Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024297.1 Corchorus olitorius cultivar O-4 contig24330, 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: 13993
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31


Found at i:1810 original size:40 final size:40

Alignment explanation


    Indices: 1755--1867  Score: 190
    Period size: 40  Copynumber: 2.8  Consensus size: 40

       1745 TTGTCATGTA

                                                *   
       1755 TAAAGTATAAACATGAATAATACCTTTTAGAAATTCTAAT
          1 TAAAGTATAAACATGAATAATACCTTTTAGAAATTCCAAT

                               *    *      *        
       1795 TAAAGTATAAACATGAATAGTACCATTTAGAGATTCCAAT
          1 TAAAGTATAAACATGAATAATACCTTTTAGAAATTCCAAT

                                             
       1835 TAAAGTATAAACATGAATAATACCTTTTAGAAA
          1 TAAAGTATAAACATGAATAATACCTTTTAGAAA

       1868 ATGTTGGCAA


Statistics
Matches: 66,  Mismatches: 7, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  40   66  1.00

ACGTcount: A:0.48, C:0.11, G:0.10, T:0.32


Consensus pattern (40 bp):   
TAAAGTATAAACATGAATAATACCTTTTAGAAATTCCAAT

Found at i:4314 original size:27 final size:27

Alignment explanation


    Indices: 4283--4356  Score: 148
    Period size: 27  Copynumber: 2.7  Consensus size: 27

       4273 TGCAATTATT

                                       
       4283 CTTACAATGTAGTTCTTAGTGCTTACA
          1 CTTACAATGTAGTTCTTAGTGCTTACA

                                       
       4310 CTTACAATGTAGTTCTTAGTGCTTACA
          1 CTTACAATGTAGTTCTTAGTGCTTACA

                                
       4337 CTTACAATGTAGTTCTTAGT
          1 CTTACAATGTAGTTCTTAGT

       4357 TTGGTAGTTT


Statistics
Matches: 47,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   47  1.00

ACGTcount: A:0.26, C:0.18, G:0.15, T:0.42


Consensus pattern (27 bp):   
CTTACAATGTAGTTCTTAGTGCTTACA

Found at i:4797 original size:18 final size:18

Alignment explanation


    Indices: 4774--4810  Score: 65
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       4764 AACAATTCTA

                              
       4774 AGTTCTAACCCTATTTGT
          1 AGTTCTAACCCTATTTGT

                     *        
       4792 AGTTCTAACTCTATTTGT
          1 AGTTCTAACCCTATTTGT

             
       4810 A
          1 A

       4811 ATTTTATTGT


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

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.24, C:0.19, G:0.11, T:0.46


Consensus pattern (18 bp):   
AGTTCTAACCCTATTTGT

Found at i:13880 original size:18 final size:20

Alignment explanation


    Indices: 13842--13880  Score: 55
    Period size: 20  Copynumber: 2.0  Consensus size: 20

      13832 GTGCTCCCGT

                          *     
      13842 TGTGATGCTCCACTTTTCAA
          1 TGTGATGCTCCACTATTCAA

                                
      13862 TGTGATGCTCC-C-ATTCAA
          1 TGTGATGCTCCACTATTCAA

             
      13880 T
          1 T

      13881 TCTAACCATT


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  18    6  0.33
  19    1  0.06
  20   11  0.61

ACGTcount: A:0.21, C:0.26, G:0.15, T:0.38


Consensus pattern (20 bp):   
TGTGATGCTCCACTATTCAA
Done.