Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007419.1 Corchorus capsularis cultivar CVL-1 contig07440, 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: 12680
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34


Found at i:2079 original size:20 final size:21

Alignment explanation


    Indices: 2042--2080  Score: 71
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       2032 GGGTCGTGAG

                                 
       2042 GCAAACCACATGGGGCGCCAA
          1 GCAAACCACATGGGGCGCCAA

                               
       2063 GCAAACCACAT-GGGCGCC
          1 GCAAACCACATGGGGCGCC

       2081 CAGCGCTAGT


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  20    7  0.39
  21   11  0.61

ACGTcount: A:0.31, C:0.36, G:0.28, T:0.05


Consensus pattern (21 bp):   
GCAAACCACATGGGGCGCCAA

Found at i:4633 original size:134 final size:134

Alignment explanation


    Indices: 4393--4656  Score: 474
    Period size: 134  Copynumber: 2.0  Consensus size: 134

       4383 ACCGCTAAAA

                       *                    *        *                       
       4393 AAGAGGATTTTGAGGTAGGGTTGATCATAAACTGACCGAACCGTTTAAACCGATCGAACCGATCA
          1 AAGAGGATTTTAAGGTAGGGTTGATCATAAACCGACCGAACAGTTTAAACCGATCGAACCGATCA

                                    *                  *                     
       4458 GTAAATGGTGCAAATGGTTCGGTGTAGGCGGTAGGTCGGTGTAGACGGTTCAAAGCATCGGTTTT
         66 GTAAATGGTGCAAATGGTTCGGTGCAGGCGGTAGGTCGGTGTAAACGGTTCAAAGCATCGGTTTT

                
       4523 GAAG
        131 GAAG

                                                                           * 
       4527 AAGAGGATTTTAAGGTAGGGTTGATCATAAACCGACCGAACAGTTTAAACCGATCGAACCGATTA
          1 AAGAGGATTTTAAGGTAGGGTTGATCATAAACCGACCGAACAGTTTAAACCGATCGAACCGATCA

                                                                             
       4592 GTAAATGGTGCAAATGGTTCGGTGCAGGCGGTAGGTCGGTGTAAACGGTTCAAAGCATCGGTTTT
         66 GTAAATGGTGCAAATGGTTCGGTGCAGGCGGTAGGTCGGTGTAAACGGTTCAAAGCATCGGTTTT

       4657 TCAGTAAGTC


Statistics
Matches: 124,  Mismatches: 6, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
 134  124  1.00

ACGTcount: A:0.29, C:0.15, G:0.30, T:0.25


Consensus pattern (134 bp):   
AAGAGGATTTTAAGGTAGGGTTGATCATAAACCGACCGAACAGTTTAAACCGATCGAACCGATCA
GTAAATGGTGCAAATGGTTCGGTGCAGGCGGTAGGTCGGTGTAAACGGTTCAAAGCATCGGTTTT
GAAG

Found at i:5607 original size:25 final size:25

Alignment explanation


    Indices: 5547--5594  Score: 87
    Period size: 25  Copynumber: 1.9  Consensus size: 25

       5537 AATCCAAATC

                            *        
       5547 TTGGCAACTTTGGTCTGCTTGAATA
          1 TTGGCAACTTTGGTCTACTTGAATA

                                   
       5572 TTGGCAACTTTGGTCTACTTGAA
          1 TTGGCAACTTTGGTCTACTTGAA

       5595 GTTATTGATC


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  25   22  1.00

ACGTcount: A:0.21, C:0.17, G:0.23, T:0.40


Consensus pattern (25 bp):   
TTGGCAACTTTGGTCTACTTGAATA

Found at i:6902 original size:33 final size:33

Alignment explanation


    Indices: 6832--6932  Score: 132
    Period size: 33  Copynumber: 3.1  Consensus size: 33

       6822 ACGTGCCTTA

                                  *** *      *
       6832 AGCCGCCCTAGTGGGGAGGCT-TATCATGGCTCA
          1 AGCCGCCCTAGTGGGGAGGCTCCGCCGTGGCT-G

                                             
       6865 AGCCGCCCTAGTGGGGAGGCTCCGCCGTGGCTG
          1 AGCCGCCCTAGTGGGGAGGCTCCGCCGTGGCTG

                   *                         
       6898 AGCCGCCTTAGTGGGGAGGCTCCGCCGTGGCTG
          1 AGCCGCCCTAGTGGGGAGGCTCCGCCGTGGCTG

              
       6931 AG
          1 AG

       6933 GGCAAAAATG


Statistics
Matches: 61,  Mismatches: 6, Indels: 2
        0.88            0.09        0.03

Matches are distributed among these distances:
  33   55  0.90
  34    6  0.10

ACGTcount: A:0.13, C:0.30, G:0.40, T:0.18


Consensus pattern (33 bp):   
AGCCGCCCTAGTGGGGAGGCTCCGCCGTGGCTG

Found at i:7240 original size:5 final size:5

Alignment explanation


    Indices: 7182--7254  Score: 58
    Period size: 5  Copynumber: 13.6  Consensus size: 5

       7172 AATTAAAATT

                              *    *                                   
       7182 AAAGA AAGAGAA AAAGG AAACA AAA-A AAATGAA AAAGA AAAGGA AAAGGA
          1 AAAGA AA-AG-A AAAGA AAAGA AAAGA AAA-G-A AAAGA AAA-GA AAA-GA

                *                      
       7232 AAAGG AAAGA AAAGA AAAGA AAA
          1 AAAGA AAAGA AAAGA AAAGA AAA

       7255 CCGTAATATG


Statistics
Matches: 57,  Mismatches: 5, Indels: 12
        0.77            0.07        0.16

Matches are distributed among these distances:
   4    4  0.07
   5   30  0.53
   6   16  0.28
   7    7  0.12

ACGTcount: A:0.75, C:0.01, G:0.22, T:0.01


Consensus pattern (5 bp):   
AAAGA

Found at i:11407 original size:67 final size:67

Alignment explanation


    Indices: 11328--11460  Score: 212
    Period size: 67  Copynumber: 2.0  Consensus size: 67

      11318 CTGTTGCTTA

                                                             *   *           
      11328 GTGGGAGAATTTGGGTAATAGAATGAACCTTTTGGGGTAAAATATTCAAGGAATTTATTTAATTG
          1 GTGGGAGAATTTGGGTAATAGAATGAACCTTTTGGGGTAAAATATTCAAAGAACTTATTTAATTG

              
      11393 TT
         66 TT

                            **                *     *                        
      11395 GTGGGAGAATTTGGGTTTTAGAATGAACCTTTTGTGGTAAGATATTCAAAGAACTTATTTAATTG
          1 GTGGGAGAATTTGGGTAATAGAATGAACCTTTTGGGGTAAAATATTCAAAGAACTTATTTAATTG

             
      11460 T
         66 T

      11461 GGCTCTACGG


Statistics
Matches: 60,  Mismatches: 6, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  67   60  1.00

ACGTcount: A:0.32, C:0.05, G:0.25, T:0.38


Consensus pattern (67 bp):   
GTGGGAGAATTTGGGTAATAGAATGAACCTTTTGGGGTAAAATATTCAAAGAACTTATTTAATTG
TT
Done.