Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017596.1 Corchorus olitorius cultivar O-4 contig17629, 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: 11777
ACGTcount: A:0.30, C:0.26, G:0.24, T:0.20


Found at i:6169 original size:76 final size:76

Alignment explanation


    Indices: 5550--6151  Score: 891
    Period size: 76  Copynumber: 7.8  Consensus size: 76

       5540 ATATTTCAAA

                             * *    *          * *                           
       5550 CAACGGCTGAGTGCCTAGACTGGCACCCCCGTTCGCCCACCAGTGAGACAGAGCGTCCACGCAGA
          1 CAACGGCTGAGTGCCTACATTGGCGCCCCCGTTCGTCTACCAGTGAGACAGAGCGTCCACGCAGA

                       
       5615 CGCCGCTCACT
         66 CGCCGCTCACT

                                          *                                  
       5626 CAACGGCTGAGTGCCTACATTGGCGCCCCCATTCGTCTACCAGTGAGACAGAGCGTCCACGCAGA
          1 CAACGGCTGAGTGCCTACATTGGCGCCCCCGTTCGTCTACCAGTGAGACAGAGCGTCCACGCAGA

              *        
       5691 CGTCGCTCACT
         66 CGCCGCTCACT

                     *                *               *                  *   
       5702 CAACGGCTGGGTGCCTACATTGGCGCGCCCGTTCGTCTACCAATGAGACAGAGCGTCCACGTAGA
          1 CAACGGCTGAGTGCCTACATTGGCGCCCCCGTTCGTCTACCAGTGAGACAGAGCGTCCACGCAGA

                       
       5767 CGCCGCTCACT
         66 CGCCGCTCACT

                                                        *            *   * * 
       5778 CAACGGCTGAGTGCCTACATTGGCGCCCCCGTTCGTCTACCAGTAAGACAGAGCGTCTACGTAAA
          1 CAACGGCTGAGTGCCTACATTGGCGCCCCCGTTCGTCTACCAGTGAGACAGAGCGTCCACGCAGA

                   *   
       5843 CGCCGCTTACT
         66 CGCCGCTCACT

                     *                                  * *                  
       5854 CAACGGCTGGGTGCCTACATTGGCGCCCCCGTTCCCCGTTCGCCCATCAGTGAGACAGAGCGTCC
          1 CAACGGCTGAGTGCCTACATTGGCGCCCCCGTT---CG-T---CTACCAGTGAGACAGAGCGTCC

                              
       5919 ACGCAGACGCCGCTCACT
         59 ACGCAGACGCCGCTCACT

                 *                           *                               
       5937 CAACGACTGAGTGCCTACATTGGCGCCCCCGTTTGTCTACCAGTGAGACAGAGCGTCCACGCAGA
          1 CAACGGCTGAGTGCCTACATTGGCGCCCCCGTTCGTCTACCAGTGAGACAGAGCGTCCACGCAGA

            *          
       6002 AGCCGCTCACT
         66 CGCCGCTCACT

                                                                             
       6013 CAACGGCTGAGTGCCTACATTGGCGCCCCCGTTCGTCTACCAGTGAGACAGAGCGTCCACGCAGA
          1 CAACGGCTGAGTGCCTACATTGGCGCCCCCGTTCGTCTACCAGTGAGACAGAGCGTCCACGCAGA

                   *   
       6078 CGCCGCTTACT
         66 CGCCGCTCACT

                     *                   *                       *          
       6089 CAACGGCTGGGTGCCTACATTGGCGCCCCTGTTCGTCTACCAGTGAGACCA-AACGTCCACGCA
          1 CAACGGCTGAGTGCCTACATTGGCGCCCCCGTTCGTCTACCAGTGAGA-CAGAGCGTCCACGCA

       6152 ACCTCCACTC


Statistics
Matches: 477,  Mismatches: 41, Indels: 16
        0.89            0.08        0.03

Matches are distributed among these distances:
  76  406  0.85
  77    2  0.00
  79    3  0.01
  80    2  0.00
  83   64  0.13

ACGTcount: A:0.20, C:0.36, G:0.26, T:0.18


Consensus pattern (76 bp):   
CAACGGCTGAGTGCCTACATTGGCGCCCCCGTTCGTCTACCAGTGAGACAGAGCGTCCACGCAGA
CGCCGCTCACT

Found at i:7954 original size:12 final size:12

Alignment explanation


    Indices: 7937--7966  Score: 51
    Period size: 12  Copynumber: 2.5  Consensus size: 12

       7927 GCACCACGAC

                      * 
       7937 GAGCAGCAGGGG
          1 GAGCAGCAGGAG

                        
       7949 GAGCAGCAGGAG
          1 GAGCAGCAGGAG

                  
       7961 GAGCAG
          1 GAGCAG

       7967 GATTGTAAGT


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  12   17  1.00

ACGTcount: A:0.30, C:0.17, G:0.53, T:0.00


Consensus pattern (12 bp):   
GAGCAGCAGGAG

Found at i:9970 original size:22 final size:22

Alignment explanation


    Indices: 9942--9984  Score: 77
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       9932 CCAACTTCCG

                            *     
       9942 AAATTCAAATTTTGAATTTTCA
          1 AAATTCAAATTTTGAAATTTCA

                                 
       9964 AAATTCAAATTTTGAAATTTC
          1 AAATTCAAATTTTGAAATTTC

       9985 GCGCCAAAAA


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

Matches are distributed among these distances:
  22   20  1.00

ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44


Consensus pattern (22 bp):   
AAATTCAAATTTTGAAATTTCA

Found at i:11743 original size:2 final size:2

Alignment explanation


    Indices: 11736--11769  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

      11726 AACTCGTATT

                                                              
      11736 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      11770 GTAATAAT


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Done.