Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007037.1 Corchorus olitorius cultivar O-4 contig07062, 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: 5400
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.36


Found at i:3150 original size:11 final size:10

Alignment explanation


    Indices: 3125--3151  Score: 54
    Period size: 10  Copynumber: 2.7  Consensus size: 10

       3115 ATCTTTCTGG

                      
       3125 GAAAAATAGT
          1 GAAAAATAGT

                      
       3135 GAAAAATAGT
          1 GAAAAATAGT

                   
       3145 GAAAAAT
          1 GAAAAAT

       3152 TCAAAAAAGA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   17  1.00

ACGTcount: A:0.63, C:0.00, G:0.19, T:0.19


Consensus pattern (10 bp):   
GAAAAATAGT

Found at i:4556 original size:197 final size:198

Alignment explanation


    Indices: 4218--4610  Score: 603
    Period size: 197  Copynumber: 2.0  Consensus size: 198

       4208 TTGTTGATAA

                                               *                     *      *
       4218 ACCCGCACGTGCAGTCTGCTAAACTCCACTGATGGTGTATTTAATTATTTTCCATTTTAATTATT
          1 ACCCGCACGTGCAGTCTGCTAAACTCCACTGATGGCGTATTTAATTATTTTCCATTTGAATTATC

                                                             *               
       4283 ATTTGATACACCGTCAGTGTAGTTTTGGAACTCCACAAGCGGGTTCAAAGGTTGACAAGTACCCC
         66 ATTTGATACACCGTCAGTGTAGTTTTGGAACTCCACAAGCGGGTTCAAAAGTTGACAAGTACCCC

                *                   *         *           *    *     *       
       4348 ATTTCAGAATTAATTAAATTTTTAGTATTTCAATTTAACCCCAAAGGGGACTCATGTCACCCTTC
        131 ATTTAAGAATTAATTAAATTTTTAATATTTCAATCTAACCCCAAAGAGGACACATGTAACCCTTC

               
       4413 TAG
        196 TAG

                              *                                         *    
       4416 ACCCGCACGTGCAGTCTGGTAAACTCCACTGTAT-GCGTATTTAATTATTTTCCA-TTGAGTTAT
          1 ACCCGCACGTGCAGTCTGCTAAACTCCACTG-ATGGCGTATTTAATTATTTTCCATTTGAATTAT

                                                                             
       4479 CATTTGATACACCGTCAGTGTAGTTTTTGG-ACTCCACAAGCGGGTTCAAAAGTTGACAAGTACC
         65 CATTTGATACACCGTCAGTGTAG-TTTTGGAACTCCACAAGCGGGTTCAAAAGTTGACAAGTACC

                              *                    **   *                    
       4543 CCATTTAAGAATTAATTAGATTTTTAATATTTCAATCTAGTCCCTAAGAGGACACATGTAACCCT
        129 CCATTTAAGAATTAATTAAATTTTTAATATTTCAATCTAACCCCAAAGAGGACACATGTAACCCT

               
       4608 TCT
        194 TCT

       4611 TGATGCGCCA


Statistics
Matches: 177,  Mismatches: 16, Indels: 5
        0.89            0.08        0.03

Matches are distributed among these distances:
 197  120  0.68
 198   55  0.31
 199    2  0.01

ACGTcount: A:0.28, C:0.21, G:0.16, T:0.34


Consensus pattern (198 bp):   
ACCCGCACGTGCAGTCTGCTAAACTCCACTGATGGCGTATTTAATTATTTTCCATTTGAATTATC
ATTTGATACACCGTCAGTGTAGTTTTGGAACTCCACAAGCGGGTTCAAAAGTTGACAAGTACCCC
ATTTAAGAATTAATTAAATTTTTAATATTTCAATCTAACCCCAAAGAGGACACATGTAACCCTTC
TAG
Done.