGA

            **                *    *               *                         
       2730 GCTCATGAATTAGAAAGACAATATAGATTATTATTACCTCCCTATTTGATTCCATAGAAAGAGGA
         66 ATTCATGAATTAGAAAGAAAATACAGATTATTATTACCTTCCTATTTGATTCCATAGAAAGAGGA

                
       2795 AGAG
        131 AGAG

       2799 ACGATGGAGT


Statistics
Matches: 404,  Mismatches: 42, Indels: 34
        0.84            0.09        0.07

Matches are distributed among these distances:
 313  109  0.27
 314    4  0.01
 315    2  0.00
 316    4  0.01
 317    3  0.01
 322    2  0.00
 324    1  0.00
 325  110  0.27
 326    3  0.01
 329    3  0.01
 330    9  0.02
 332   20  0.05
 333  134  0.33

ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30


Consensus pattern (322 bp):   
AGCAGAACAATTCTAGTATCAATGGTTGTCTTGGTATATTGTGTTCATGTACTAAATAAATATGA
ATTCATGAATTAGAAAGAAAATACAGATTATTATTACCTTCCTATTTGATTCCATAGAAAGAGGA
AGAGTCACTCAATATCAATGATAAATAAATACTCAGGCATTAAAGATGCTGAAGTTATTTCAGGA
CTTAGTGCAGTCTGAGGATCACTTGGGACAATCACCAACTGCAAAAGGAAATCACTGGCCCACTT
TTTGTAATCAAAAAGAAAAAAGAAGAAGAAAAGAAGAATAAGTTGTTTGCACAATAATGTGC

Found at i:3636 original size:22 final size:21

Alignment explanation


    Indices: 3611--3660  Score: 64
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       3601 GGAAAATATC

                                  
       3611 ACACTGCACGGACACCGTACGA
          1 ACACTGCACGGAC-CCGTACGA

                       * **      
       3633 ACACTGCACGGGCTTGTACGA
          1 ACACTGCACGGACCCGTACGA

                   
       3654 ACACTGC
          1 ACACTGC

       3661 GCATGGGCCG


Statistics
Matches: 25,  Mismatches: 3, Indels: 1
        0.86            0.10        0.03

Matches are distributed among these distances:
  21   13  0.52
  22   12  0.48

ACGTcount: A:0.28, C:0.34, G:0.24, T:0.14


Consensus pattern (21 bp):   
ACACTGCACGGACCCGTACGA
Done.