Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017720.1 Corchorus olitorius cultivar O-4 contig17753, 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: 8313
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--94  Score: 188
    Period size: 2  Copynumber: 47.0  Consensus size: 2

                                                                          
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC

                                                                          
         43 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC

                          
         85 TC TC TC TC TC
          1 TC TC TC TC TC

         95 GTCCACGCTC


Statistics
Matches: 92,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   92  1.00

ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50


Consensus pattern (2 bp):   
TC

Found at i:5714 original size:30 final size:27

Alignment explanation


    Indices: 5629--5711  Score: 121
    Period size: 30  Copynumber: 3.0  Consensus size: 27

       5619 GTTAATTTAG

                                       
       5629 ACTTATTATTATTATAATAATTATTAA
          1 ACTTATTATTATTATAATAATTATTAA

                              *           
       5656 ACTTATTATTAGTGGTATTATAATTATTAA
          1 ACTTATTATTA-T--TATAATAATTATTAA

                        *             
       5686 ACTTATTATTATAATAATAATTATTA
          1 ACTTATTATTATTATAATAATTATTA

       5712 TTAGTAATAT


Statistics
Matches: 50,  Mismatches: 3, Indels: 6
        0.85            0.05        0.10

Matches are distributed among these distances:
  27   23  0.46
  28    1  0.02
  29    1  0.02
  30   25  0.50

ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51


Consensus pattern (27 bp):   
ACTTATTATTATTATAATAATTATTAA
Done.