Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013793.1 Corchorus olitorius cultivar O-4 contig13826, 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: 6331
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36


Found at i:3348 original size:99 final size:99

Alignment explanation


    Indices: 3232--3423  Score: 341
    Period size: 99  Copynumber: 1.9  Consensus size: 99

       3222 ATTATATAAT

                                                                       *     
       3232 GAAATGTTTGATTTTTGACAAACCTGAAGATTGATCAGTACTGAGGAGTTGAAAGGAAGTAG-AA
          1 GAAATGTTTGATTTTTGACAAACCTGAAGATTGATCAGTACTGAGGAGTTGAAAGGAAGCAGCAA

                                               
       3296 GCTGAGTTGGTGAGAGGAAAAAACAAAAGAAGGGG
         66 -CTGAGTTGGTGAGAGGAAAAAACAAAAGAAGGGG

                                                    *                        
       3331 GAAATGTTTGATTTTTGACAAACCTGAAGATTGATCAGTATTGAGGAGTTGAAAGGAAGCAGCAA
          1 GAAATGTTTGATTTTTGACAAACCTGAAGATTGATCAGTACTGAGGAGTTGAAAGGAAGCAGCAA

                                  *     
       3396 CTGAGTTGGTGAGAGGAAAAAAGAAAAG
         66 CTGAGTTGGTGAGAGGAAAAAACAAAAG

       3424 GGGGGAGGGA


Statistics
Matches: 89,  Mismatches: 3, Indels: 2
        0.95            0.03        0.02

Matches are distributed among these distances:
  99   87  0.98
 100    2  0.02

ACGTcount: A:0.40, C:0.07, G:0.30, T:0.23


Consensus pattern (99 bp):   
GAAATGTTTGATTTTTGACAAACCTGAAGATTGATCAGTACTGAGGAGTTGAAAGGAAGCAGCAA
CTGAGTTGGTGAGAGGAAAAAACAAAAGAAGGGG

Found at i:5403 original size:5 final size:5

Alignment explanation


    Indices: 5392--5467  Score: 115
    Period size: 5  Copynumber: 16.0  Consensus size: 5

       5382 GTGTTTTATG

                                      *                                
       5392 CAAAA -AAAA -AAAA CAAAA -ACAA -AAAA CAAAA CAAAA CAAAA CAAAA
          1 CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA

                                               
       5438 CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA
          1 CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA

       5468 AACATTATTG


Statistics
Matches: 67,  Mismatches: 2, Indels: 4
        0.92            0.03        0.05

Matches are distributed among these distances:
   4   14  0.21
   5   53  0.79

ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00


Consensus pattern (5 bp):   
CAAAA

Done.