Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013578.1 Corchorus capsularis cultivar CVL-1 contig13599, 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: 22594
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28


Found at i:9934 original size:22 final size:22

Alignment explanation


    Indices: 9906--9965  Score: 65
    Period size: 22  Copynumber: 2.9  Consensus size: 22

       9896 GAACTTCGTG

                               *  
       9906 TTTGAAGAATATTTGAAGATAA
          1 TTTGAAGAATATTTGAAGACAA

                                  
       9928 TTTGAAG---ATTTGAAGACAA
          1 TTTGAAGAATATTTGAAGACAA

                           *    
       9947 -TTGAAGAATTATTTCAAGA
          1 TTTGAAGAA-TATTTGAAGA

       9966 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   11  0.34
  22   15  0.47

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


Consensus pattern (22 bp):   
TTTGAAGAATATTTGAAGACAA

Found at i:9940 original size:19 final size:18

Alignment explanation


    Indices: 9916--9953  Score: 58
    Period size: 19  Copynumber: 2.1  Consensus size: 18

       9906 TTTGAAGAAT

                     *         
       9916 ATTTGAAGATAATTTGAAG
          1 ATTTGAAGACAA-TTGAAG

                              
       9935 ATTTGAAGACAATTGAAG
          1 ATTTGAAGACAATTGAAG

             
       9953 A
          1 A

       9954 ATTATTTCAA


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

Matches are distributed among these distances:
  18    7  0.39
  19   11  0.61

ACGTcount: A:0.45, C:0.03, G:0.21, T:0.32


Consensus pattern (18 bp):   
ATTTGAAGACAATTGAAG

Found at i:15127 original size:22 final size:22

Alignment explanation


    Indices: 15099--15158  Score: 65
    Period size: 22  Copynumber: 2.9  Consensus size: 22

      15089 GAAATTCGTG

                               *  
      15099 TTTGAAGAATATTTGAAGATAA
          1 TTTGAAGAATATTTGAAGACAA

                                  
      15121 TTTGAAG---ATTTGAAGACAA
          1 TTTGAAGAATATTTGAAGACAA

                           *    
      15140 -TTGAAGAATTATTTCAAGA
          1 TTTGAAGAA-TATTTGAAGA

      15159 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   11  0.34
  22   15  0.47

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


Consensus pattern (22 bp):   
TTTGAAGAATATTTGAAGACAA

Found at i:15133 original size:19 final size:18

Alignment explanation


    Indices: 15109--15146  Score: 58
    Period size: 19  Copynumber: 2.1  Consensus size: 18

      15099 TTTGAAGAAT

                     *         
      15109 ATTTGAAGATAATTTGAAG
          1 ATTTGAAGACAA-TTGAAG

                              
      15128 ATTTGAAGACAATTGAAG
          1 ATTTGAAGACAATTGAAG

             
      15146 A
          1 A

      15147 ATTATTTCAA


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

Matches are distributed among these distances:
  18    7  0.39
  19   11  0.61

ACGTcount: A:0.45, C:0.03, G:0.21, T:0.32


Consensus pattern (18 bp):   
ATTTGAAGACAATTGAAG

Found at i:16503 original size:6 final size:6

Alignment explanation


    Indices: 16492--16528  Score: 58
    Period size: 6  Copynumber: 6.3  Consensus size: 6

      16482 ATAATTGCCA

                                          *             
      16492 TAGATT TAGATT TAGATT TAGATT TACATT TA-ATT TA
          1 TAGATT TAGATT TAGATT TAGATT TAGATT TAGATT TA

      16529 CTTTGCTTAG


Statistics
Matches: 30,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
   5    5  0.17
   6   25  0.83

ACGTcount: A:0.35, C:0.03, G:0.11, T:0.51


Consensus pattern (6 bp):   
TAGATT

Found at i:16566 original size:15 final size:15

Alignment explanation


    Indices: 16546--16575  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

      16536 TAGATTTTAG

                    *      
      16546 TTTAATTGTTTTCTT
          1 TTTAATTGCTTTCTT

                           
      16561 TTTAATTGCTTTCTT
          1 TTTAATTGCTTTCTT

      16576 AAAATCCCCT


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.13, C:0.10, G:0.07, T:0.70


Consensus pattern (15 bp):   
TTTAATTGCTTTCTT

Found at i:21358 original size:15 final size:17

Alignment explanation


    Indices: 21338--21380  Score: 54
    Period size: 18  Copynumber: 2.6  Consensus size: 17

      21328 CTTGTGAAGA

                        *    
      21338 TTGAAAATTAG-GT-CT
          1 TTGAAAATTAGCCTCCT

                              
      21353 TTGAAAATTCAGCCTCCT
          1 TTGAAAATT-AGCCTCCT

                      
      21371 TTGAAAATTA
          1 TTGAAAATTA

      21381 CCTTGGTTCC


Statistics
Matches: 24,  Mismatches: 1, Indels: 4
        0.83            0.03        0.14

Matches are distributed among these distances:
  15    9  0.38
  16    2  0.08
  17    2  0.08
  18   11  0.46

ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37


Consensus pattern (17 bp):   
TTGAAAATTAGCCTCCT
Done.