Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014563.1 Corchorus olitorius cultivar O-4 contig14596, 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: 3919
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32


Found at i:88 original size:38 final size:38

Alignment explanation


    Indices: 46--270  Score: 299
    Period size: 38  Copynumber: 5.9  Consensus size: 38

         36 ACTTTCAACA

                                      **  *        
         46 AAGCGATCAAATTT-ATTATTCGCTTTTGATCAAGACCC
          1 AAGCGATC-AATTTCATTATTCGCTTAGGACCAAGACCC

                       *             *           *
         84 AAGCGATCAATGTCATTATTCGCTTGGGACCAAGACCT
          1 AAGCGATCAATTTCATTATTCGCTTAGGACCAAGACCC

                 *                 *              
        122 AAGCGCTCAATTTCATTATTCGCCTAGGACCAAGACCC
          1 AAGCGATCAATTTCATTATTCGCTTAGGACCAAGACCC

                          *    *     *   *       *
        160 AAGCGATCAATTTCTTTATCCGCTTGGGATCAAGACCT
          1 AAGCGATCAATTTCATTATTCGCTTAGGACCAAGACCC

                                                  
        198 AAGCGATCAATTTCATTATTCGCTTAGGACCAAGACCC
          1 AAGCGATCAATTTCATTATTCGCTTAGGACCAAGACCC

                          *          *         
        236 AAGCGATCAATTTCTTTATTCGCTTGGGACCAAGA
          1 AAGCGATCAATTTCATTATTCGCTTAGGACCAAGA

        271 TTAATAAATT


Statistics
Matches: 162,  Mismatches: 24, Indels: 2
        0.86            0.13        0.01

Matches are distributed among these distances:
  37    4  0.02
  38  158  0.98

ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29


Consensus pattern (38 bp):   
AAGCGATCAATTTCATTATTCGCTTAGGACCAAGACCC

Found at i:184 original size:76 final size:76

Alignment explanation


    Indices: 46--270  Score: 344
    Period size: 76  Copynumber: 3.0  Consensus size: 76

         36 ACTTTCAACA

                                    * **  *                   *  *           
         46 AAGCGATCAAATTT-ATTATTCGCTTTTGATCAAGACCCAAGCGATCAATGTCATTATTCGCTTG
          1 AAGCGATC-AATTTCATTATTCGCCTAGGACCAAGACCCAAGCGATCAATTTCTTTATTCGCTTG

                        
        110 GGACCAAGACCT
         65 GGACCAAGACCT

                 *                                                   *       
        122 AAGCGCTCAATTTCATTATTCGCCTAGGACCAAGACCCAAGCGATCAATTTCTTTATCCGCTTGG
          1 AAGCGATCAATTTCATTATTCGCCTAGGACCAAGACCCAAGCGATCAATTTCTTTATTCGCTTGG

              *        
        187 GATCAAGACCT
         66 GACCAAGACCT

                                   *                                         
        198 AAGCGATCAATTTCATTATTCGCTTAGGACCAAGACCCAAGCGATCAATTTCTTTATTCGCTTGG
          1 AAGCGATCAATTTCATTATTCGCCTAGGACCAAGACCCAAGCGATCAATTTCTTTATTCGCTTGG

                    
        263 GACCAAGA
         66 GACCAAGA

        271 TTAATAAATT


Statistics
Matches: 135,  Mismatches: 13, Indels: 2
        0.90            0.09        0.01

Matches are distributed among these distances:
  75    5  0.04
  76  130  0.96

ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29


Consensus pattern (76 bp):   
AAGCGATCAATTTCATTATTCGCCTAGGACCAAGACCCAAGCGATCAATTTCTTTATTCGCTTGG
GACCAAGACCT

Found at i:3777 original size:57 final size:57

Alignment explanation


    Indices: 3708--3862  Score: 296
    Period size: 56  Copynumber: 2.8  Consensus size: 57

       3698 GTTTTTTTTT

                                                                     
       3708 CTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGCTTTTGTGCTCTAACTTTTGC
          1 CTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGCTTTTGTGCTCTAACTTTTGC

                                                                     
       3765 CTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGC-TTTGTGCTCTAACTTTTGC
          1 CTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGCTTTTGTGCTCTAACTTTTGC

                                                       
       3821 CTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAG-TTTTGT
          1 CTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGCTTTTGT

       3863 AAGTAGTTTA


Statistics
Matches: 97,  Mismatches: 0, Indels: 3
        0.97            0.00        0.03

Matches are distributed among these distances:
  56   60  0.62
  57   37  0.38

ACGTcount: A:0.18, C:0.24, G:0.20, T:0.38


Consensus pattern (57 bp):   
CTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGCTTTTGTGCTCTAACTTTTGC

Done.