Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012665.1 Corchorus capsularis cultivar CVL-1 contig12686, 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: 10097
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:52 original size:34 final size:34

Alignment explanation


    Indices: 9--77  Score: 102
    Period size: 34  Copynumber: 2.0  Consensus size: 34

          1 ATCGCAAA

                             *        **      
          9 TTTTTTTTTTAGAAAAATCGGAAAAAGGAAAAAC
          1 TTTTTTTTTTAGAAAAAACGGAAAAAACAAAAAC

                              *               
         43 TTTTTTTTTTAGAAAAAAGGGAAAAAACAAAAAC
          1 TTTTTTTTTTAGAAAAAACGGAAAAAACAAAAAC

             
         77 T
          1 T

         78 AATTCTTGGA


Statistics
Matches: 31,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  34   31  1.00

ACGTcount: A:0.49, C:0.06, G:0.13, T:0.32


Consensus pattern (34 bp):   
TTTTTTTTTTAGAAAAAACGGAAAAAACAAAAAC

Found at i:370 original size:6 final size:6

Alignment explanation


    Indices: 355--392  Score: 69
    Period size: 6  Copynumber: 6.5  Consensus size: 6

        345 AAAACAAAGC

                                                         
        355 AAAT-T AAATCT AAATCT AAATCT AAATCT AAATCT AAA
          1 AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT AAA

        393 GCAGATTAAT


Statistics
Matches: 32,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
   5    4  0.12
   6   28  0.88

ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32


Consensus pattern (6 bp):   
AAATCT

Found at i:4900 original size:15 final size:16

Alignment explanation


    Indices: 4868--4901  Score: 52
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       4858 AAAGAAGAAT

                 *          
       4868 TAAAATTAAATCTAAC
          1 TAAAAGTAAATCTAAC

                            
       4884 TAAAAGTAAAT-TAAC
          1 TAAAAGTAAATCTAAC

               
       4899 TAA
          1 TAA

       4902 GAAAGCAATC


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  15    7  0.41
  16   10  0.59

ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29


Consensus pattern (16 bp):   
TAAAAGTAAATCTAAC
Done.