Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004875.1 Corchorus capsularis cultivar CVL-1 contig04893, 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: 7881
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.31


Found at i:2370 original size:6 final size:6

Alignment explanation


    Indices: 2359--2383  Score: 50
    Period size: 6  Copynumber: 4.2  Consensus size: 6

       2349 AGACTTGCGC

                                         
       2359 CCCAAG CCCAAG CCCAAG CCCAAG C
          1 CCCAAG CCCAAG CCCAAG CCCAAG C

       2384 AGACAAAGAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   19  1.00

ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00


Consensus pattern (6 bp):   
CCCAAG

Found at i:4950 original size:102 final size:102

Alignment explanation


    Indices: 4821--5025  Score: 295
    Period size: 102  Copynumber: 2.0  Consensus size: 102

       4811 TTGTTTCATG

                                  *                         *           *    
       4821 TGCATCATAGCGAAGGAGCGAGCAGAGATCAACGAGTCAA-TTGACTTTGACAAGCATCTGAATC
          1 TGCATCATAGCGAAGGAGCGAGAAGAGATCAACGAGT-AAGTTGACTTGGACAAGCATCTCAATC

              **   *                    *         
       4885 TTTGAAGGGACTTGACAGGCAACCGTGAGAGGATATCT
         65 TTACAAGAGACTTGACAGGCAACCGTGACAGGATATCT

                      *                     *                   *  *         
       4923 TGCATCATAGTGAAGGAGCGAGAAGAGATCAAGGAGTAAGTTGACTTGGACATGCTTCTCAATCT
          1 TGCATCATAGCGAAGGAGCGAGAAGAGATCAACGAGTAAGTTGACTTGGACAAGCATCTCAATCT

                                                 
       4988 TACAAGAGACTTGACAGGCAACCGTGACAGGATATCT
         66 TACAAGAGACTTGACAGGCAACCGTGACAGGATATCT

             
       5025 T
          1 T

       5026 CCATGATTTC


Statistics
Matches: 91,  Mismatches: 11, Indels: 2
        0.88            0.11        0.02

Matches are distributed among these distances:
 101    2  0.02
 102   89  0.98

ACGTcount: A:0.33, C:0.18, G:0.27, T:0.22


Consensus pattern (102 bp):   
TGCATCATAGCGAAGGAGCGAGAAGAGATCAACGAGTAAGTTGACTTGGACAAGCATCTCAATCT
TACAAGAGACTTGACAGGCAACCGTGACAGGATATCT
Done.