Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024282.1 Corchorus olitorius cultivar O-4 contig24315, 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: 4664
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.32


Found at i:347 original size:15 final size:16

Alignment explanation


    Indices: 321--356  Score: 65
    Period size: 15  Copynumber: 2.3  Consensus size: 16

        311 TTTGCTTTGT

                            
        321 TTTCTAGTTTAATTGC
          1 TTTCTAGTTTAATTGC

                            
        337 TTTCT-GTTTAATTGC
          1 TTTCTAGTTTAATTGC

                 
        352 TTTCT
          1 TTTCT

        357 TTCAACCTCT


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  15   15  0.75
  16    5  0.25

ACGTcount: A:0.14, C:0.14, G:0.11, T:0.61


Consensus pattern (16 bp):   
TTTCTAGTTTAATTGC

Found at i:2124 original size:21 final size:22

Alignment explanation


    Indices: 2108--2199  Score: 120
    Period size: 21  Copynumber: 4.4  Consensus size: 22

       2098 AGCTTCCTTG

                                  
       2108 ATGAACTTGGAACCTT-CTCCA
          1 ATGAACTTGGAACCTTCCTCCA

                                  
       2129 ATGAACTTGGAACCTT-CTCCA
          1 ATGAACTTGGAACCTTCCTCCA

                *           *     
       2150 ATGAGCTTGGAA-CTTGCTCCA
          1 ATGAACTTGGAACCTTCCTCCA

                *           *     
       2171 ATGAGCTTGGAA-CTTGCTCCA
          1 ATGAACTTGGAACCTTCCTCCA

                    
       2192 ATGAACTT
          1 ATGAACTT

       2200 CTAGCATCTT


Statistics
Matches: 68,  Mismatches: 2, Indels: 2
        0.94            0.03        0.03

Matches are distributed among these distances:
  20    3  0.04
  21   65  0.96

ACGTcount: A:0.27, C:0.25, G:0.18, T:0.29


Consensus pattern (22 bp):   
ATGAACTTGGAACCTTCCTCCA

Found at i:2160 original size:42 final size:42

Alignment explanation


    Indices: 2108--2199  Score: 134
    Period size: 42  Copynumber: 2.2  Consensus size: 42

       2098 AGCTTCCTTG

                                                        
       2108 ATGAACTTGGAACCTT-CTCCAATGAACTTGGAACCTT-CTCCA
          1 ATGAACTTGGAA-CTTGCTCCAATGAACTTGGAA-CTTGCTCCA

                *                    *                
       2150 ATGAGCTTGGAACTTGCTCCAATGAGCTTGGAACTTGCTCCA
          1 ATGAACTTGGAACTTGCTCCAATGAACTTGGAACTTGCTCCA

                    
       2192 ATGAACTT
          1 ATGAACTT

       2200 CTAGCATCTT


Statistics
Matches: 45,  Mismatches: 3, Indels: 4
        0.87            0.06        0.08

Matches are distributed among these distances:
  41    6  0.13
  42   39  0.87

ACGTcount: A:0.27, C:0.25, G:0.18, T:0.29


Consensus pattern (42 bp):   
ATGAACTTGGAACTTGCTCCAATGAACTTGGAACTTGCTCCA
Done.