Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016015.1 Corchorus olitorius cultivar O-4 contig16048, 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: 10587
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32


Found at i:14 original size:3 final size:3

Alignment explanation


    Indices: 1--56  Score: 78
    Period size: 3  Copynumber: 18.0  Consensus size: 3

                                                                          
          1 TAA TATA TAA TAA TAA TAA TAAA TAA T-A TATA TAA TAA TAA TAA TAA
          1 TAA TA-A TAA TAA TAA TAA T-AA TAA TAA TA-A TAA TAA TAA TAA TAA

                       
         48 TAA TAA TAA
          1 TAA TAA TAA

         57 GAGGGGAAAG


Statistics
Matches: 49,  Mismatches: 0, Indels: 8
        0.86            0.00        0.14

Matches are distributed among these distances:
   2    2  0.04
   3   38  0.78
   4    9  0.18

ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36


Consensus pattern (3 bp):   
TAA

Found at i:2573 original size:21 final size:21

Alignment explanation


    Indices: 2549--2588  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       2539 TTGTTTAAGA

                 *       *       
       2549 GAGAAGTCGACTTGAGCAAGG
          1 GAGAAATCGACTTAAGCAAGG

                               
       2570 GAGAAATCGACTTAAGCAA
          1 GAGAAATCGACTTAAGCAA

       2589 ATCAATTTCA


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.40, C:0.15, G:0.30, T:0.15


Consensus pattern (21 bp):   
GAGAAATCGACTTAAGCAAGG

Found at i:5262 original size:29 final size:30

Alignment explanation


    Indices: 5210--5269  Score: 86
    Period size: 29  Copynumber: 2.0  Consensus size: 30

       5200 GAAGTTCGTG

                               *      *    
       5210 TTTGAAGACTCATTGAAGACTTATTTGAAGA
          1 TTTGAAGACT-ATTGAAGAATTATTTCAAGA

                                          
       5241 TTTGAAGACT-TTGAAGAATTATTTCAAGA
          1 TTTGAAGACTATTGAAGAATTATTTCAAGA

       5270 GGAAAGAATT


Statistics
Matches: 27,  Mismatches: 2, Indels: 2
        0.87            0.06        0.06

Matches are distributed among these distances:
  29   17  0.63
  31   10  0.37

ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37


Consensus pattern (30 bp):   
TTTGAAGACTATTGAAGAATTATTTCAAGA
Done.