Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016956.1 Corchorus olitorius cultivar O-4 contig16989, 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: 9458
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30


Found at i:4237 original size:21 final size:21

Alignment explanation


    Indices: 4207--4246  Score: 71
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       4197 CTAAAAACAG

                 *               
       4207 GACAAGTCCTGCCCAGGACTT
          1 GACAACTCCTGCCCAGGACTT

                               
       4228 GACAACTCCTGCCCAGGAC
          1 GACAACTCCTGCCCAGGAC

       4247 CTGGTCTGTT


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.25, C:0.38, G:0.23, T:0.15


Consensus pattern (21 bp):   
GACAACTCCTGCCCAGGACTT

Found at i:4304 original size:50 final size:50

Alignment explanation


    Indices: 4229--4350  Score: 190
    Period size: 50  Copynumber: 2.4  Consensus size: 50

       4219 CCAGGACTTG

                              *             *                 
       4229 ACAACTCCTGCCCAGGACCTGGTCTGTTGAAAGACGGAAGAAAAATCAGA
          1 ACAACTCCTGCCCAGGACTTGGTCTGTTGAAAAACGGAAGAAAAATCAGA

                                              *         *     
       4279 ACAACTCCTGCCCAGGACTTGGTCTGTTGAAAAATGGAAGAAAATTCAGA
          1 ACAACTCCTGCCCAGGACTTGGTCTGTTGAAAAACGGAAGAAAAATCAGA

                *     *           
       4329 ACAAGTCCTGTCCAGGACTTGG
          1 ACAACTCCTGCCCAGGACTTGG

       4351 ACAACTCCTG


Statistics
Matches: 66,  Mismatches: 6, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  50   66  1.00

ACGTcount: A:0.34, C:0.23, G:0.24, T:0.20


Consensus pattern (50 bp):   
ACAACTCCTGCCCAGGACTTGGTCTGTTGAAAAACGGAAGAAAAATCAGA

Found at i:4359 original size:22 final size:22

Alignment explanation


    Indices: 4329--4371  Score: 68
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       4319 AAAATTCAGA

                *     *           
       4329 ACAAGTCCTGTCCAGGACTTGG
          1 ACAACTCCTGCCCAGGACTTGG

                                 
       4351 ACAACTCCTGCCCAGGACTTG
          1 ACAACTCCTGCCCAGGACTTG

       4372 TTGCAGAAAA


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.23, C:0.33, G:0.23, T:0.21


Consensus pattern (22 bp):   
ACAACTCCTGCCCAGGACTTGG

Found at i:5584 original size:61 final size:61

Alignment explanation


    Indices: 5512--5640  Score: 240
    Period size: 61  Copynumber: 2.1  Consensus size: 61

       5502 TTTTGTGCAG

                  *                                                      
       5512 CAAGTTTGGGAGACAAAAGGCTGTTTGGATTGCATAAAGAACACTTTTCTTTTGATTCACT
          1 CAAGTTAGGGAGACAAAAGGCTGTTTGGATTGCATAAAGAACACTTTTCTTTTGATTCACT

                                                 *                       
       5573 CAAGTTAGGGAGACAAAAGGCTGTTTGGATTGCATAAGGAACACTTTTCTTTTGATTCACT
          1 CAAGTTAGGGAGACAAAAGGCTGTTTGGATTGCATAAAGAACACTTTTCTTTTGATTCACT

                   
       5634 CAAGTTA
          1 CAAGTTA

       5641 TTGCTCTTAA


Statistics
Matches: 66,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  61   66  1.00

ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33


Consensus pattern (61 bp):   
CAAGTTAGGGAGACAAAAGGCTGTTTGGATTGCATAAAGAACACTTTTCTTTTGATTCACT
Done.