Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016112.1 Corchorus capsularis cultivar CVL-1 contig16133, 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: 17613
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32


Found at i:4875 original size:19 final size:17

Alignment explanation


    Indices: 4851--4893  Score: 50
    Period size: 19  Copynumber: 2.4  Consensus size: 17

       4841 TAGACTTAGA

                              
       4851 TTTAATTTACTTTGCTTT
          1 TTTAATTTACTTT-CTTT

                   * *        
       4869 GTTTAATCTGCTTTCTTT
          1 -TTTAATTTACTTTCTTT

                   
       4887 TTTAATT
          1 TTTAATT

       4894 GATCTTTTAA


Statistics
Matches: 21,  Mismatches: 3, Indels: 2
        0.81            0.12        0.08

Matches are distributed among these distances:
  17    6  0.29
  18    4  0.19
  19   11  0.52

ACGTcount: A:0.16, C:0.12, G:0.07, T:0.65


Consensus pattern (17 bp):   
TTTAATTTACTTTCTTT

Found at i:6571 original size:12 final size:12

Alignment explanation


    Indices: 6554--6584  Score: 53
    Period size: 12  Copynumber: 2.6  Consensus size: 12

       6544 AAGGCAAAAC

                        
       6554 CTCAACCAAGGT
          1 CTCAACCAAGGT

                     *  
       6566 CTCAACCAATGT
          1 CTCAACCAAGGT

                   
       6578 CTCAACC
          1 CTCAACC

       6585 TCCAAGTCCA


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  12   18  1.00

ACGTcount: A:0.32, C:0.39, G:0.10, T:0.19


Consensus pattern (12 bp):   
CTCAACCAAGGT

Found at i:15884 original size:6 final size:6

Alignment explanation


    Indices: 15873--15899  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

      15863 AAAGCAAAGC

                                           
      15873 AAATCT AAATCT AAATCT AAATCT AAA
          1 AAATCT AAATCT AAATCT AAATCT AAA

      15900 GCAAACAATA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30


Consensus pattern (6 bp):   
AAATCT

Found at i:17084 original size:45 final size:45

Alignment explanation


    Indices: 17031--17177  Score: 244
    Period size: 45  Copynumber: 3.3  Consensus size: 45

      17021 CAAAGCGATG

                                                         
      17031 ATGG-TTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAA
          1 ATGGTTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAA

                             *                *          
      17075 ATGGTTTTTCAAAAAGACTCATGGTTTTCAAAAGATTTTGATAAA
          1 ATGGTTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAA

                                                          
      17120 ATGGTTTTTCAAAAAGAGTCATAGG-TTTCAAAAGGTTTTGATAAA
          1 ATGGTTTTTCAAAAAGAGTCAT-GGTTTTCAAAAGGTTTTGATAAA

                    *    
      17165 ATGGTTTTCCAAA
          1 ATGGTTTTTCAAA

      17178 GTTGTGTTTT


Statistics
Matches: 96,  Mismatches: 5, Indels: 3
        0.92            0.05        0.03

Matches are distributed among these distances:
  44    4  0.04
  45   90  0.94
  46    2  0.02

ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37


Consensus pattern (45 bp):   
ATGGTTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAA

Found at i:17531 original size:5 final size:5

Alignment explanation


    Indices: 17512--17546  Score: 52
    Period size: 5  Copynumber: 6.8  Consensus size: 5

      17502 TGAAAAAGAA

                             *                       
      17512 AAAAG AAAGAG AAAAT AAAAG AAAAG AAAAG AAAA
          1 AAAAG AAA-AG AAAAG AAAAG AAAAG AAAAG AAAA

      17547 AAAGAAAGTA


Statistics
Matches: 27,  Mismatches: 2, Indels: 2
        0.87            0.06        0.06

Matches are distributed among these distances:
   5   22  0.81
   6    5  0.19

ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03


Consensus pattern (5 bp):   
AAAAG

Found at i:17531 original size:16 final size:16

Alignment explanation


    Indices: 17512--17551  Score: 57
    Period size: 15  Copynumber: 2.6  Consensus size: 16

      17502 TGAAAAAGAA

                           *
      17512 AAAAGAAAGAGAAAAT
          1 AAAAGAAAGAGAAAAG

                            
      17528 AAAAGAAA-AGAAAAG
          1 AAAAGAAAGAGAAAAG

                      
      17543 AAAA-AAAGA
          1 AAAAGAAAGA

      17552 AAGTAGAAAG


Statistics
Matches: 22,  Mismatches: 1, Indels: 3
        0.85            0.04        0.12

Matches are distributed among these distances:
  14    3  0.14
  15   11  0.50
  16    8  0.36

ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03


Consensus pattern (16 bp):   
AAAAGAAAGAGAAAAG

Found at i:17573 original size:12 final size:13

Alignment explanation


    Indices: 17550--17578  Score: 51
    Period size: 12  Copynumber: 2.3  Consensus size: 13

      17540 AAGAAAAAAA

                         
      17550 GAAAGTAGAAAGT
          1 GAAAGTAGAAAGT

                         
      17563 GAAAGTA-AAAGT
          1 GAAAGTAGAAAGT

                
      17575 GAAA
          1 GAAA

      17579 ATTAAAAAGT


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  12    9  0.56
  13    7  0.44

ACGTcount: A:0.59, C:0.00, G:0.28, T:0.14


Consensus pattern (13 bp):   
GAAAGTAGAAAGT
Done.