Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016390.1 Corchorus olitorius cultivar O-4 contig16423, 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: 25626
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33


Found at i:12858 original size:120 final size:120

Alignment explanation


    Indices: 12645--12897  Score: 409
    Period size: 120  Copynumber: 2.1  Consensus size: 120

      12635 CTCACTAGTG

                                                                             
      12645 TTAA-TAAAAGAAAGGCAAATTATACAATACACCGACGGTGGAGTTTAGCAGACTACACAAGCGA
          1 TTAATTAAAA-AAAGGCAAATTATACAATACACCGACGGTGGAGTTTAGCAGACTACACAAGCGA

               *                    *                               
      12709 GTCTTGAAGGGTGACATGTGTCCTTTAGGGACTAGATTGAAATATTTAAAACTTAA
         65 GTCCTGAAGGGTGACATGTGTCCTCTAGGGACTAGATTGAAATATTTAAAACTTAA

                  *                   *       *                   *        * 
      12765 TTAATTCAAAAAAGGCAAATTATACAGTACACCGGCGGTGGAGTTTAGCAGACTTCACAAGCGGG
          1 TTAATTAAAAAAAGGCAAATTATACAATACACCGACGGTGGAGTTTAGCAGACTACACAAGCGAG

                                             *                *    
      12830 TCCTGAAGGGTGACATGTGTCCTCTAGGGACTATATTGAAATATTTAAAATTTAA
         66 TCCTGAAGGGTGACATGTGTCCTCTAGGGACTAGATTGAAATATTTAAAACTTAA

                         
      12885 TTAATTAAAAAAA
          1 TTAATTAAAAAAA

      12898 TGGACATGTG


Statistics
Matches: 122,  Mismatches: 10, Indels: 2
        0.91            0.07        0.01

Matches are distributed among these distances:
 120  118  0.97
 121    4  0.03

ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27


Consensus pattern (120 bp):   
TTAATTAAAAAAAGGCAAATTATACAATACACCGACGGTGGAGTTTAGCAGACTACACAAGCGAG
TCCTGAAGGGTGACATGTGTCCTCTAGGGACTAGATTGAAATATTTAAAACTTAA

Found at i:15045 original size:6 final size:6

Alignment explanation


    Indices: 15036--15077  Score: 54
    Period size: 6  Copynumber: 7.5  Consensus size: 6

      15026 AAATTGGAAA

                                     *                          
      15036 AAAAAG AAAAAG AAAAAG -AAAGG AAAAA- AAAAAG -AAAAG AAA
          1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAA

      15078 GCACATAAGT


Statistics
Matches: 31,  Mismatches: 2, Indels: 6
        0.79            0.05        0.15

Matches are distributed among these distances:
   5   14  0.45
   6   17  0.55

ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00


Consensus pattern (6 bp):   
AAAAAG

Found at i:15052 original size:16 final size:16

Alignment explanation


    Indices: 15033--15077  Score: 65
    Period size: 16  Copynumber: 2.8  Consensus size: 16

      15023 TTGAAATTGG

                             
      15033 AAAA-AAAAGAAAAAGA
          1 AAAAGAAAAGAAAAA-A

                    *       
      15049 AAAAGAAAGGAAAAAA
          1 AAAAGAAAAGAAAAAA

                         
      15065 AAAAGAAAAGAAA
          1 AAAAGAAAAGAAA

      15078 GCACATAAGT


Statistics
Matches: 26,  Mismatches: 2, Indels: 2
        0.87            0.07        0.07

Matches are distributed among these distances:
  16   17  0.65
  17    9  0.35

ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00


Consensus pattern (16 bp):   
AAAAGAAAAGAAAAAA

Found at i:15053 original size:12 final size:12

Alignment explanation


    Indices: 15036--15077  Score: 54
    Period size: 11  Copynumber: 3.8  Consensus size: 12

      15026 AAATTGGAAA

                        
      15036 AAAAAGAAAAAG
          1 AAAAAGAAAAAG

                      * 
      15048 AAAAAG-AAAGG
          1 AAAAAGAAAAAG

                        
      15059 AAAAA-AAAAAG
          1 AAAAAGAAAAAG

                     
      15070 -AAAAGAAA
          1 AAAAAGAAA

      15078 GCACATAAGT


Statistics
Matches: 26,  Mismatches: 2, Indels: 5
        0.79            0.06        0.15

Matches are distributed among these distances:
  10    4  0.15
  11   16  0.62
  12    6  0.23

ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00


Consensus pattern (12 bp):   
AAAAAGAAAAAG

Found at i:17534 original size:21 final size:21

Alignment explanation


    Indices: 17508--17551  Score: 88
    Period size: 21  Copynumber: 2.1  Consensus size: 21

      17498 ATGAATGGAT

                                 
      17508 TATTGTTACCGGAGTAAATAA
          1 TATTGTTACCGGAGTAAATAA

                                 
      17529 TATTGTTACCGGAGTAAATAA
          1 TATTGTTACCGGAGTAAATAA

              
      17550 TA
          1 TA

      17552 AATAGAATTT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   23  1.00

ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34


Consensus pattern (21 bp):   
TATTGTTACCGGAGTAAATAA
Done.