Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009144.1 Corchorus capsularis cultivar CVL-1 contig09165, 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: 30913
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:4054 original size:108 final size:108

Alignment explanation


    Indices: 3865--4082  Score: 418
    Period size: 108  Copynumber: 2.0  Consensus size: 108

       3855 TTCTTCCTTG

                                                                             
       3865 TCTCGTCTTGAACTCGAGGATTTTGCAGGGCTCTTGGGTTCCATTTTCTCCTCTGCAGAGATGTC
          1 TCTCGTCTTGAACTCGAGGATTTTGCAGGGCTCTTGGGTTCCATTTTCTCCTCTGCAGAGATGTC

                                                       
       3930 TCCTCCTGTCAAACCCCCAGATCCCCACGCTATTCTCAACTTC
         66 TCCTCCTGTCAAACCCCCAGATCCCCACGCTATTCTCAACTTC

                                                             *          *    
       3973 TCTCGTCTTGAACTCGAGGATTTTGCAGGGCTCTTGGGTTCCATTTTCTTCTCTGCAGAGTTGTC
          1 TCTCGTCTTGAACTCGAGGATTTTGCAGGGCTCTTGGGTTCCATTTTCTCCTCTGCAGAGATGTC

                                                       
       4038 TCCTCCTGTCAAACCCCCAGATCCCCACGCTATTCTCAACTTC
         66 TCCTCCTGTCAAACCCCCAGATCCCCACGCTATTCTCAACTTC

              
       4081 TC
          1 TC

       4083 AAGATTCTCG


Statistics
Matches: 108,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
 108  108  1.00

ACGTcount: A:0.16, C:0.33, G:0.17, T:0.33


Consensus pattern (108 bp):   
TCTCGTCTTGAACTCGAGGATTTTGCAGGGCTCTTGGGTTCCATTTTCTCCTCTGCAGAGATGTC
TCCTCCTGTCAAACCCCCAGATCCCCACGCTATTCTCAACTTC

Found at i:19947 original size:2 final size:2

Alignment explanation


    Indices: 19935--19967  Score: 57
    Period size: 2  Copynumber: 16.0  Consensus size: 2

      19925 AGATTAAGTG

                                                            
      19935 TA TA CTA 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

      19968 GTATTAATTG


Statistics
Matches: 30,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   2   28  0.93
   3    2  0.07

ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48


Consensus pattern (2 bp):   
TA

Found at i:26739 original size:78 final size:78

Alignment explanation


    Indices: 26650--26896  Score: 370
    Period size: 78  Copynumber: 3.2  Consensus size: 78

      26640 GTTTTTTAAT

                          **                     *  *                        
      26650 TAAAATAGTAAAATATTAAAATATAATAGTTATAAGGTTAATAGATTTAATTATATAAAAATAGA
          1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA

                        *
      26715 GTTTTTAGTTGAA
         66 GTTTTTAGTTGAG

                  *             *                                            
      26728 TAAAATTGTAAAATGGTAAAGTATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
          1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA

                         
      26793 GTTTTTAGTTGAG
         66 GTTTTTAGTTGAG

                                   *           *       *         *           
      26806 TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTATATTTAATTAAATAAAAATAGA
          1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA

                    *    
      26871 GTTTTTAGCTGAG
         66 GTTTTTAGTTGAG

                          
      26884 TAAAACTA-TAAAA
          1 TAAAA-TAGTAAAA

      26897 ACCTAAACAA


Statistics
Matches: 154,  Mismatches: 14, Indels: 2
        0.91            0.08        0.01

Matches are distributed among these distances:
  78  152  0.99
  79    2  0.01

ACGTcount: A:0.50, C:0.01, G:0.13, T:0.36


Consensus pattern (78 bp):   
TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
GTTTTTAGTTGAG
Done.