Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017297.1 Corchorus olitorius cultivar O-4 contig17330, 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: 5079
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:662 original size:15 final size:15

Alignment explanation


    Indices: 632--673  Score: 75
    Period size: 15  Copynumber: 2.7  Consensus size: 15

        622 TTACTTTGCT

                            
        632 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                           
        648 TTGTTTTCTGTTTAA
          1 TTGTTTTCTGTTTAA

                       
        663 TTGTTTTCTGT
          1 TTGTTTTCTGT

        674 CAACCTCTGT


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   17  0.65
  16    9  0.35

ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:3399 original size:41 final size:41

Alignment explanation


    Indices: 3349--3442  Score: 161
    Period size: 41  Copynumber: 2.3  Consensus size: 41

       3339 CACATAAGGC

                                                     
       3349 CCGGCCAGGACCGGCCATGCAGAGCCGCAAAACAAGCTAGG
          1 CCGGCCAGGACCGGCCATGCAGAGCCGCAAAACAAGCTAGG

                                *    *               
       3390 CCGGCCAGGACCGGCCATGCCGAGCTGCAAAACAAGCTAGG
          1 CCGGCCAGGACCGGCCATGCAGAGCCGCAAAACAAGCTAGG

                   *    
       3431 CCGGCCATGACC
          1 CCGGCCAGGACC

       3443 TGGCTACCCG


Statistics
Matches: 50,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  41   50  1.00

ACGTcount: A:0.27, C:0.36, G:0.31, T:0.06


Consensus pattern (41 bp):   
CCGGCCAGGACCGGCCATGCAGAGCCGCAAAACAAGCTAGG

Found at i:3678 original size:16 final size:16

Alignment explanation


    Indices: 3657--3702  Score: 83
    Period size: 16  Copynumber: 2.9  Consensus size: 16

       3647 TTTCTTTGCA

                            
       3657 TGCTTTGATTGATTAT
          1 TGCTTTGATTGATTAT

                            
       3673 TGCTTTGATTGATTAT
          1 TGCTTTGATTGATTAT

              *           
       3689 TGTTTTGATTGATT
          1 TGCTTTGATTGATT

       3703 GCCTATTTCT


Statistics
Matches: 29,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  16   29  1.00

ACGTcount: A:0.17, C:0.04, G:0.20, T:0.59


Consensus pattern (16 bp):   
TGCTTTGATTGATTAT
Done.