Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016239.1 Corchorus capsularis cultivar CVL-1 contig16260, 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: 9482
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31


Found at i:2805 original size:11 final size:11

Alignment explanation


    Indices: 2789--2820  Score: 55
    Period size: 11  Copynumber: 2.9  Consensus size: 11

       2779 TCCAAGTTCG

                       
       2789 TATTTGAAGAT
          1 TATTTGAAGAT

                       
       2800 TATTTGAAGAT
          1 TATTTGAAGAT

            *         
       2811 AATTTGAAGA
          1 TATTTGAAGA

       2821 ATTGAAGACC


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  11   20  1.00

ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41


Consensus pattern (11 bp):   
TATTTGAAGAT

Found at i:4235 original size:22 final size:23

Alignment explanation


    Indices: 4191--4238  Score: 64
    Period size: 21  Copynumber: 2.2  Consensus size: 23

       4181 TAGATTTAGA

                      *            
       4191 TTTAATTTACTTTGCCTTTTTTT
          1 TTTAATTTACATTGCCTTTTTTT

                               *   
       4214 TTTAATTTA-ATTG-CTTTCTTT
          1 TTTAATTTACATTGCCTTTTTTT

                
       4235 TTTA
          1 TTTA

       4239 TTGATAATTT


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  21   11  0.48
  22    3  0.13
  23    9  0.39

ACGTcount: A:0.17, C:0.10, G:0.04, T:0.69


Consensus pattern (23 bp):   
TTTAATTTACATTGCCTTTTTTT

Found at i:8289 original size:2 final size:2

Alignment explanation


    Indices: 8282--8329  Score: 87
    Period size: 2  Copynumber: 24.0  Consensus size: 2

       8272 TTGATCCTTG

                                                          *               
       8282 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                    
       8324 AT AT AT
          1 AT AT AT

       8330 GCATTCAAAA


Statistics
Matches: 44,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   2   44  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:8892 original size:11 final size:11

Alignment explanation


    Indices: 8876--8907  Score: 55
    Period size: 11  Copynumber: 2.9  Consensus size: 11

       8866 TCGAAGTTTG

                       
       8876 TATTTGAAGAT
          1 TATTTGAAGAT

                       
       8887 TATTTGAAGAT
          1 TATTTGAAGAT

            *         
       8898 AATTTGAAGA
          1 TATTTGAAGA

       8908 ATTGAAGACC


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  11   20  1.00

ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41


Consensus pattern (11 bp):   
TATTTGAAGAT

Found at i:8914 original size:19 final size:18

Alignment explanation


    Indices: 8890--8928  Score: 51
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       8880 TGAAGATTAT

                   *           
       8890 TTGAAGATAATTTGAAGAA
          1 TTGAAGACAA-TTGAAGAA

                    *         
       8909 TTGAAGACCATTGAAGAA
          1 TTGAAGACAATTGAAGAA

              
       8927 TT
          1 TT

       8929 ATTTCAAGAA


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  18   10  0.56
  19    8  0.44

ACGTcount: A:0.44, C:0.05, G:0.21, T:0.31


Consensus pattern (18 bp):   
TTGAAGACAATTGAAGAA
Done.