Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013661.1 Corchorus olitorius cultivar O-4 contig13694, 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: 13836
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:2732 original size:51 final size:51

Alignment explanation


    Indices: 2630--2732  Score: 129
    Period size: 51  Copynumber: 2.0  Consensus size: 51

       2620 TGTTCTTCAA

                                     *  *             * **     
       2630 TATTTCCTTGTTTCAATCTTGTCTCTGGGCAAAAGAACACTCTTTTAGTGT
          1 TATTTCCTTGTTTCAATCTTGTCTCCGGACAAAAGAACACTCGTACAGTGT

                                                                 
       2681 TATTTCCTTGTTTCAATCTTGTCTCCGGACATAAA-AACACT-GTACACGTGT
          1 TATTTCCTTGTTTCAATCTTGTCTCCGGACA-AAAGAACACTCGTACA-GTGT

             
       2732 T
          1 T

       2733 TCTCTCTCAG


Statistics
Matches: 45,  Mismatches: 5, Indels: 4
        0.83            0.09        0.07

Matches are distributed among these distances:
  50    2  0.04
  51   40  0.89
  52    3  0.07

ACGTcount: A:0.23, C:0.21, G:0.15, T:0.41


Consensus pattern (51 bp):   
TATTTCCTTGTTTCAATCTTGTCTCCGGACAAAAGAACACTCGTACAGTGT

Found at i:7137 original size:39 final size:39

Alignment explanation


    Indices: 7093--7168  Score: 116
    Period size: 39  Copynumber: 1.9  Consensus size: 39

       7083 CAAAAACCAT

                                       *           
       7093 AAAATTGCTCAGAAAGATAAGATGGCATGTGGGGGTGTG
          1 AAAATTGCTCAGAAAGATAAGATGGCACGTGGGGGTGTG

                      *          *    *          
       7132 AAAATTGCTCCGAAAGATAAGGTGGCCCGTGGGGGTG
          1 AAAATTGCTCAGAAAGATAAGATGGCACGTGGGGGTG

       7169 CGTGCGGAGA


Statistics
Matches: 33,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  39   33  1.00

ACGTcount: A:0.30, C:0.12, G:0.37, T:0.21


Consensus pattern (39 bp):   
AAAATTGCTCAGAAAGATAAGATGGCACGTGGGGGTGTG

Found at i:9683 original size:38 final size:38

Alignment explanation


    Indices: 9628--9702  Score: 114
    Period size: 38  Copynumber: 2.0  Consensus size: 38

       9618 TAGTAAGCAA

                        *      *                  
       9628 AAGGATTTGTGGGAGGTTCTAAATGTTGCTAAAGACTG
          1 AAGGATTTGTGGAAGGTTCAAAATGTTGCTAAAGACTG

                                        * *      
       9666 AAGGATTTGTGGAAGGTTCAAAATGTTGTTGAAGACT
          1 AAGGATTTGTGGAAGGTTCAAAATGTTGCTAAAGACT

       9703 CAAGAATCTC


Statistics
Matches: 33,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  38   33  1.00

ACGTcount: A:0.31, C:0.07, G:0.31, T:0.32


Consensus pattern (38 bp):   
AAGGATTTGTGGAAGGTTCAAAATGTTGCTAAAGACTG

Found at i:13800 original size:2 final size:2

Alignment explanation


    Indices: 13793--13836  Score: 88
    Period size: 2  Copynumber: 22.0  Consensus size: 2

      13783 TCAATTTCGG

                                                                          
      13793 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
          1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA

              
      13835 GA
          1 GA


Statistics
Matches: 42,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   42  1.00

ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00


Consensus pattern (2 bp):   
GA

Done.