Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017636.1 Corchorus olitorius cultivar O-4 contig17669, 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: 28976
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:2643 original size:57 final size:56

Alignment explanation


    Indices: 2577--2705  Score: 231
    Period size: 57  Copynumber: 2.3  Consensus size: 56

       2567 ATACATGCCA

                                                    *                
       2577 AATTACTAAAGATTCAATTCAGACATAAGATCAATACTGATCTCAATTCAATAAATT
          1 AATTACTAAAGATTCAATTCAGACATAAGATCAATACTGAAC-CAATTCAATAAATT

             *                                                      
       2634 AGTTACTAAAGATTCAATTCAGACATAAGATCAATACTGAACCAATTCAATAAATT
          1 AATTACTAAAGATTCAATTCAGACATAAGATCAATACTGAACCAATTCAATAAATT

                            
       2690 AATTACTAAAGATTCA
          1 AATTACTAAAGATTCA

       2706 CTAAGATAAC


Statistics
Matches: 69,  Mismatches: 3, Indels: 1
        0.95            0.04        0.01

Matches are distributed among these distances:
  56   29  0.42
  57   40  0.58

ACGTcount: A:0.47, C:0.16, G:0.08, T:0.30


Consensus pattern (56 bp):   
AATTACTAAAGATTCAATTCAGACATAAGATCAATACTGAACCAATTCAATAAATT

Found at i:2954 original size:24 final size:24

Alignment explanation


    Indices: 2902--2957  Score: 62
    Period size: 24  Copynumber: 2.3  Consensus size: 24

       2892 TAACTTATTC

                                    
       2902 AATCAACATCGCATATATAAGACA
          1 AATCAACATCGCATATATAAGACA

            *                *        
       2926 TATCAAGCAT-GCATATTTCAAG-CA
          1 AATCAA-CATCGCATATAT-AAGACA

                    
       2950 AATCAACA
          1 AATCAACA

       2958 CTATTCATCA


Statistics
Matches: 27,  Mismatches: 3, Indels: 5
        0.77            0.09        0.14

Matches are distributed among these distances:
  23    2  0.07
  24   19  0.70
  25    6  0.22

ACGTcount: A:0.46, C:0.21, G:0.09, T:0.23


Consensus pattern (24 bp):   
AATCAACATCGCATATATAAGACA

Found at i:16793 original size:19 final size:18

Alignment explanation


    Indices: 16760--16795  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      16750 TTGAGATAAT

                              
      16760 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
      16778 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

      16796 TAAGTCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA

Found at i:23158 original size:19 final size:18

Alignment explanation


    Indices: 23125--23160  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      23115 TTGAGATAAT

                              
      23125 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
      23143 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

      23161 TAAGTCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA
Done.