Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016610.1 Corchorus olitorius cultivar O-4 contig16643, 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: 15782
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30


Found at i:5546 original size:2 final size:2

Alignment explanation


    Indices: 5539--5567  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       5529 AATGCGGCGC

                                                       
       5539 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       5568 ATTAGCAAGA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:14564 original size:262 final size:262

Alignment explanation


    Indices: 14092--14618  Score: 991
    Period size: 262  Copynumber: 2.0  Consensus size: 262

      14082 GCATCTAATG

                  *                             *                            
      14092 TAGCAATAGGTGCAGTTCTCACTCAAAATGGACATCCTATTGCCTATTTTAGCAAGAAATTATCT
          1 TAGCAACAGGTGCAGTTCTCACTCAAAATGGACATCATATTGCCTATTTTAGCAAGAAATTATCT

                                                                             
      14157 CCAAGTATGCAGAGCGCATCAGCCTATGTGCGTGAGATGTTTGCCATAACTGAAGCAGTCAAAAA
         66 CCAAGTATGCAGAGCGCATCAGCCTATGTGCGTGAGATGTTTGCCATAACTGAAGCAGTCAAAAA

                *                                                            
      14222 ATGGTGGCAATATCTCTTGGGGCGGCCATTTGAGATCTTTACGGACCAGCAGAGTCTTCGGGGCT
        131 ATGGCGGCAATATCTCTTGGGGCGGCCATTTGAGATCTTTACGGACCAGCAGAGTCTTCGGGGCT

                                     *                                       
      14287 TAATGAACCAGACCATACAGACTCCTGAGCAACATAAATGGCTTACAAAGCTTCTGGGATTTCAG
        196 TAATGAACCAGACCATACAGACTCCCGAGCAACATAAATGGCTTACAAAGCTTCTGGGATTTCAG

              
      14352 TA
        261 TA

                                           *                                 
      14354 TAGCAACAGGTGCAGTTCTCACTCAAAATGGGCATCATATTGCCTATTTTAGCAAGAAATTATCT
          1 TAGCAACAGGTGCAGTTCTCACTCAAAATGGACATCATATTGCCTATTTTAGCAAGAAATTATCT

                                 *                                           
      14419 CCAAGTATGCAGAGCGCATCATCCTATGTGCGTGAGATGTTTGCCATAACTGAAGCAGTCAAAAA
         66 CCAAGTATGCAGAGCGCATCAGCCTATGTGCGTGAGATGTTTGCCATAACTGAAGCAGTCAAAAA

                                                                             
      14484 ATGGCGGCAATATCTCTTGGGGCGGCCATTTGAGATCTTTACGGACCAGCAGAGTCTTCGGGGCT
        131 ATGGCGGCAATATCTCTTGGGGCGGCCATTTGAGATCTTTACGGACCAGCAGAGTCTTCGGGGCT

                                                        *                    
      14549 TAATGAACCAGACCATACAGACTCCCGAGCAACATAAATGGCTTGCAAAGCTTCTGGGATTTCAG
        196 TAATGAACCAGACCATACAGACTCCCGAGCAACATAAATGGCTTACAAAGCTTCTGGGATTTCAG

              
      14614 TA
        261 TA

               
      14616 TAG
          1 TAG

      14619 TATTCATTAC


Statistics
Matches: 258,  Mismatches: 7, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
 262  258  1.00

ACGTcount: A:0.30, C:0.22, G:0.23, T:0.26


Consensus pattern (262 bp):   
TAGCAACAGGTGCAGTTCTCACTCAAAATGGACATCATATTGCCTATTTTAGCAAGAAATTATCT
CCAAGTATGCAGAGCGCATCAGCCTATGTGCGTGAGATGTTTGCCATAACTGAAGCAGTCAAAAA
ATGGCGGCAATATCTCTTGGGGCGGCCATTTGAGATCTTTACGGACCAGCAGAGTCTTCGGGGCT
TAATGAACCAGACCATACAGACTCCCGAGCAACATAAATGGCTTACAAAGCTTCTGGGATTTCAG
TA
Done.