Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001552.1 Corchorus capsularis cultivar CVL-1 contig01552, 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: 5348
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33


Found at i:186 original size:2 final size:2

Alignment explanation


    Indices: 179--208  Score: 51
    Period size: 2  Copynumber: 15.0  Consensus size: 2

        169 AACAATTTAT

                                     *                  
        179 TA TA TA TA TA TA TA TA TT TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

        209 GAATGAAGAA


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (2 bp):   
TA

Found at i:2416 original size:2 final size:2

Alignment explanation


    Indices: 2403--2436  Score: 59
    Period size: 2  Copynumber: 16.5  Consensus size: 2

       2393 TATTTTGAAG

                                                              
       2403 AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT A

       2437 CACACACACA


Statistics
Matches: 31,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   2   29  0.94
   3    2  0.06

ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47


Consensus pattern (2 bp):   
AT

Found at i:5051 original size:30 final size:28

Alignment explanation


    Indices: 5016--5087  Score: 92
    Period size: 28  Copynumber: 2.5  Consensus size: 28

       5006 GAAGTTTATT

                   *                      
       5016 GGGCAAATC-TCCTAAATTTGAAAATTCAA
          1 GGGCAAAACGTCCT-AATTTG-AAATTCAA

                           *             
       5045 GAGGCAAAACGTCCTGATTTGAAATTCAA
          1 G-GGCAAAACGTCCTAATTTGAAATTCAA

                          
       5074 GGGCAAAACGTCCT
          1 GGGCAAAACGTCCT

       5088 TCACGTACCC


Statistics
Matches: 39,  Mismatches: 2, Indels: 5
        0.85            0.04        0.11

Matches are distributed among these distances:
  28   13  0.33
  29   10  0.26
  30   12  0.31
  31    4  0.10

ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24


Consensus pattern (28 bp):   
GGGCAAAACGTCCTAATTTGAAATTCAA

Found at i:5083 original size:28 final size:30

Alignment explanation


    Indices: 5031--5087  Score: 100
    Period size: 28  Copynumber: 2.0  Consensus size: 30

       5021 AATCTCCTAA

                                          
       5031 ATTTGAAAATTCAAGAGGCAAAACGTCCTG
          1 ATTTGAAAATTCAAGAGGCAAAACGTCCTG

                                         
       5061 ATTTG-AAATTCAAG-GGCAAAACGTCCT
          1 ATTTGAAAATTCAAGAGGCAAAACGTCCT

       5088 TCACGTACCC


Statistics
Matches: 27,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
  28   13  0.48
  29    9  0.33
  30    5  0.19

ACGTcount: A:0.39, C:0.18, G:0.19, T:0.25


Consensus pattern (30 bp):   
ATTTGAAAATTCAAGAGGCAAAACGTCCTG
Done.