Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006806.1 Corchorus olitorius cultivar O-4 contig06831, 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, 983

Length: 1639
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.28


Found at i:881 original size:47 final size:47

Alignment explanation


    Indices: 825--1626  Score: 998
    Period size: 47  Copynumber: 16.8  Consensus size: 47

        815 TTAAATCAGA

                             *                          *  
        825 GTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTAATTCCGG
          1 GTAATTAAACTAAAGAGTAAGAGAAGAAGAAAACAGTTTAATTCTGG

                             *                 *           
        872 GTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAATTTAATTCTGG
          1 GTAATTAAACTAAAGAGTAAGAGAAGAAGAAAACAGTTTAATTCTGG

            *                   * *                               
        919 ATAATTAAACTAAAGAGTAAAAAAAGAAGTAAACAGATGCTAGTTTAATTCTGG
          1 GTAATTAAACTAAAGAGTAAGAGAAGAAG--AA-A-A--C-AGTTTAATTCTGG

                          * *                *          *  
        973 GTAATTAAACTAAAAATTAAGAGAAGAAGAAAAGAGTTTAATTCCGG
          1 GTAATTAAACTAAAGAGTAAGAGAAGAAGAAAACAGTTTAATTCTGG

                *         *              *   *           * 
       1020 GTAAGTAAACTAAAAAGTAAGAGAAGAAGGAAAGAGTTTAATTCTAG
          1 GTAATTAAACTAAAGAGTAAGAGAAGAAGAAAACAGTTTAATTCTGG

                                          *   *             
       1067 GTAATTAAACT-AAGAAGTAAGAGAAGAAGGAAAGAGTTTAATTCTGG
          1 GTAATTAAACTAAAG-AGTAAGAGAAGAAGAAAACAGTTTAATTCTGG

                          * *     *          *             
       1114 GTAATTAAACTAAAAATTAAGAAAAGAAGAAAAGAGTTTAATTCTGG
          1 GTAATTAAACTAAAGAGTAAGAGAAGAAGAAAACAGTTTAATTCTGG

                          *  *               *             
       1161 GTAATTAAACTAAATAGCAAGAGAAGAAGAAAAGAGTTTAATTCTGG
          1 GTAATTAAACTAAAGAGTAAGAGAAGAAGAAAACAGTTTAATTCTGG

                   *                      *   *             
       1208 GTAATTATACTATAA-AGTAAGAGAAGAAGGAAAGAGTTTAATTCTGG
          1 GTAATTAAACTA-AAGAGTAAGAGAAGAAGAAAACAGTTTAATTCTGG

                          * *           *                  
       1255 GTAATTAAACTAAAAATTAAGAGAAGAAAAAAACAGTTTAATTCTGG
          1 GTAATTAAACTAAAGAGTAAGAGAAGAAGAAAACAGTTTAATTCTGG

                            ** *               *           
       1302 GTAATTAAACTAAAGAACAGGAGAAGAAGAAAACAATTTAATTCTGG
          1 GTAATTAAACTAAAGAGTAAGAGAAGAAGAAAACAGTTTAATTCTGG

                          *                  *             
       1349 GTAATTAAACTAAAAAGTAAGAGAAGAAGAAAAGAGTTTAATTCTGG
          1 GTAATTAAACTAAAGAGTAAGAGAAGAAGAAAACAGTTTAATTCTGG

                             *                 *           
       1396 GTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAATTTAATTCTGG
          1 GTAATTAAACTAAAGAGTAAGAGAAGAAGAAAACAGTTTAATTCTGG

                                                    **             
       1443 GTAATTAAACTAAAGAGTGAAAGCAGAAGTAA-ACAGAGGTTAGTTTAATTCTGG
          1 GTAATTAAACTAAAGAGT--AAG-AGAAG-AAGA-A-A--ACAGTTTAATTCTGG

                          *              *   *             
       1497 GTAATTAAACTAAAAAGTAAGAGAAGAAGGAAAGAGTTTAATTCTGG
          1 GTAATTAAACTAAAGAGTAAGAGAAGAAGAAAACAGTTTAATTCTGG

                             *    *                        
       1544 GTAATTAAACTAAAGAGCAAGAAAAGAAGAAAACAGTTTAATTCTGG
          1 GTAATTAAACTAAAGAGTAAGAGAAGAAGAAAACAGTTTAATTCTGG

                                *        *      
       1591 GTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAG
          1 GTAATTAAACTAAAGAGTAAGAGAAGAAGAAAACAG

       1627 AGGTTAGTTT


Statistics
Matches: 664,  Mismatches: 71, Indels: 40
        0.86            0.09        0.05

Matches are distributed among these distances:
  46    4  0.01
  47  557  0.84
  48    4  0.01
  49    6  0.01
  50   11  0.02
  51   10  0.02
  52    6  0.01
  53    1  0.00
  54   65  0.10

ACGTcount: A:0.50, C:0.06, G:0.20, T:0.23


Consensus pattern (47 bp):   
GTAATTAAACTAAAGAGTAAGAGAAGAAGAAAACAGTTTAATTCTGG

Done.