Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003212.1 Corchorus capsularis cultivar CVL-1 contig03220, 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, 609

Length: 1016
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.28


Found at i:99 original size:35 final size:35

Alignment explanation


    Indices: 19--120  Score: 168
    Period size: 35  Copynumber: 2.9  Consensus size: 35

          9 AGTAAGTTCT

                                                
         19 AAGACTTAATTTCACAAGAATTAAGTTAAAATAGCA
          1 AAGACTTAATTTCACAAGAATTAAG-TAAAATAGCA

                                         *  *  
         55 AAGACTTAATTTCACAAGAATTAAGTAAATTATCA
          1 AAGACTTAATTTCACAAGAATTAAGTAAAATAGCA

                          *                
         90 AAGACTTAATTTCAAAAGAATTAAGTAAAAT
          1 AAGACTTAATTTCACAAGAATTAAGTAAAAT

        121 TAGGTAAAAT


Statistics
Matches: 62,  Mismatches: 4, Indels: 1
        0.93            0.06        0.01

Matches are distributed among these distances:
  35   37  0.60
  36   25  0.40

ACGTcount: A:0.51, C:0.10, G:0.10, T:0.29


Consensus pattern (35 bp):   
AAGACTTAATTTCACAAGAATTAAGTAAAATAGCA

Found at i:138 original size:46 final size:45

Alignment explanation


    Indices: 73--166  Score: 152
    Period size: 46  Copynumber: 2.1  Consensus size: 45

         63 ATTTCACAAG

                          *                              
         73 AATTAAGTAAATTATCAAAGACTTAATTTCAAAAGAATTAAGTAA
          1 AATTAAGTAAATTAGCAAAGACTTAATTTCAAAAGAATTAAGTAA

                 *                          *             
        118 AATTAGGTAAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAA
          1 AATTAAGT-AAATTAGCAAAGACTTAATTTCAAAAGAATTAAGTAA

               
        164 AAT
          1 AAT

        167 CAGCAAAGAT


Statistics
Matches: 45,  Mismatches: 3, Indels: 1
        0.92            0.06        0.02

Matches are distributed among these distances:
  45    7  0.16
  46   38  0.84

ACGTcount: A:0.52, C:0.07, G:0.11, T:0.30


Consensus pattern (45 bp):   
AATTAAGTAAATTAGCAAAGACTTAATTTCAAAAGAATTAAGTAA

Found at i:325 original size:33 final size:33

Alignment explanation


    Indices: 242--358  Score: 119
    Period size: 33  Copynumber: 3.5  Consensus size: 33

        232 AGGCAAAAGA

                     *            *             
        242 AGACTGAAAGAAGACTGACAA-AAGACTAGAAAGTT
          1 AGACTGAAAAAAGACTGA-AATTAGACTA-AAA-TT

                   * **                      
        277 AGACTGACATCAGACTGAAATTAGACTAAAATT
          1 AGACTGAAAAAAGACTGAAATTAGACTAAAATT

                              *        *     
        310 AGACTGAAAAAAGACTGATATTAGACTGAAATT
          1 AGACTGAAAAAAGACTGAAATTAGACTAAAATT

            *      *        
        343 GGACTGATAAAAGACT
          1 AGACTGAAAAAAGACT

        359 AGCTTAATTT


Statistics
Matches: 70,  Mismatches: 11, Indels: 4
        0.82            0.13        0.05

Matches are distributed among these distances:
  33   44  0.63
  34    5  0.07
  35   21  0.30

ACGTcount: A:0.48, C:0.12, G:0.20, T:0.21


Consensus pattern (33 bp):   
AGACTGAAAAAAGACTGAAATTAGACTAAAATT

Found at i:335 original size:11 final size:11

Alignment explanation


    Indices: 242--349  Score: 92
    Period size: 11  Copynumber: 9.6  Consensus size: 11

        232 AGGCAAAAGA

                     **
        242 AGACTGAAAGA
          1 AGACTGAAATT

                       *
        253 AGACTGACAA-A
          1 AGACTGA-AATT

                         
        264 AGACTAGAAAGTT
          1 AGACT-GAAA-TT

                   *  *
        277 AGACTGACATC
          1 AGACTGAAATT

                       
        288 AGACTGAAATT
          1 AGACTGAAATT

                 *     
        299 AGACTAAAATT
          1 AGACTGAAATT

                     **
        310 AGACTGAAAAA
          1 AGACTGAAATT

                   *   
        321 AGACTGATATT
          1 AGACTGAAATT

                       
        332 AGACTGAAATT
          1 AGACTGAAATT

            *      
        343 GGACTGA
          1 AGACTGA

        350 TAAAAGACTA


Statistics
Matches: 79,  Mismatches: 14, Indels: 8
        0.78            0.14        0.08

Matches are distributed among these distances:
  11   67  0.85
  12    7  0.09
  13    5  0.06

ACGTcount: A:0.47, C:0.12, G:0.20, T:0.20


Consensus pattern (11 bp):   
AGACTGAAATT

Done.