Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016952.1 Corchorus olitorius cultivar O-4 contig16985, 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: 5320
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30


Found at i:4384 original size:13 final size:13

Alignment explanation


    Indices: 4366--4392  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

       4356 AAATTAAAAA

                         
       4366 AAAAAGAAGAAGG
          1 AAAAAGAAGAAGG

                         
       4379 AAAAAGAAGAAGG
          1 AAAAAGAAGAAGG

             
       4392 A
          1 A

       4393 GGAAAAATGG


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00


Consensus pattern (13 bp):   
AAAAAGAAGAAGG

Found at i:4388 original size:16 final size:16

Alignment explanation


    Indices: 4363--4399  Score: 56
    Period size: 16  Copynumber: 2.3  Consensus size: 16

       4353 TTTAAATTAA

                            
       4363 AAAAAAAAGAAGAAGG
          1 AAAAAAAAGAAGAAGG

                 *      *   
       4379 AAAAAGAAGAAGGAGG
          1 AAAAAAAAGAAGAAGG

                 
       4395 AAAAA
          1 AAAAA

       4400 TGGGCTAGGC


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  16   19  1.00

ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00


Consensus pattern (16 bp):   
AAAAAAAAGAAGAAGG

Found at i:5310 original size:27 final size:28

Alignment explanation


    Indices: 5242--5314  Score: 87
    Period size: 28  Copynumber: 2.6  Consensus size: 28

       5232 TTAATATGTC

                    *         *      *  
       5242 AAAATTACTGTTTTACCCTTGGTCGGCT
          1 AAAATTACAGTTTTACCCCTGGTCGACT

                                    *    
       5270 AAAATTACCA-TTTTACCCCTGGTTGACT
          1 AAAATTA-CAGTTTTACCCCTGGTCGACT

                              
       5298 -AAATTACAGTTTTACCC
          1 AAAATTACAGTTTTACCC

       5315 TTAAAT


Statistics
Matches: 39,  Mismatches: 4, Indels: 5
        0.81            0.08        0.10

Matches are distributed among these distances:
  26    2  0.05
  27   14  0.36
  28   22  0.56
  29    1  0.03

ACGTcount: A:0.27, C:0.23, G:0.12, T:0.37


Consensus pattern (28 bp):   
AAAATTACAGTTTTACCCCTGGTCGACT
Done.