Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017063.1 Corchorus olitorius cultivar O-4 contig17096, 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: 10902
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.30


Found at i:1581 original size:76 final size:76

Alignment explanation


    Indices: 1431--1574  Score: 177
    Period size: 76  Copynumber: 1.9  Consensus size: 76

       1421 ACAAGGACCC

                                                               *           * 
       1431 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
          1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT

                       
       1496 GGGCAGTGTCA
         66 GGGCAGTGTCA

                    *     *              *                            **     
       1507 CGACTCCAGCTGGGTGCCCACATGGTT-CGTCTGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
          1 CGACTCCACCTGGGCGCCCACATGGTTGCCT-TG-AGCACCCATGTGGTTT-GCCTGAGAACCCA

                  
       1569 GATGGG
         63 GATGGG

       1575 TTGTGTCTTA


Statistics
Matches: 58,  Mismatches: 7, Indels: 6
        0.82            0.10        0.08

Matches are distributed among these distances:
  75    6  0.10
  76   50  0.86
  77    2  0.03

ACGTcount: A:0.17, C:0.31, G:0.29, T:0.23


Consensus pattern (76 bp):   
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA

Found at i:8715 original size:10 final size:10

Alignment explanation


    Indices: 8697--8748  Score: 68
    Period size: 10  Copynumber: 5.1  Consensus size: 10

       8687 AAAAGTAACT

                      
       8697 AAGAAAAATA
          1 AAGAAAAATA

              *        
       8707 AATAAAAATAA
          1 AAGAAAAAT-A

                      
       8718 AAGAAAAATA
          1 AAGAAAAATA

             *        
       8728 ACGAAAAATA
          1 AAGAAAAATA

             *        
       8738 ACGAAAAATA
          1 AAGAAAAATA

             
       8748 A
          1 A

       8749 TAAAAAGATA


Statistics
Matches: 38,  Mismatches: 3, Indels: 2
        0.88            0.07        0.05

Matches are distributed among these distances:
  10   29  0.76
  11    9  0.24

ACGTcount: A:0.77, C:0.04, G:0.08, T:0.12


Consensus pattern (10 bp):   
AAGAAAAATA

Found at i:8722 original size:21 final size:20

Alignment explanation


    Indices: 8697--8754  Score: 73
    Period size: 21  Copynumber: 2.9  Consensus size: 20

       8687 AAAAGTAACT

                                 
       8697 AAGAAAAATAAATAAAAATAA
          1 AAGAAAAATAAATAAAAAT-A

                       **       
       8718 AAGAAAAATAACGAAAAATA
          1 AAGAAAAATAAATAAAAATA

             *                
       8738 ACGAAAAAT-AATAAAAA
          1 AAGAAAAATAAATAAAAA

       8755 GATAAGGATA


Statistics
Matches: 32,  Mismatches: 5, Indels: 2
        0.82            0.13        0.05

Matches are distributed among these distances:
  19    6  0.19
  20    9  0.28
  21   17  0.53

ACGTcount: A:0.78, C:0.03, G:0.07, T:0.12


Consensus pattern (20 bp):   
AAGAAAAATAAATAAAAATA

Found at i:8754 original size:10 final size:10

Alignment explanation


    Indices: 8700--8759  Score: 50
    Period size: 10  Copynumber: 5.8  Consensus size: 10

       8690 AGTAACTAAG

                      
       8700 AAAAATAA-A
          1 AAAAATAACA

                     * 
       8709 TAAAAATAAAA
          1 -AAAAATAACA

                      *
       8720 GAAAAATAACG
          1 -AAAAATAACA

                     *
       8731 AAAAATAACG
          1 AAAAATAACA

                    * 
       8741 AAAAATAATA
          1 AAAAATAACA

                     
       8751 AAAAGATAA
          1 AAAA-ATAA

       8760 GGATAAGAAA


Statistics
Matches: 43,  Mismatches: 5, Indels: 3
        0.84            0.10        0.06

Matches are distributed among these distances:
  10   30  0.70
  11   13  0.30

ACGTcount: A:0.77, C:0.03, G:0.07, T:0.13


Consensus pattern (10 bp):   
AAAAATAACA

Found at i:10484 original size:76 final size:76

Alignment explanation


    Indices: 10334--10477  Score: 177
    Period size: 76  Copynumber: 1.9  Consensus size: 76

      10324 ACAAGGACCC

                                                               *           * 
      10334 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
          1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT

                       
      10399 GGGCAGTGTCA
         66 GGGCAGTGTCA

                    *     *              *                            **     
      10410 CGACTCCAGCTGGGTGCCCACATGGTT-CGTCTGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
          1 CGACTCCACCTGGGCGCCCACATGGTTGCCT-TG-AGCACCCATGTGGTTT-GCCTGAGAACCCA

                  
      10472 GATGGG
         63 GATGGG

      10478 TTGTGTCTTA


Statistics
Matches: 58,  Mismatches: 7, Indels: 6
        0.82            0.10        0.08

Matches are distributed among these distances:
  75    6  0.10
  76   50  0.86
  77    2  0.03

ACGTcount: A:0.17, C:0.31, G:0.29, T:0.23


Consensus pattern (76 bp):   
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Done.