Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010974.1 Corchorus olitorius cultivar O-4 contig11006, 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: 1809
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28


Found at i:281 original size:154 final size:154

Alignment explanation


    Indices: 1--836  Score: 1379
    Period size: 154  Copynumber: 5.4  Consensus size: 154

                                                  *                    *     
          1 ATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAAAGAGCTAAAAACTTCACAGTGCACTAA
          1 ATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA

                             *       *      *             *                  
         66 TCTCACCAAAATGATTACAGTTAGTTCATAAATAATGGAAAGAAAAACATTGAGGTTTGCCAAAT
         66 TCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAAT

                                    
        131 CGAAGACGATTCAAAACGGAACTA
        131 CGAAGACGATTCAAAACGGAACTA

                                                                    **       
        155 ATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACACAGGACTAA
          1 ATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA

                                                 *                           
        220 TCTCACCAAAATGATTATAGTTACG-CCATAAACAATCGAAAGAAAAGCATTGAGGTTTGCCAAA
         66 TCTCACCAAAATGATTATAGTTA-GTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAA

                        *          * 
        284 TCGAAGACGATTAAAAACGGAACAA
        130 TCGAAGACGATTCAAAACGGAACTA

                   *                               *            *            
        309 ATGGGCCGCGATAGGCCCAAAATAACAAGTGTTCCAAATAAGCTAAAAACTTAACAGTGGACTAA
          1 ATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA

                                                                             
        374 TCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAAT
         66 TCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAAT

                                    
        439 CGAAGACGATTCAAAACGGAACTA
        131 CGAAGACGATTCAAAACGGAACTA

                                                 *        *       *          
        463 ATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAATTGAGCTAAGAACTTCATAGTGGACTAA
          1 ATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA

                 *      *           *             *          *               
        528 TCTCATCAAAATCATTATAGTTAGGCCATAAACAACT-TAAAGAAAAGCTTTGAGGTTTGCCAAA
         66 TCTCACCAAAATGATTATAGTTAGTCCATAAACAA-TGGAAAGAAAAGCATTGAGGTTTGCCAAA

                    *        *       
        592 TCGAAGACTATTCAAAATGGAACTA
        130 TCGAAGACGATTCAAAACGGAACTA

                                                                             
        617 ATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
          1 ATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA

                            *               *                                
        682 TCTCACCAAAATGATTGTAGTTAGTCCATAAAAAATGGAAAGAAAAGCATTGAGGTTTGCCAAAT
         66 TCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAAT

                                    
        747 CGAAGACGATTCAAAACGGAACTA
        131 CGAAGACGATTCAAAACGGAACTA

                           *  *                                          *   
        771 ATGGGCCCCGATAGGTCCGAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAGTAA
          1 ATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA

             
        836 T
         66 T

        837 GATGCGCCAA


Statistics
Matches: 631,  Mismatches: 47, Indels: 8
        0.92            0.07        0.01

Matches are distributed among these distances:
 153    2  0.00
 154  627  0.99
 155    2  0.00

ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21


Consensus pattern (154 bp):   
ATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
TCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAAT
CGAAGACGATTCAAAACGGAACTA

Found at i:971 original size:21 final size:21

Alignment explanation


    Indices: 945--986  Score: 75
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        935 TAAGGAAGAA

                                 
        945 GTTTCAAGCTCATCAGAGTTG
          1 GTTTCAAGCTCATCAGAGTTG

                          *      
        966 GTTTCAAGCTCATCGGAGTTG
          1 GTTTCAAGCTCATCAGAGTTG

        987 CCTAAGATGT


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.21, C:0.19, G:0.26, T:0.33


Consensus pattern (21 bp):   
GTTTCAAGCTCATCAGAGTTG
Done.