Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024328.1 Corchorus olitorius cultivar O-4 contig24361, 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: 8178
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30


Found at i:105 original size:21 final size:21

Alignment explanation


    Indices: 79--191  Score: 158
    Period size: 21  Copynumber: 5.4  Consensus size: 21

         69 TGCTAGAAGT

                                 
         79 TCATTGGAGCAAGTTCCAAGC
          1 TCATTGGAGCAAGTTCCAAGC

                                 
        100 TCATTGGAGCAAGTTCCAAGC
          1 TCATTGGAGCAAGTTCCAAGC

                       *        *
        121 TCATTGGAGCAGGTTCCAAGT
          1 TCATTGGAGCAAGTTCCAAGC

                                 *
        142 TCATTGGAG-AAGGTTCCAAGA
          1 TCATTGGAGCAA-GTTCCAAGC

                            *     
        163 TCATTGGAG-AAGGTTTCAAGC
          1 TCATTGGAGCAA-GTTCCAAGC

                    
        184 TCATTGGA
          1 TCATTGGA

        192 AATGCCTAAG


Statistics
Matches: 85,  Mismatches: 6, Indels: 2
        0.91            0.06        0.02

Matches are distributed among these distances:
  20    1  0.01
  21   84  0.99

ACGTcount: A:0.28, C:0.19, G:0.27, T:0.27


Consensus pattern (21 bp):   
TCATTGGAGCAAGTTCCAAGC

Found at i:1795 original size:21 final size:21

Alignment explanation


    Indices: 1771--1862  Score: 132
    Period size: 21  Copynumber: 4.4  Consensus size: 21

       1761 CTTAGGCATT

                         *       
       1771 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *            
       1792 TCCAATGATCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *          * 
       1813 TCCAATGAACTTGGAACCTGC
          1 TCCAATGAGCTTGGAACCTTC

                                  
       1834 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                    
       1855 TCCAATGA
          1 TCCAATGA

       1863 ACTTCTAGCA


Statistics
Matches: 64,  Mismatches: 6, Indels: 2
        0.89            0.08        0.03

Matches are distributed among these distances:
  20    2  0.03
  21   62  0.97

ACGTcount: A:0.27, C:0.27, G:0.17, T:0.28


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC

Found at i:3722 original size:11 final size:11

Alignment explanation


    Indices: 3706--3730  Score: 50
    Period size: 11  Copynumber: 2.3  Consensus size: 11

       3696 CCATATCCCT

                       
       3706 CTCGGATTGAA
          1 CTCGGATTGAA

                       
       3717 CTCGGATTGAA
          1 CTCGGATTGAA

               
       3728 CTC
          1 CTC

       3731 TCATCTTCCT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   14  1.00

ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28


Consensus pattern (11 bp):   
CTCGGATTGAA

Found at i:7266 original size:75 final size:75

Alignment explanation


    Indices: 7166--7390  Score: 299
    Period size: 75  Copynumber: 3.0  Consensus size: 75

       7156 TTAAATAAAT

                    * *                                                   *  
       7166 TGAGAAAACATCAAAACAGGGCGAAAATGTTCTCCCACGTTAAAAGTTGATGGGAGCTATCAATA
          1 TGAGAAAAGACCAAAACAGGGCGAAAATGTTCTCCCACGTTAAAAGTTGATGGGAGCTATCAGTA

             *        
       7231 AATTCCAGAG
         66 ATTTCCAGAG

                        *    *         *       *      *                 **   
       7241 TGAGAAAAGACCGAAACGGGGCGAAAAGGTTCTCCTACGTTAGAAGTTGATGGGAGCTATTGGTA
          1 TGAGAAAAGACCAAAACAGGGCGAAAATGTTCTCCCACGTTAAAAGTTGATGGGAGCTATCAGTA

                 *    
       7306 ATTTCTAGAG
         66 ATTTCCAGAG

                            *                 *                 *            
       7316 TGAGAAAAGACCAAAATAGGGCG-AAATGGTTCTTCCACGTTAAAAGTTGATTGGAGCTATCAGT
          1 TGAGAAAAGACCAAAACAGGGCGAAAAT-GTTCTCCCACGTTAAAAGTTGATGGGAGCTATCAGT

                       
       7380 AATTTCCAGAG
         65 AATTTCCAGAG

       7391 GGTATTCAAA


Statistics
Matches: 126,  Mismatches: 23, Indels: 2
        0.83            0.15        0.01

Matches are distributed among these distances:
  74    3  0.02
  75  123  0.98

ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24


Consensus pattern (75 bp):   
TGAGAAAAGACCAAAACAGGGCGAAAATGTTCTCCCACGTTAAAAGTTGATGGGAGCTATCAGTA
ATTTCCAGAG
Done.