Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016470.1 Corchorus olitorius cultivar O-4 contig16503, 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: 9444
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.29


Found at i:4266 original size:16 final size:16

Alignment explanation


    Indices: 4245--4285  Score: 73
    Period size: 16  Copynumber: 2.6  Consensus size: 16

       4235 CATCTCTAGT

                  *         
       4245 ATGTCATAACACTGGG
          1 ATGTCAAAACACTGGG

                            
       4261 ATGTCAAAACACTGGG
          1 ATGTCAAAACACTGGG

                     
       4277 ATGTCAAAA
          1 ATGTCAAAA

       4286 ACTTCCTTTG


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  16   24  1.00

ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22


Consensus pattern (16 bp):   
ATGTCAAAACACTGGG

Found at i:8353 original size:121 final size:122

Alignment explanation


    Indices: 8139--8428  Score: 442
    Period size: 121  Copynumber: 2.4  Consensus size: 122

       8129 AATGTTATGA

                                  *            *         *                   
       8139 CCGACCGGCAGGCGATCGACAAGGACCATCCCTGATCGAGTAT-GAAATGATGAAGCCCTCAAGG
          1 CCGACCGGCAGGCGATCGACAATGACCATCCCTGACCGAGTATGGGAATGATGAAGCCCTCAAGG

                                                *                    
       8203 GGCCCAACGCCAACAGGCGAGCGATCAGGCAAGGCCTAGCTCGACCTAGTATGGCCC
         66 GGCCCAACGCCAACAGGCGAGCGATCAGGCAAGGCCGAGCTCGACCTAGTATGGCCC

                       *      *               *                              
       8260 CCGACCGGCAGACGATCGGCAATGACCAT-CCTGGCCGAGTATGGGAATGATGAAGCCCTCAAGG
          1 CCGACCGGCAGGCGATCGACAATGACCATCCCTGACCGAGTATGGGAATGATGAAGCCCTCAAGG

                          *                                          
       8324 GGCCCAACGCCAACGGGCGAGCGATCAGGCAAGGCCGAGCTCGACCTAGTATGGCCC
         66 GGCCCAACGCCAACAGGCGAGCGATCAGGCAAGGCCGAGCTCGACCTAGTATGGCCC

              * *   *                             *          
       8381 CCCATCGGTAGGCGATCGAC-ATGAACCATCCCTGACCAAGTATGGGAA
          1 CCGACCGGCAGGCGATCGACAATG-ACCATCCCTGACCGAGTATGGGAA

       8429 ATGAAGAAAA


Statistics
Matches: 151,  Mismatches: 15, Indels: 5
        0.88            0.09        0.03

Matches are distributed among these distances:
 120   14  0.09
 121  121  0.80
 122   16  0.11

ACGTcount: A:0.27, C:0.31, G:0.30, T:0.13


Consensus pattern (122 bp):   
CCGACCGGCAGGCGATCGACAATGACCATCCCTGACCGAGTATGGGAATGATGAAGCCCTCAAGG
GGCCCAACGCCAACAGGCGAGCGATCAGGCAAGGCCGAGCTCGACCTAGTATGGCCC

Found at i:8736 original size:25 final size:25

Alignment explanation


    Indices: 8572--8729  Score: 280
    Period size: 25  Copynumber: 6.3  Consensus size: 25

       8562 TCGCATATGT

                      *   **  *      
       8572 AGAACGCCCGCCGAATGCGAAGCGG
          1 AGAACGCCCGTCGAGCGCCAAGCGG

                                     
       8597 AGAACGCCCGTCGAGCGCCAAGCGG
          1 AGAACGCCCGTCGAGCGCCAAGCGG

                                     
       8622 AGAACGCCCGTCGAGCGCCAAGCGG
          1 AGAACGCCCGTCGAGCGCCAAGCGG

                                     
       8647 AGAACGCCCGTCGAGCGCCAAGCGG
          1 AGAACGCCCGTCGAGCGCCAAGCGG

                                     
       8672 AGAACGCCCGTCGAGCGCCAAGCGG
          1 AGAACGCCCGTCGAGCGCCAAGCGG

                                     
       8697 AGAACGCCCGTCGAGCGCCAAGCGG
          1 AGAACGCCCGTCGAGCGCCAAGCGG

                    
       8722 AGAACGCC
          1 AGAACGCC

       8730 TGCCGAGTGA


Statistics
Matches: 129,  Mismatches: 4, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  25  129  1.00

ACGTcount: A:0.25, C:0.35, G:0.35, T:0.04


Consensus pattern (25 bp):   
AGAACGCCCGTCGAGCGCCAAGCGG

Found at i:9055 original size:30 final size:30

Alignment explanation


    Indices: 9021--9098  Score: 149
    Period size: 30  Copynumber: 2.6  Consensus size: 30

       9011 AAGTTCGTGT

                                          
       9021 TTGAAGACCATTTGAAGATAAATTGGAGAC
          1 TTGAAGACCATTTGAAGATAAATTGGAGAC

                                          
       9051 TTGAAGACCATTTGAAGATAAATTGGAGAC
          1 TTGAAGACCATTTGAAGATAAATTGGAGAC

                               
       9081 TTGAAGACCA-TTGAAGAT
          1 TTGAAGACCATTTGAAGAT

       9099 TTATTTCAAG


Statistics
Matches: 48,  Mismatches: 0, Indels: 1
        0.98            0.00        0.02

Matches are distributed among these distances:
  29    8  0.17
  30   40  0.83

ACGTcount: A:0.40, C:0.10, G:0.23, T:0.27


Consensus pattern (30 bp):   
TTGAAGACCATTTGAAGATAAATTGGAGAC
Done.