Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015277.1 Corchorus olitorius cultivar O-4 contig15310, 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: 7219
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.34


Found at i:257 original size:19 final size:19

Alignment explanation


    Indices: 233--273  Score: 55
    Period size: 19  Copynumber: 2.2  Consensus size: 19

        223 GAACAGTGGC

                   *           
        233 CGGCGGCGGTGGTGACCGG
          1 CGGCGGCAGTGGTGACCGG

                  *       *    
        252 CGGCGGTAGTGGTGGCCGG
          1 CGGCGGCAGTGGTGACCGG

               
        271 CGG
          1 CGG

        274 TGGTTGGTTT


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  19   19  1.00

ACGTcount: A:0.05, C:0.24, G:0.59, T:0.12


Consensus pattern (19 bp):   
CGGCGGCAGTGGTGACCGG

Found at i:855 original size:18 final size:16

Alignment explanation


    Indices: 832--878  Score: 62
    Period size: 15  Copynumber: 2.9  Consensus size: 16

        822 AAAAATATAA

                              
        832 AAAAAAAGAGAAAAGGAG
          1 AAAAAAAGAGAAAA--AG

                            
        850 AAAAAAAGA-AAAAAG
          1 AAAAAAAGAGAAAAAG

                           
        865 AAAAAAA-AGAAAAA
          1 AAAAAAAGAGAAAAA

        879 AAATAAATTA


Statistics
Matches: 28,  Mismatches: 0, Indels: 5
        0.85            0.00        0.15

Matches are distributed among these distances:
  14    1  0.04
  15   14  0.50
  17    4  0.14
  18    9  0.32

ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00


Consensus pattern (16 bp):   
AAAAAAAGAGAAAAAG

Found at i:859 original size:16 final size:16

Alignment explanation


    Indices: 831--879  Score: 71
    Period size: 16  Copynumber: 2.9  Consensus size: 16

        821 AAAAAATATA

                           * 
        831 AAAAAAAAGAGAAAAGG
          1 AAAAAAAAGA-AAAAAG

                             
        848 AGAAAAAAAGAAAAAAG
          1 A-AAAAAAAGAAAAAAG

                           
        865 AAAAAAAAGAAAAAA
          1 AAAAAAAAGAAAAAA

        880 AATAAATTAA


Statistics
Matches: 30,  Mismatches: 1, Indels: 3
        0.88            0.03        0.09

Matches are distributed among these distances:
  16   14  0.47
  17    7  0.23
  18    9  0.30

ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00


Consensus pattern (16 bp):   
AAAAAAAAGAAAAAAG

Found at i:870 original size:8 final size:8

Alignment explanation


    Indices: 832--880  Score: 55
    Period size: 9  Copynumber: 5.9  Consensus size: 8

        822 AAAAATATAA

                    
        832 AAAAAAAG
          1 AAAAAAAG

                   *  
        840 AGAAAAGGAG
          1 A-AAAA-AAG

                    
        850 AAAAAAAG
          1 AAAAAAAG

                    
        858 -AAAAAAG
          1 AAAAAAAG

                     
        865 AAAAAAAAG
          1 -AAAAAAAG

                   
        874 AAAAAAA
          1 AAAAAAA

        881 ATAAATTAAG


Statistics
Matches: 35,  Mismatches: 2, Indels: 8
        0.78            0.04        0.18

Matches are distributed among these distances:
   7    7  0.20
   8   10  0.29
   9   15  0.43
  10    3  0.09

ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00


Consensus pattern (8 bp):   
AAAAAAAG
Done.