Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008290.1 Corchorus capsularis cultivar CVL-1 contig08311, 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: 8138
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32


Found at i:853 original size:16 final size:16

Alignment explanation


    Indices: 832--863  Score: 64
    Period size: 16  Copynumber: 2.0  Consensus size: 16

        822 TGGGGATTAT

                            
        832 CTTATGATTGCTGACG
          1 CTTATGATTGCTGACG

                            
        848 CTTATGATTGCTGACG
          1 CTTATGATTGCTGACG

        864 ACACGATCAT


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:0.19, C:0.19, G:0.25, T:0.38


Consensus pattern (16 bp):   
CTTATGATTGCTGACG

Found at i:985 original size:20 final size:20

Alignment explanation


    Indices: 960--999  Score: 53
    Period size: 20  Copynumber: 2.0  Consensus size: 20

        950 TTTTTTCTAT

                                
        960 AAAAAAAATTGCGTCGAAAA
          1 AAAAAAAATTGCGTCGAAAA

                  **   *        
        980 AAAAAATTTTGTGTCGAAAA
          1 AAAAAAAATTGCGTCGAAAA

       1000 CAAATTTAGG


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  20   17  1.00

ACGTcount: A:0.55, C:0.07, G:0.15, T:0.23


Consensus pattern (20 bp):   
AAAAAAAATTGCGTCGAAAA

Found at i:5095 original size:11 final size:11

Alignment explanation


    Indices: 5079--5110  Score: 55
    Period size: 11  Copynumber: 2.9  Consensus size: 11

       5069 GAAGTTCGTG

                       
       5079 TTTGAAGATTA
          1 TTTGAAGATTA

                     * 
       5090 TTTGAAGATAA
          1 TTTGAAGATTA

                      
       5101 TTTGAAGATT
          1 TTTGAAGATT

       5111 TGAAGACAAT


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  11   19  1.00

ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44


Consensus pattern (11 bp):   
TTTGAAGATTA

Found at i:5104 original size:22 final size:22

Alignment explanation


    Indices: 5079--5138  Score: 65
    Period size: 22  Copynumber: 2.9  Consensus size: 22

       5069 GAAGTTCGTG

                               *  
       5079 TTTGAAGATTATTTGAAGATAA
          1 TTTGAAGATTATTTGAAGACAA

                                  
       5101 TTTGAAG---ATTTGAAGACAA
          1 TTTGAAGATTATTTGAAGACAA

                           *    
       5120 TTT-AAGAATTATTTCAAGA
          1 TTTGAAG-ATTATTTGAAGA

       5139 AGCAAGAATT


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

Matches are distributed among these distances:
  18    3  0.09
  19   14  0.44
  22   15  0.47

ACGTcount: A:0.42, C:0.03, G:0.17, T:0.38


Consensus pattern (22 bp):   
TTTGAAGATTATTTGAAGACAA

Found at i:5113 original size:19 final size:18

Alignment explanation


    Indices: 5089--5126  Score: 58
    Period size: 19  Copynumber: 2.1  Consensus size: 18

       5079 TTTGAAGATT

                     *         
       5089 ATTTGAAGATAATTTGAAG
          1 ATTTGAAGACAATTT-AAG

                              
       5108 ATTTGAAGACAATTTAAG
          1 ATTTGAAGACAATTTAAG

             
       5126 A
          1 A

       5127 ATTATTTCAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  18    4  0.22
  19   14  0.78

ACGTcount: A:0.45, C:0.03, G:0.18, T:0.34


Consensus pattern (18 bp):   
ATTTGAAGACAATTTAAG

Found at i:6477 original size:6 final size:6

Alignment explanation


    Indices: 6466--6496  Score: 55
    Period size: 6  Copynumber: 5.3  Consensus size: 6

       6456 ATAATTGCCA

                                                 
       6466 TAGATT TAGATT TAGATT TAGATT TA-ATT TA
          1 TAGATT TAGATT TAGATT TAGATT TAGATT TA

       6497 CTTTGCTTAG


Statistics
Matches: 25,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   5    5  0.20
   6   20  0.80

ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52


Consensus pattern (6 bp):   
TAGATT

Done.