Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021631.1 Corchorus olitorius cultivar O-4 contig21664, 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: 21248
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:6739 original size:48 final size:50

Alignment explanation


    Indices: 6655--6748  Score: 131
    Period size: 48  Copynumber: 1.9  Consensus size: 50

       6645 TTTTTCAAAA

                                                     *        
       6655 ACGCAACACAAAAAATTTAAAAACGCAAAAATCAAAAAAAATTTTTTATG
          1 ACGCAACACAAAAAATTTAAAAACGCAAAAATCAAAAAAAAATTTTTATG

                      *              *                     
       6705 ACGCAA-ACACAAAA-TTAAAAACGGACAAAA-CAAAAAAAAATTTT
          1 ACGCAACACAAAAAATTTAAAAACGCA-AAAATCAAAAAAAAATTTT

       6749 AGGTTTAAAA


Statistics
Matches: 40,  Mismatches: 3, Indels: 4
        0.85            0.06        0.09

Matches are distributed among these distances:
  48   23  0.57
  49   11  0.28
  50    6  0.15

ACGTcount: A:0.61, C:0.15, G:0.06, T:0.18


Consensus pattern (50 bp):   
ACGCAACACAAAAAATTTAAAAACGCAAAAATCAAAAAAAAATTTTTATG

Found at i:6900 original size:29 final size:30

Alignment explanation


    Indices: 6859--6931  Score: 112
    Period size: 30  Copynumber: 2.4  Consensus size: 30

       6849 AGTCTATTTT

                                           
       6859 CCTTCCCCTGGCAAAAACCAGAAAAAGTT-C
          1 CCTTCCCC-GGCAAAAACCAGAAAAAGTTAC

                          *        *      
       6889 CCTTCCCCGGCAAATACCAGAAACAGTTAC
          1 CCTTCCCCGGCAAAAACCAGAAAAAGTTAC

                         
       6919 CCTTCCCCGGCAA
          1 CCTTCCCCGGCAA

       6932 CGGCGCCAAA


Statistics
Matches: 40,  Mismatches: 2, Indels: 2
        0.91            0.05        0.05

Matches are distributed among these distances:
  29   18  0.45
  30   22  0.55

ACGTcount: A:0.32, C:0.38, G:0.14, T:0.16


Consensus pattern (30 bp):   
CCTTCCCCGGCAAAAACCAGAAAAAGTTAC

Found at i:11305 original size:126 final size:126

Alignment explanation


    Indices: 11077--11310  Score: 369
    Period size: 126  Copynumber: 1.9  Consensus size: 126

      11067 AAACGCAAAC

                                         *   *  *        *                   
      11077 TTTTTTTTTTTGAATTTTCACTATTTTTCTATAGAAGATAATAGTGTAAGAACCCTAAATCTAAA
          1 TTTTTTTTTTTGAATTTTCACTATTTTTCAATAAAACATAATAGTATAAGAACCCTAAATCTAAA

                           *    *                                        
      11142 ATTTCAAGTAAATCGCACCACTAATGAATGCAAAACAAAAATCTTTAATCCTCCCTGTGAT
         66 ATTTCAAGTAAATCGAACCAATAATGAATGCAAAACAAAAATCTTTAATCCTCCCTGTGAT

                                                 *  *                        
      11203 TTTTTTTTTTTGAATTTTCACTATTTTTCAATAAAACCTAGTAGTATAAGAACCCTAAATCTAAA
          1 TTTTTTTTTTTGAATTTTCACTATTTTTCAATAAAACATAATAGTATAAGAACCCTAAATCTAAA

                     *                    * *          
      11268 ATTTCAAGTCAATCGAACCAATAATGAATGTAGAACAAAAATC
         66 ATTTCAAGTAAATCGAACCAATAATGAATGCAAAACAAAAATC

      11311 ACAAAATTCA


Statistics
Matches: 97,  Mismatches: 11, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
 126   97  1.00

ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37


Consensus pattern (126 bp):   
TTTTTTTTTTTGAATTTTCACTATTTTTCAATAAAACATAATAGTATAAGAACCCTAAATCTAAA
ATTTCAAGTAAATCGAACCAATAATGAATGCAAAACAAAAATCTTTAATCCTCCCTGTGAT

Found at i:14303 original size:21 final size:20

Alignment explanation


    Indices: 14256--14314  Score: 66
    Period size: 21  Copynumber: 3.0  Consensus size: 20

      14246 CTGTTTGGCA

                       *        
      14256 ACTGTACAGATGAGATTA-C
          1 ACTGTACAGATAAGATTATC

             *         *        *
      14275 ATTGTACAGATTAGATTATGT
          1 ACTGTACAGATAAGATTAT-C

                               
      14296 ACTGTACAGATAAGATTAT
          1 ACTGTACAGATAAGATTAT

      14315 TAGAGCAGCG


Statistics
Matches: 33,  Mismatches: 5, Indels: 2
        0.82            0.12        0.05

Matches are distributed among these distances:
  19   16  0.48
  21   17  0.52

ACGTcount: A:0.37, C:0.10, G:0.19, T:0.34


Consensus pattern (20 bp):   
ACTGTACAGATAAGATTATC

Found at i:16789 original size:19 final size:19

Alignment explanation


    Indices: 16765--16802  Score: 76
    Period size: 19  Copynumber: 2.0  Consensus size: 19

      16755 CACACTTTCG

                               
      16765 AAATTAGGCTCTCCGCACA
          1 AAATTAGGCTCTCCGCACA

                               
      16784 AAATTAGGCTCTCCGCACA
          1 AAATTAGGCTCTCCGCACA

      16803 GCGAAGCGCG


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   19  1.00

ACGTcount: A:0.32, C:0.32, G:0.16, T:0.21


Consensus pattern (19 bp):   
AAATTAGGCTCTCCGCACA
Done.