Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013812.1 Corchorus olitorius cultivar O-4 contig13845, 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: 5296
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29


Found at i:3540 original size:78 final size:77

Alignment explanation


    Indices: 3406--3622  Score: 312
    Period size: 78  Copynumber: 2.8  Consensus size: 77

       3396 GGCCACAGCA

                *                                           *                
       3406 CCAGGGCAGAGGCCCGACTGCCGCTGGGCGCCCAGGCAGAACGCCCAAACGCCCAGGCGACAGGC
          1 CCAGAGCAGA-GCCCGACTGCCGCTGGGCGCCCAGGCAGAACGCCCAAGCGCCCAGGCGACAGGC

                  *      
       3471 ACCCAGGCCCCAG
         65 ACCCAGACCCCAG

                                                                             
       3484 CCAGAGCAGAGACCCGACTGCCGCTGGGCGCCCAGGCAGAACGCCCAAGCGCCCAGGCGACAGGC
          1 CCAGAGCAGAG-CCCGACTGCCGCTGGGCGCCCAGGCAGAACGCCCAAGCGCCCAGGCGACAGGC

             *           
       3549 ATCCAGACCCCAG
         65 ACCCAGACCCCAG

             *      *       *                        *                     
       3562 CTAGAGCAAAGCCCGATTGCCGCTGGGCGCCCAGGC-GAAATGCCTC-AGCGCCCAGGCGACA
          1 CCAGAGCAGAGCCCGACTGCCGCTGGGCGCCCAGGCAG-AACGCC-CAAGCGCCCAGGCGACA

       3623 AGGCTCAGCG


Statistics
Matches: 128,  Mismatches: 8, Indels: 7
        0.90            0.06        0.05

Matches are distributed among these distances:
  76    1  0.01
  77   45  0.35
  78   82  0.64

ACGTcount: A:0.23, C:0.40, G:0.32, T:0.05


Consensus pattern (77 bp):   
CCAGAGCAGAGCCCGACTGCCGCTGGGCGCCCAGGCAGAACGCCCAAGCGCCCAGGCGACAGGCA
CCCAGACCCCAG

Found at i:3612 original size:21 final size:21

Alignment explanation


    Indices: 3588--3637  Score: 75
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       3578 TTGCCGCTGG

                                  
       3588 GCGCCCAGGCGA-AATGCCTCA
          1 GCGCCCAGGCGACAA-GCCTCA

                            *    
       3609 GCGCCCAGGCGACAAGGCTCA
          1 GCGCCCAGGCGACAAGCCTCA

                    
       3630 GCGCCCAG
          1 GCGCCCAG

       3638 CTCGATCCCT


Statistics
Matches: 27,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  21   25  0.93
  22    2  0.07

ACGTcount: A:0.22, C:0.40, G:0.32, T:0.06


Consensus pattern (21 bp):   
GCGCCCAGGCGACAAGCCTCA

Done.