Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016762.1 Corchorus olitorius cultivar O-4 contig16795, 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: 13266
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32


Found at i:387 original size:36 final size:36

Alignment explanation


    Indices: 347--416  Score: 113
    Period size: 36  Copynumber: 1.9  Consensus size: 36

        337 GAGATTTTGG

                         *      *               
        347 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
          1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA

                                       *      
        383 AGAAATATGATAACCAAAATCACAAAAGATGTAA
          1 AGAAATATGATAACCAAAATCACAAAAAATGTAA

        417 GGTTATTGAA


Statistics
Matches: 31,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  36   31  1.00

ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21


Consensus pattern (36 bp):   
AGAAATATGATAACCAAAATCACAAAAAATGTAATA

Found at i:3296 original size:2 final size:2

Alignment explanation


    Indices: 3289--3318  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       3279 CTTTAACTAG

                                                        
       3289 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

       3319 ATGATTTTTT


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:3619 original size:13 final size:13

Alignment explanation


    Indices: 3601--3638  Score: 51
    Period size: 13  Copynumber: 2.8  Consensus size: 13

       3591 AAGTAATAAT

                         
       3601 AACAAAAAGAAAA
          1 AACAAAAAGAAAA

                           
       3614 AACAAAAAGACCAAA
          1 AACAAAAAGA--AAA

                       
       3629 AA-AAAAAGAA
          1 AACAAAAAGAA

       3639 TTCAGAAATG


Statistics
Matches: 23,  Mismatches: 0, Indels: 5
        0.82            0.00        0.18

Matches are distributed among these distances:
  12    1  0.04
  13   10  0.43
  14    7  0.30
  15    5  0.22

ACGTcount: A:0.82, C:0.11, G:0.08, T:0.00


Consensus pattern (13 bp):   
AACAAAAAGAAAA

Found at i:5877 original size:22 final size:21

Alignment explanation


    Indices: 5852--5895  Score: 61
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       5842 TGGTCAAGCA

                      *           
       5852 TGATAGGGAATGAATTTTGCTT
          1 TGAT-GGGAAAGAATTTTGCTT

                *                
       5874 TGATTGGAAAGAATTTTGCTT
          1 TGATGGGAAAGAATTTTGCTT

             
       5895 T
          1 T

       5896 AAATAGACAA


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  21   16  0.80
  22    4  0.20

ACGTcount: A:0.27, C:0.05, G:0.25, T:0.43


Consensus pattern (21 bp):   
TGATGGGAAAGAATTTTGCTT

Found at i:12085 original size:25 final size:25

Alignment explanation


    Indices: 12057--12106  Score: 82
    Period size: 25  Copynumber: 2.0  Consensus size: 25

      12047 GCTTCGCTGC

                              *      
      12057 GGGTTTTTCATGGTTAATGAAGTGT
          1 GGGTTTTTCATGGTTAATAAAGTGT

                    *                
      12082 GGGTTTTTTATGGTTAATAAAGTGT
          1 GGGTTTTTCATGGTTAATAAAGTGT

      12107 TTGTGATTAT


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  25   23  1.00

ACGTcount: A:0.22, C:0.02, G:0.30, T:0.46


Consensus pattern (25 bp):   
GGGTTTTTCATGGTTAATAAAGTGT
Done.