Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013742.1 Corchorus olitorius cultivar O-4 contig13775, 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: 7730
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:103 original size:62 final size:63

Alignment explanation


    Indices: 1--157  Score: 235
    Period size: 62  Copynumber: 2.4  Consensus size: 63

                  *                      *                                  
          1 AAAATTTTTGACACCAGAAGATTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCA-TG
          1 AAAATTATTGACACCAGAAG-TTGTCATAGCAAATTATTATCTTGACACCAGAAGTTGTCACTG

                                                                             
         64 AAAATTATTGACACCAGAAGTTGTCATAGCAAATTATTATCTTGACACCAGAAGTTGTCATGCTG
          1 AAAATTATTGACACCAGAAGTTGTCATAGCAAATTATTATCTTGACACCAGAAGTTGTCA--CTG

                            *            
        129 AGGAAATTATTGACACTAGAAGTTGTCAT
          1 A--AAATTATTGACACCAGAAGTTGTCAT

        158 CCTAAGATTG


Statistics
Matches: 86,  Mismatches: 3, Indels: 6
        0.91            0.03        0.06

Matches are distributed among these distances:
  62   39  0.45
  63   19  0.22
  65    3  0.03
  67   25  0.29

ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32


Consensus pattern (63 bp):   
AAAATTATTGACACCAGAAGTTGTCATAGCAAATTATTATCTTGACACCAGAAGTTGTCACTG

Found at i:109 original size:34 final size:34

Alignment explanation


    Indices: 8--124  Score: 174
    Period size: 34  Copynumber: 3.6  Consensus size: 34

          1 AAAATTT

                                  *            
          8 TTGACACCAGAAGATTGTCATATCAAATTATTATC
          1 TTGACACCAGAAG-TTGTCATAGCAAATTATTATC

                                              
         43 TTGACACCAGAAGTTGTCAT-G-AAA--ATTA--
          1 TTGACACCAGAAGTTGTCATAGCAAATTATTATC

                                              
         71 TTGACACCAGAAGTTGTCATAGCAAATTATTATC
          1 TTGACACCAGAAGTTGTCATAGCAAATTATTATC

                                
        105 TTGACACCAGAAGTTGTCAT
          1 TTGACACCAGAAGTTGTCAT

        125 GCTGAGGAAA


Statistics
Matches: 75,  Mismatches: 1, Indels: 13
        0.84            0.01        0.15

Matches are distributed among these distances:
  28   20  0.27
  29    1  0.01
  30    7  0.09
  32    7  0.09
  34   27  0.36
  35   13  0.17

ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32


Consensus pattern (34 bp):   
TTGACACCAGAAGTTGTCATAGCAAATTATTATC

Found at i:7226 original size:21 final size:21

Alignment explanation


    Indices: 7202--7268  Score: 57
    Period size: 21  Copynumber: 3.2  Consensus size: 21

       7192 AATTCTCTGT

                                 
       7202 AAATTAAGAAATACTCAACTC
          1 AAATTAAGAAATACTCAACTC

                *         *   **  *
       7223 AAATCATAGAAA-ATTC-TTTGT
          1 AAATTA-AGAAATACTCAACT-C

                                 
       7244 AAATTAAGAAATACTCAACTC
          1 AAATTAAGAAATACTCAACTC

                
       7265 AAAT
          1 AAAT

       7269 CATGATCCTT


Statistics
Matches: 32,  Mismatches: 10, Indels: 8
        0.64            0.20        0.16

Matches are distributed among these distances:
  20    6  0.19
  21   20  0.62
  22    6  0.19

ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28


Consensus pattern (21 bp):   
AAATTAAGAAATACTCAACTC

Found at i:7248 original size:42 final size:42

Alignment explanation


    Indices: 7189--7271  Score: 157
    Period size: 42  Copynumber: 2.0  Consensus size: 42

       7179 GCTAAGTCTT

                                                      
       7189 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
          1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA

                     *                               
       7231 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATCAT
          1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCAT

       7272 GATCCTTAGC


Statistics
Matches: 40,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  42   40  1.00

ACGTcount: A:0.47, C:0.16, G:0.07, T:0.30


Consensus pattern (42 bp):   
GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA

Found at i:7407 original size:56 final size:57

Alignment explanation


    Indices: 7335--7449  Score: 187
    Period size: 57  Copynumber: 2.0  Consensus size: 57

       7325 TTTATTTTGT

                                                                     
       7335 AGAATAATTAAGTAGAGAT-AGGGGGATAGGATTTATTATAACATTTATTGTGCGAA
          1 AGAATAATTAAGTAGAGATAAGGGGGATAGGATTTATTATAACATTTATTGTGCGAA

                                         *        *           *  *   
       7391 AGAATAATTAAGTAGAGATAAGGGGGATATGATTTATTTTAACATTTATTTTGTGAA
          1 AGAATAATTAAGTAGAGATAAGGGGGATAGGATTTATTATAACATTTATTGTGCGAA

              
       7448 AG
          1 AG

       7450 GAAACAAATA


Statistics
Matches: 54,  Mismatches: 4, Indels: 1
        0.92            0.07        0.02

Matches are distributed among these distances:
  56   19  0.35
  57   35  0.65

ACGTcount: A:0.39, C:0.03, G:0.23, T:0.35


Consensus pattern (57 bp):   
AGAATAATTAAGTAGAGATAAGGGGGATAGGATTTATTATAACATTTATTGTGCGAA

Found at i:7693 original size:2 final size:2

Alignment explanation


    Indices: 7686--7723  Score: 76
    Period size: 2  Copynumber: 19.0  Consensus size: 2

       7676 AGAGAATGGT

                                                                    
       7686 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       7724 CTACTAA


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   36  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Done.