Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011358.1 Corchorus olitorius cultivar O-4 contig11391, 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: 6611
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.34


Found at i:3737 original size:29 final size:29

Alignment explanation


    Indices: 3480--3738  Score: 329
    Period size: 29  Copynumber: 8.9  Consensus size: 29

       3470 GAACCTAGAG

                              *      * * 
       3480 TATGCAAAAATGACCAAACTGCCCCAGAA
          1 TATGCAAAAATGACCAAAATGCCCCTGGA

             *  *   *      *             
       3509 TGTGTAAAGATGACCGAAATGCCCCTGGA
          1 TATGCAAAAATGACCAAAATGCCCCTGGA

             *  *                    *   
       3538 TGTGTAAAAATGACCAAAATGCCCCCGGA
          1 TATGCAAAAATGACCAAAATGCCCCTGGA

                                     * * 
       3567 TATGCAAAAATGACCAAAATGCCCCCGTA
          1 TATGCAAAAATGACCAAAATGCCCCTGGA

                                     * * 
       3596 TATGCAAAAATGACCAAAATGCCCCCGTA
          1 TATGCAAAAATGACCAAAATGCCCCTGGA

                                         
       3625 TATGCAAAAATGACCAAAATGCCCCTGGA
          1 TATGCAAAAATGACCAAAATGCCCCTGGA

                                * **   * 
       3654 TATGCAAAAATGACCAAAATTCATCTGAA
          1 TATGCAAAAATGACCAAAATGCCCCTGGA

             *   *                       
       3683 TGTGCGAAAATGACCAAAATGCCCCTGGA
          1 TATGCAAAAATGACCAAAATGCCCCTGGA

                                *      
       3712 TATGCAAAAATGACCAAAATTCCCCTG
          1 TATGCAAAAATGACCAAAATGCCCCTG

       3739 AGCGTGCGAA


Statistics
Matches: 202,  Mismatches: 28, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  29  202  1.00

ACGTcount: A:0.40, C:0.24, G:0.17, T:0.19


Consensus pattern (29 bp):   
TATGCAAAAATGACCAAAATGCCCCTGGA

Found at i:5777 original size:144 final size:144

Alignment explanation


    Indices: 5517--5802  Score: 563
    Period size: 144  Copynumber: 2.0  Consensus size: 144

       5507 TTAAGTTATT

                                                                             
       5517 TCCATCTTGATGTGGATATGGAATTTTGGTTCAAGTTGGTTTCACAGAGAAAGAATAGGCTCTTT
          1 TCCATCTTGATGTGGATATGGAATTTTGGTTCAAGTTGGTTTCACAGAGAAAGAATAGGCTCTTT

                                                                             
       5582 TAGGACATAGGCAAAGTCTTGACACAAACCGAAAGACTTTTTCTTGTTTTATTCTTAAAAACCCT
         66 TAGGACATAGGCAAAGTCTTGACACAAACCGAAAGACTTTTTCTTGTTTTATTCTTAAAAACCCT

                          
       5647 CTTCATTCCTTTGG
        131 CTTCATTCCTTTGG

                                                       *                     
       5661 TCCATCTTGATGTGGATATGGAATTTTGGTTCAAGTTGGTTTCGCAGAGAAAGAATAGGCTCTTT
          1 TCCATCTTGATGTGGATATGGAATTTTGGTTCAAGTTGGTTTCACAGAGAAAGAATAGGCTCTTT

                                                                             
       5726 TAGGACATAGGCAAAGTCTTGACACAAACCGAAAGACTTTTTCTTGTTTTATTCTTAAAAACCCT
         66 TAGGACATAGGCAAAGTCTTGACACAAACCGAAAGACTTTTTCTTGTTTTATTCTTAAAAACCCT

                        
       5791 CTTCATTCCTTT
        131 CTTCATTCCTTT

       5803 AGTCGTTGCC


Statistics
Matches: 141,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
 144  141  1.00

ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36


Consensus pattern (144 bp):   
TCCATCTTGATGTGGATATGGAATTTTGGTTCAAGTTGGTTTCACAGAGAAAGAATAGGCTCTTT
TAGGACATAGGCAAAGTCTTGACACAAACCGAAAGACTTTTTCTTGTTTTATTCTTAAAAACCCT
CTTCATTCCTTTGG
Done.