Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018018.1 Corchorus olitorius cultivar O-4 contig18051, 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: 25513
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:5306 original size:76 final size:76

Alignment explanation


    Indices: 5156--5299  Score: 175
    Period size: 76  Copynumber: 1.9  Consensus size: 76

       5146 ACAAGGACCC

                                              **               *           * 
       5156 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
          1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAAAACCCATGTGGTTTGCCTGAGAACCCAGAT

                       
       5221 GGGCAGTGTCA
         66 GGGCAGTGTCA

                    *     *              *                           **      
       5232 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAAACCCATGT-GTTTCGCCTGATCACCCAG
          1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTGAAAACCCATGTGGTTT-GCCTGAGAACCCAG

                 
       5295 ATGGG
         64 ATGGG

       5300 TTGTGTCTTA


Statistics
Matches: 57,  Mismatches: 9, Indels: 4
        0.81            0.13        0.06

Matches are distributed among these distances:
  75    4  0.07
  76   49  0.86
  77    4  0.07

ACGTcount: A:0.18, C:0.30, G:0.28, T:0.24


Consensus pattern (76 bp):   
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAAAACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA

Found at i:21328 original size:61 final size:59

Alignment explanation


    Indices: 21222--21356  Score: 189
    Period size: 61  Copynumber: 2.3  Consensus size: 59

      21212 ACCGTACATG

                               *               *                       
      21222 TCCCTCTACTTACAAAAAAGCATCAATTTGGTCCCGTACTACAAAAGCTGCCAATAAAA
          1 TCCCTCTACTTACAAAAAAACATCAATTTGGTCCCCTACTACAAAAGCTGCCAATAAAA

                  *                                             *    **  
      21281 TCCCTCCACTTACAACAAAAACATCAATTTGGTCCCCCTACTACAAAAGCTGTCAATTTAA
          1 TCCCTCTACTTACAA-AAAAACATCAATTTGGT-CCCCTACTACAAAAGCTGCCAATAAAA

                   *       
      21342 TCCCTCTTCTTACAA
          1 TCCCTCTACTTACAA

      21357 TTTGGTGTCA


Statistics
Matches: 66,  Mismatches: 8, Indels: 2
        0.87            0.11        0.03

Matches are distributed among these distances:
  59   14  0.21
  60   16  0.24
  61   36  0.55

ACGTcount: A:0.36, C:0.30, G:0.07, T:0.27


Consensus pattern (59 bp):   
TCCCTCTACTTACAAAAAAACATCAATTTGGTCCCCTACTACAAAAGCTGCCAATAAAA

Found at i:22346 original size:31 final size:29

Alignment explanation


    Indices: 22273--22357  Score: 93
    Period size: 29  Copynumber: 2.8  Consensus size: 29

      22263 TGAAATCAAA

                                       *   
      22273 TTGTAAGTAGAGGGACTC-AATTGACAGTTT
          1 TTGT-AGTAGAGGGAC-CAAATTGACAATTT

                                         
      22303 TTGTAGTAGAGGGACCAAATTGA-AATTT
          1 TTGTAGTAGAGGGACCAAATTGACAATTT

                                 *     
      22331 TTGTATCGGTAGAGGGACCAACTTGAC
          1 TTGTA---GTAGAGGGACCAAATTGAC

      22358 TTTTTTAATT


Statistics
Matches: 48,  Mismatches: 2, Indels: 8
        0.83            0.03        0.14

Matches are distributed among these distances:
  28   10  0.21
  29   17  0.35
  30    4  0.08
  31   17  0.35

ACGTcount: A:0.31, C:0.12, G:0.27, T:0.31


Consensus pattern (29 bp):   
TTGTAGTAGAGGGACCAAATTGACAATTT

Found at i:22363 original size:31 final size:27

Alignment explanation


    Indices: 22273--22363  Score: 92
    Period size: 31  Copynumber: 3.1  Consensus size: 27

      22263 TGAAATCAAA

                                          
      22273 TTGTAAGTAGAGGGACTCAATTGACAGTTT
          1 TTGT-AGTAGAGGGAC-CAATTGACA-TTT

                                   *    
      22303 TTGTAGTAGAGGGACCAAATTGAAATTT
          1 TTGTAGTAGAGGGACC-AATTGACATTT

                                       *   
      22331 TTGTATCGGTAGAGGGACCAACTTGACTTTT
          1 TTGTA---GTAGAGGGACCAA-TTGACATTT

              
      22362 TT
          1 TT

      22364 AATTTTTATT


Statistics
Matches: 53,  Mismatches: 3, Indels: 9
        0.82            0.05        0.14

Matches are distributed among these distances:
  28    9  0.17
  29   18  0.34
  30    6  0.11
  31   20  0.38

ACGTcount: A:0.29, C:0.11, G:0.25, T:0.35


Consensus pattern (27 bp):   
TTGTAGTAGAGGGACCAATTGACATTT
Done.