Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016217.1 Corchorus olitorius cultivar O-4 contig16250, 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: 6658
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:3883 original size:7 final size:7

Alignment explanation


    Indices: 3866--3899  Score: 61
    Period size: 7  Copynumber: 5.0  Consensus size: 7

       3856 TGCTTGTTTT

                   
       3866 CAAAAAA
          1 CAAAAAA

                   
       3873 -AAAAAA
          1 CAAAAAA

                   
       3879 CAAAAAA
          1 CAAAAAA

                   
       3886 CAAAAAA
          1 CAAAAAA

                   
       3893 CAAAAAA
          1 CAAAAAA

       3900 ATACTACCTG


Statistics
Matches: 26,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   6    6  0.23
   7   20  0.77

ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00


Consensus pattern (7 bp):   
CAAAAAA

Found at i:4767 original size:19 final size:19

Alignment explanation


    Indices: 4743--4782  Score: 80
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       4733 TTAGGGATCC

                               
       4743 AGTAGATAATTATTTGAAT
          1 AGTAGATAATTATTTGAAT

                               
       4762 AGTAGATAATTATTTGAAT
          1 AGTAGATAATTATTTGAAT

              
       4781 AG
          1 AG

       4783 ACATTAGAAT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   21  1.00

ACGTcount: A:0.42, C:0.00, G:0.17, T:0.40


Consensus pattern (19 bp):   
AGTAGATAATTATTTGAAT

Found at i:6412 original size:22 final size:22

Alignment explanation


    Indices: 6183--6417  Score: 168
    Period size: 22  Copynumber: 10.5  Consensus size: 22

       6173 CTCCAACGTA

                 *              **
       6183 GAAATATTGATAACCACACTGC
          1 GAAATTTTGATAACCACACTAT

                *   *      *  * * 
       6205 GAAAATTTCATAACCTCATTGT
          1 GAAATTTTGATAACCACACTAT

                   *       * *    
       6227 GAAATTTCGATAACCTCTCTAT
          1 GAAATTTTGATAACCACACTAT

                *             * * 
       6249 GAAAATTTGATAACCACAATGT
          1 GAAATTTTGATAACCACACTAT

                                * 
       6271 GAAATTTTGATAACCACACTGT
          1 GAAATTTTGATAACCACACTAT

                  *            *  
       6293 GAAATTCTGATAACCACACAAT
          1 GAAATTTTGATAACCACACTAT

               *           *          
       6315 GAAGTTTTGATAACCTCATTGTCTAT
          1 GAAATTTTGATAACCACA----CTAT

                         *    *   
       6341 GAAATTTTGATAATCACATTAT
          1 GAAATTTTGATAACCACACTAT

                 *   *   * *      
       6363 -AAA-ATTGGTAATCGCACTAT
          1 GAAATTTTGATAACCACACTAT

                                *  
       6383 GAAAATTTTGATAACCACACCAT
          1 G-AAATTTTGATAACCACACTAT

                   *    
       6406 GAAATTTCGATA
          1 GAAATTTTGATA

       6418 GCTTCCCTAT


Statistics
Matches: 165,  Mismatches: 41, Indels: 14
        0.75            0.19        0.06

Matches are distributed among these distances:
  20   13  0.08
  21    3  0.02
  22  118  0.72
  23   13  0.08
  26   18  0.11

ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32


Consensus pattern (22 bp):   
GAAATTTTGATAACCACACTAT
Done.