Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017474.1 Corchorus olitorius cultivar O-4 contig17507, 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: 30833
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34


Found at i:5841 original size:18 final size:17

Alignment explanation


    Indices: 5808--5843  Score: 54
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       5798 GCCGGACTAT

                *            
       5808 GAAGTAGAGGAGAAGGA
          1 GAAGGAGAGGAGAAGGA

                              
       5825 GAAGGAGAGGTAGAAGGA
          1 GAAGGAGAGG-AGAAGGA

             
       5843 G
          1 G

       5844 GAGTGAGAGC


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  17    9  0.53
  18    8  0.47

ACGTcount: A:0.44, C:0.00, G:0.50, T:0.06


Consensus pattern (17 bp):   
GAAGGAGAGGAGAAGGA

Found at i:7198 original size:29 final size:30

Alignment explanation


    Indices: 7156--7212  Score: 98
    Period size: 29  Copynumber: 1.9  Consensus size: 30

       7146 TCTAAAGAAA

                 *                        
       7156 TTTTGTAAATAAGGATGACACATTGTTTTT
          1 TTTTGCAAATAAGGATGACACATTGTTTTT

                                        
       7186 TTTTGCAAA-AAGGATGACACATTGTTT
          1 TTTTGCAAATAAGGATGACACATTGTTT

       7213 AACCATTCAA


Statistics
Matches: 26,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  29   18  0.69
  30    8  0.31

ACGTcount: A:0.32, C:0.09, G:0.18, T:0.42


Consensus pattern (30 bp):   
TTTTGCAAATAAGGATGACACATTGTTTTT

Found at i:8852 original size:16 final size:16

Alignment explanation


    Indices: 8833--8864  Score: 64
    Period size: 16  Copynumber: 2.0  Consensus size: 16

       8823 TATTTTACCC

                            
       8833 TTTTTAACATTTAAGA
          1 TTTTTAACATTTAAGA

                            
       8849 TTTTTAACATTTAAGA
          1 TTTTTAACATTTAAGA

       8865 AAAATTTAAG


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50


Consensus pattern (16 bp):   
TTTTTAACATTTAAGA
Done.