Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013579.1 Corchorus olitorius cultivar O-4 contig13612, 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: 4110
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33


Found at i:2790 original size:10 final size:9

Alignment explanation


    Indices: 2766--2823  Score: 50
    Period size: 10  Copynumber: 6.4  Consensus size: 9

       2756 ATTTCTTACC

                 *   
       2766 CTTATCTTT
          1 CTTATTTTT

                     
       2775 -TTATTTTT
          1 CTTATTTTT

                      
       2783 CGTTATTTTT
          1 C-TTATTTTT

                      
       2793 CTT-TTTCTT
          1 CTTATTT-TT

                     
       2802 -TTATTTTT
          1 CTTATTTTT

             *        
       2810 GTTTATTTTT
          1 -CTTATTTTT

                
       2820 CTTA
          1 CTTA

       2824 GTTACTTTTA


Statistics
Matches: 41,  Mismatches: 2, Indels: 12
        0.75            0.04        0.22

Matches are distributed among these distances:
   8   14  0.34
   9   10  0.24
  10   17  0.41

ACGTcount: A:0.10, C:0.10, G:0.03, T:0.76


Consensus pattern (9 bp):   
CTTATTTTT

Found at i:2797 original size:16 final size:17

Alignment explanation


    Indices: 2772--2809  Score: 51
    Period size: 16  Copynumber: 2.3  Consensus size: 17

       2762 TACCCTTATC

                             
       2772 TTTTTATTTTTC-GTTA
          1 TTTTTATTTTTCTGTTA

                 *       *   
       2788 TTTTTCTTTTTCTTTTA
          1 TTTTTATTTTTCTGTTA

                 
       2805 TTTTT
          1 TTTTT

       2810 GTTTATTTTT


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  16   11  0.58
  17    8  0.42

ACGTcount: A:0.08, C:0.08, G:0.03, T:0.82


Consensus pattern (17 bp):   
TTTTTATTTTTCTGTTA

Found at i:3988 original size:21 final size:21

Alignment explanation


    Indices: 3949--3997  Score: 55
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       3939 TCAATGCTTT

                         **       
       3949 AGGAATGCAAGAGGGATTTCAA
          1 AGGAA-GCAAGAGCCATTTCAA

                               * 
       3971 AGGAAGCAAGAGCCATTTCCA
          1 AGGAAGCAAGAGCCATTTCAA

                   
       3992 A-GAAGC
          1 AGGAAGC

       3998 TACAATTCTC


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  20    5  0.21
  21   14  0.58
  22    5  0.21

ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14


Consensus pattern (21 bp):   
AGGAAGCAAGAGCCATTTCAA
Done.