Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006302.1 Corchorus olitorius cultivar O-4 contig06327, 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: 13543
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.29


Found at i:133 original size:27 final size:27

Alignment explanation


    Indices: 101--183  Score: 103
    Period size: 32  Copynumber: 2.9  Consensus size: 27

         91 AAGCCAAATT

                                       
        101 ACAGATCTTAAGCCCTTAACTCAAACC
          1 ACAGATCTTAAGCCCTTAACTCAAACC

                       *                    
        128 ACAGATCTTAAACCCTTAATTTTACTCAAACC
          1 ACAGATCTTAAGCCCTT-A----ACTCAAACC

             *                      
        160 ATAGATCTTAAGCCCTTAACTCAA
          1 ACAGATCTTAAGCCCTTAACTCAA

        184 CACTTGTTAA


Statistics
Matches: 48,  Mismatches: 3, Indels: 10
        0.79            0.05        0.16

Matches are distributed among these distances:
  27   22  0.46
  28    1  0.02
  31    1  0.02
  32   24  0.50

ACGTcount: A:0.37, C:0.29, G:0.06, T:0.28


Consensus pattern (27 bp):   
ACAGATCTTAAGCCCTTAACTCAAACC

Found at i:642 original size:20 final size:20

Alignment explanation


    Indices: 619--658  Score: 71
    Period size: 20  Copynumber: 2.0  Consensus size: 20

        609 GAGAGAAAAG

                                
        619 CGACGGAGAGAAGAGAGATT
          1 CGACGGAGAGAAGAGAGATT

                          *     
        639 CGACGGAGAGAAGATAGATT
          1 CGACGGAGAGAAGAGAGATT

        659 TGTCAAATTC


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.40, C:0.10, G:0.38, T:0.12


Consensus pattern (20 bp):   
CGACGGAGAGAAGAGAGATT

Found at i:7497 original size:13 final size:13

Alignment explanation


    Indices: 7479--7503  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       7469 AGCAGTTAGC

                         
       7479 AAGAAAGGAGAAG
          1 AAGAAAGGAGAAG

                        
       7492 AAGAAAGGAGAA
          1 AAGAAAGGAGAA

       7504 TATTCGAACT


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00


Consensus pattern (13 bp):   
AAGAAAGGAGAAG

Found at i:12772 original size:31 final size:31

Alignment explanation


    Indices: 12734--12795  Score: 88
    Period size: 31  Copynumber: 2.0  Consensus size: 31

      12724 GAGTTTTGTA

                         *   ***           
      12734 AAACTTTTGAATCGCCTGTTATACCCTTATT
          1 AAACTTTTGAATCACCTAACATACCCTTATT

                                           
      12765 AAACTTTTGAATCACCTAACATACCCTTATT
          1 AAACTTTTGAATCACCTAACATACCCTTATT

      12796 TTTTCGAATA


Statistics
Matches: 27,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  31   27  1.00

ACGTcount: A:0.31, C:0.24, G:0.06, T:0.39


Consensus pattern (31 bp):   
AAACTTTTGAATCACCTAACATACCCTTATT
Done.