Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017981.1 Corchorus olitorius cultivar O-4 contig18014, 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: 10146
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31


Found at i:8197 original size:2 final size:2

Alignment explanation


    Indices: 8192--8226  Score: 52
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       8182 GTGTGTGCAT

                                                 *     *        
       8192 GA GA GA GA GA GA GA GA GA GA GA GA GG GA GG GA GA G
          1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G

       8227 CTTTCCAAGA


Statistics
Matches: 29,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00


Consensus pattern (2 bp):   
GA

Found at i:8325 original size:8 final size:7

Alignment explanation


    Indices: 8312--8371  Score: 57
    Period size: 8  Copynumber: 8.0  Consensus size: 7

       8302 ACAAGTTTTC

                    
       8312 AAAAAGTA
          1 AAAAAG-A

                   
       8320 AAAAAGA
          1 AAAAAGA

                *  
       8327 AAAAGGA
          1 AAAAAGA

             *     
       8334 AGAAAGA
          1 AAAAAGA

                    
       8341 AAGAAAGA
          1 AA-AAAGA

                    
       8349 AAGAAAGA
          1 AA-AAAGA

                    
       8357 AAGAAAGA
          1 AA-AAAGA

              *    
       8365 AAGAAGA
          1 AAAAAGA

       8372 GAGACAGTTC


Statistics
Matches: 46,  Mismatches: 5, Indels: 3
        0.85            0.09        0.06

Matches are distributed among these distances:
   7   17  0.37
   8   29  0.63

ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02


Consensus pattern (7 bp):   
AAAAAGA

Found at i:8342 original size:4 final size:4

Alignment explanation


    Indices: 8328--8369  Score: 75
    Period size: 4  Copynumber: 10.5  Consensus size: 4

       8318 TAAAAAAGAA

                 *                                              
       8328 AAAG GAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AA
          1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AA

       8370 GAGAGACAGT


Statistics
Matches: 36,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   4   36  1.00

ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00


Consensus pattern (4 bp):   
AAAG

Done.