Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003333.1 Corchorus capsularis cultivar CVL-1 contig03341, 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, 682

Length: 1137
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34


Found at i:51 original size:11 final size:11

Alignment explanation


    Indices: 35--64  Score: 51
    Period size: 11  Copynumber: 2.7  Consensus size: 11

         25 AAAGTTCGTG

                     * 
         35 TTTGAAGATTA
          1 TTTGAAGATAA

                       
         46 TTTGAAGATAA
          1 TTTGAAGATAA

                    
         57 TTTGAAGA
          1 TTTGAAGA

         65 ATTGAAGACA


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

Matches are distributed among these distances:
  11   18  1.00

ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40


Consensus pattern (11 bp):   
TTTGAAGATAA

Found at i:63 original size:22 final size:22

Alignment explanation


    Indices: 35--94  Score: 65
    Period size: 22  Copynumber: 2.9  Consensus size: 22

         25 AAAGTTCGTG

                               *  
         35 TTTGAAGATTATTTGAAGATAA
          1 TTTGAAGATTATTTGAAGACAA

                                  
         57 TTTGAAGA--A-TTGAAGACAA
          1 TTTGAAGATTATTTGAAGACAA

                           *    
         76 -TTGAAGAATTATTTCAAGA
          1 TTTGAAG-ATTATTTGAAGA

         95 AGCAAGAATT


Statistics
Matches: 32,  Mismatches: 2, Indels: 8
        0.76            0.05        0.19

Matches are distributed among these distances:
  18    6  0.19
  19   10  0.31
  20    1  0.03
  21    1  0.03
  22   14  0.44

ACGTcount: A:0.43, C:0.03, G:0.18, T:0.35


Consensus pattern (22 bp):   
TTTGAAGATTATTTGAAGACAA

Found at i:81 original size:18 final size:19

Alignment explanation


    Indices: 47--85  Score: 62
    Period size: 18  Copynumber: 2.1  Consensus size: 19

         37 TGAAGATTAT

                   *           
         47 TTGAAGATAATTTGAAGAA
          1 TTGAAGACAATTTGAAGAA

                               
         66 TTGAAGACAA-TTGAAGAA
          1 TTGAAGACAATTTGAAGAA

              
         84 TT
          1 TT

         86 ATTTCAAGAA


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  18   10  0.53
  19    9  0.47

ACGTcount: A:0.46, C:0.03, G:0.21, T:0.31


Consensus pattern (19 bp):   
TTGAAGACAATTTGAAGAA
Done.