Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014075.1 Corchorus olitorius cultivar O-4 contig14108, 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: 4312
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.29


Found at i:723 original size:168 final size:168

Alignment explanation


    Indices: 445--760  Score: 551
    Period size: 168  Copynumber: 1.9  Consensus size: 168

        435 TGATAATGAT

                      *                             *                        
        445 AATGAGAATGCCAATGTTGGTGGTAATGGAGCTGGTCAAGGTGATAAAATAGTTGAAGAGGAACA
          1 AATGAGAATGACAATGTTGGTGGTAATGGAGCTGGTCAAGCTGATAAAATAGTTGAAGAGGAACA

                                     *                                       
        510 ACCTGAAGAAGTTCATGTTGAAGATTCTGTTCAAATTGAAGTTGCTGATGTAGCTGCTCCAACTG
         66 ACCTGAAGAAGTTCATGTTGAAGATCCTGTTCAAATTGAAGTTGCTGATGTAGCTGCTCCAACTG

                                                  
        575 GTCAAGTTAATGGTGTTGGGTTTGGAGGTTTTCAGGAA
        131 GTCAAGTTAATGGTGTTGGGTTTGGAGGTTTTCAGGAA

                                         *               *    *              
        613 AATGAGAATGACAATGTTGGTGGTAATGGTGCTGGTCAAGCTGATCAAATGGTTGAAGAGGAACA
          1 AATGAGAATGACAATGTTGGTGGTAATGGAGCTGGTCAAGCTGATAAAATAGTTGAAGAGGAACA

                         *                   **                              
        678 ACCTGAAGAAGTTGATGTTGAAGATCCTGTTCATGTTGAAGTTGCTGATGTAGCTGCTCCAACTG
         66 ACCTGAAGAAGTTCATGTTGAAGATCCTGTTCAAATTGAAGTTGCTGATGTAGCTGCTCCAACTG

                              
        743 GTCAAGTTAATGGTGTTG
        131 GTCAAGTTAATGGTGTTG

        761 AACATGTTCA


Statistics
Matches: 139,  Mismatches: 9, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
 168  139  1.00

ACGTcount: A:0.29, C:0.11, G:0.30, T:0.30


Consensus pattern (168 bp):   
AATGAGAATGACAATGTTGGTGGTAATGGAGCTGGTCAAGCTGATAAAATAGTTGAAGAGGAACA
ACCTGAAGAAGTTCATGTTGAAGATCCTGTTCAAATTGAAGTTGCTGATGTAGCTGCTCCAACTG
GTCAAGTTAATGGTGTTGGGTTTGGAGGTTTTCAGGAA

Found at i:1057 original size:24 final size:24

Alignment explanation


    Indices: 1025--1113  Score: 160
    Period size: 24  Copynumber: 3.7  Consensus size: 24

       1015 GGTCAGAGAG

                       *            
       1025 AAAATGCTGGTGATGGTGGGGCTC
          1 AAAATGCTGGTAATGGTGGGGCTC

                             *      
       1049 AAAATGCTGGTAATGGTTGGGCTC
          1 AAAATGCTGGTAATGGTGGGGCTC

                                    
       1073 AAAATGCTGGTAATGGTGGGGCTC
          1 AAAATGCTGGTAATGGTGGGGCTC

                             
       1097 AAAATGCTGGTAATGGT
          1 AAAATGCTGGTAATGGT

       1114 TGAAAATATT


Statistics
Matches: 62,  Mismatches: 3, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  24   62  1.00

ACGTcount: A:0.26, C:0.11, G:0.36, T:0.27


Consensus pattern (24 bp):   
AAAATGCTGGTAATGGTGGGGCTC

Found at i:4261 original size:20 final size:20

Alignment explanation


    Indices: 4236--4277  Score: 75
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       4226 TGAAACCAGT

                                
       4236 TTATGGTTGTTATTTTAATG
          1 TTATGGTTGTTATTTTAATG

                       *        
       4256 TTATGGTTGTTGTTTTAATG
          1 TTATGGTTGTTATTTTAATG

              
       4276 TT
          1 TT

       4278 TATTTTGAAC


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   21  1.00

ACGTcount: A:0.17, C:0.00, G:0.21, T:0.62


Consensus pattern (20 bp):   
TTATGGTTGTTATTTTAATG
Done.