Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012426.1 Corchorus olitorius cultivar O-4 contig12459, 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: 10567
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:1395 original size:21 final size:21

Alignment explanation


    Indices: 1356--1395  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       1346 AGGAGATGCC

                        *        
       1356 AAAGATGCCATTTGATCCATT
          1 AAAGATGCCATTAGATCCATT

                          *    
       1377 AAAGATGCCATTAGGTCCA
          1 AAAGATGCCATTAGATCCA

       1396 ATGACAAGAG


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28


Consensus pattern (21 bp):   
AAAGATGCCATTAGATCCATT

Found at i:2785 original size:52 final size:51

Alignment explanation


    Indices: 2607--2788  Score: 229
    Period size: 52  Copynumber: 3.5  Consensus size: 51

       2597 ACTAAAACCC

                               *           * *        *         
       2607 GGTGGGAACTTTCCCAATTCGAAAAAGAACCTACTTGAATACATTGAAAACT
          1 GGTGGGAACTTTCCCAATTTGAAAAAG-ACCAAATTGAATACTTTGAAAACT

             *                            * *                   
       2659 GATGGGAACTTTCCCAATTTGAAAAAGAGCTAGATTGAATACTTTGAAAACT
          1 GGTGGGAACTTTCCCAATTTGAAAAAGA-CCAAATTGAATACTTTGAAAACT

            *              * *                                  
       2711 AGTGGGAACTTTCCCGACTTGAAAAAGACCAAAATTGAATACTTTGAAAACT
          1 GGTGGGAACTTTCCCAATTTGAAAAAGACC-AAATTGAATACTTTGAAAACT

                          **          
       2763 GGTGGGAACTTTCCTGATTTGAAAAA
          1 GGTGGGAACTTTCCCAATTTGAAAAA

       2789 TAGCTAAATG


Statistics
Matches: 112,  Mismatches: 16, Indels: 4
        0.85            0.12        0.03

Matches are distributed among these distances:
  51    2  0.02
  52  110  0.98

ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27


Consensus pattern (51 bp):   
GGTGGGAACTTTCCCAATTTGAAAAAGACCAAATTGAATACTTTGAAAACT

Found at i:9278 original size:42 final size:42

Alignment explanation


    Indices: 9219--9299  Score: 153
    Period size: 42  Copynumber: 1.9  Consensus size: 42

       9209 TAAGGATCAG

                                                      
       9219 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
          1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT

                                         *         
       9261 GATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTTC
          1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC

       9300 AAGACTTAGC


Statistics
Matches: 38,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  42   38  1.00

ACGTcount: A:0.30, C:0.07, G:0.16, T:0.47


Consensus pattern (42 bp):   
GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
Done.