Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012687.1 Corchorus olitorius cultivar O-4 contig12720, 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: 3985
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31


Found at i:2619 original size:28 final size:28

Alignment explanation


    Indices: 2586--2702  Score: 144
    Period size: 28  Copynumber: 3.9  Consensus size: 28

       2576 ACTAAAACCT

                                        
       2586 GATGGGAACTTTCCCAATTTGAAAACTG
          1 GATGGGAACTTTCCCAATTTGAAAACTG

                                           
       2614 GATGGGAACTTTCCCAATTTGAAAACTAAAG
          1 GATGGGAACTTTCCCAATTTGAAAACT---G

                                            *
       2645 AACTTGATGGGAACTTTCCCAATTTGAAAACTT
          1 -----GATGGGAACTTTCCCAATTTGAAAACTG

                    *                
       2678 GATGGGAAGTTTCCCAATTTGAAAA
          1 GATGGGAACTTTCCCAATTTGAAAA

       2703 GAGCTAAATT


Statistics
Matches: 79,  Mismatches: 2, Indels: 16
        0.81            0.02        0.16

Matches are distributed among these distances:
  28   51  0.65
  31    1  0.01
  36   27  0.34

ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29


Consensus pattern (28 bp):   
GATGGGAACTTTCCCAATTTGAAAACTG

Found at i:2660 original size:64 final size:62

Alignment explanation


    Indices: 2554--2702  Score: 235
    Period size: 64  Copynumber: 2.4  Consensus size: 62

       2544 CCAAAAATGA

                           *                                               
       2554 GGGAACTTTCCCTAAATTGAAAACTAAAACCTGATGGGAACTTTCCCAATTTGAAAACTGGAT
          1 GGGAACTTTCCC-AATTTGAAAACTAAAACCTGATGGGAACTTTCCCAATTTGAAAACTGGAT

                                           *                            *   
       2617 GGGAACTTTCCCAATTTGAAAACTAAAGAACTTGATGGGAACTTTCCCAATTTGAAAACTTGAT
          1 GGGAACTTTCCCAATTTGAAAACT-AA-AACCTGATGGGAACTTTCCCAATTTGAAAACTGGAT

                 *                
       2681 GGGAAGTTTCCCAATTTGAAAA
          1 GGGAACTTTCCCAATTTGAAAA

       2703 GAGCTAAATT


Statistics
Matches: 80,  Mismatches: 4, Indels: 3
        0.92            0.05        0.03

Matches are distributed among these distances:
  62   11  0.14
  63   14  0.17
  64   55  0.69

ACGTcount: A:0.36, C:0.17, G:0.18, T:0.28


Consensus pattern (62 bp):   
GGGAACTTTCCCAATTTGAAAACTAAAACCTGATGGGAACTTTCCCAATTTGAAAACTGGAT
Done.