Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022219.1 Corchorus olitorius cultivar O-4 contig22252, 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: 11759
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30


Found at i:6901 original size:16 final size:16

Alignment explanation


    Indices: 6880--6916  Score: 65
    Period size: 16  Copynumber: 2.3  Consensus size: 16

       6870 GTTTTGGCGG

                            
       6880 AAAAAGAAAATAAAAT
          1 AAAAAGAAAATAAAAT

                          * 
       6896 AAAAAGAAAATAAAGT
          1 AAAAAGAAAATAAAAT

                 
       6912 AAAAA
          1 AAAAA

       6917 CCCATTAACC


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  16   20  1.00

ACGTcount: A:0.81, C:0.00, G:0.08, T:0.11


Consensus pattern (16 bp):   
AAAAAGAAAATAAAAT

Found at i:8011 original size:24 final size:24

Alignment explanation


    Indices: 7980--8064  Score: 95
    Period size: 24  Copynumber: 3.7  Consensus size: 24

       7970 GAATTTGGGT

                     *              
       7980 GAAAATGTAAAAGAAAATGTTGTG
          1 GAAAATGTAGAAGAAAATGTTGTG

               *       **   *       
       8004 GAAGATGTAGATCAAACTG-T-T-
          1 GAAAATGTAGAAGAAAATGTTGTG

                   *                
       8025 GAAAATGCAGAAGAAAATGTTGTG
          1 GAAAATGTAGAAGAAAATGTTGTG

                            
       8049 GAAAATGTAGAAGAAA
          1 GAAAATGTAGAAGAAA

       8065 GTGCTGCAGA


Statistics
Matches: 47,  Mismatches: 11, Indels: 6
        0.73            0.17        0.09

Matches are distributed among these distances:
  21   14  0.30
  22    2  0.04
  23    2  0.04
  24   29  0.62

ACGTcount: A:0.48, C:0.04, G:0.26, T:0.22


Consensus pattern (24 bp):   
GAAAATGTAGAAGAAAATGTTGTG

Found at i:8220 original size:12 final size:12

Alignment explanation


    Indices: 8198--8330  Score: 167
    Period size: 12  Copynumber: 11.1  Consensus size: 12

       8188 CTCCAGATCC

                        
       8198 AGTTGAGGAAAG
          1 AGTTGAGGAAAG

                * *     
       8210 AGTTCATGAAAG
          1 AGTTGAGGAAAG

                  *     
       8222 AGTTGAAGAAAG
          1 AGTTGAGGAAAG

                        
       8234 AGTTGAGGAAAG
          1 AGTTGAGGAAAG

                  *  *  
       8246 AGTTGAAGACAG
          1 AGTTGAGGAAAG

                *       
       8258 AGTTCAGGAAAG
          1 AGTTGAGGAAAG

                *       
       8270 AGTTCAGGAAAG
          1 AGTTGAGGAAAG

                  *   * 
       8282 AGTTGAAGAACG
          1 AGTTGAGGAAAG

                        
       8294 AGTTGAGGAAAG
          1 AGTTGAGGAAAG

                  *     
       8306 AGTTGAAGAAAG
          1 AGTTGAGGAAAG

                *       
       8318 AGTTCAGGAAAG
          1 AGTTGAGGAAAG

             
       8330 A
          1 A

       8331 ATGGAGGAAG


Statistics
Matches: 103,  Mismatches: 18, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  12  103  1.00

ACGTcount: A:0.44, C:0.05, G:0.35, T:0.17


Consensus pattern (12 bp):   
AGTTGAGGAAAG

Done.