Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016372.1 Corchorus olitorius cultivar O-4 contig16405, 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: 38393
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--40  Score: 80
    Period size: 2  Copynumber: 20.0  Consensus size: 2

                                                                       
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

         41 TTTACATATT


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   38  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:2239 original size:18 final size:18

Alignment explanation


    Indices: 2213--2248  Score: 63
    Period size: 18  Copynumber: 2.0  Consensus size: 18

       2203 TTGGTTCACT

                              
       2213 TCCTCCGATTTTTGAAAA
          1 TCCTCCGATTTTTGAAAA

                *             
       2231 TCCTTCGATTTTTGAAAA
          1 TCCTCCGATTTTTGAAAA

       2249 GGAACGTCAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.28, C:0.19, G:0.11, T:0.42


Consensus pattern (18 bp):   
TCCTCCGATTTTTGAAAA

Found at i:4962 original size:31 final size:32

Alignment explanation


    Indices: 4924--4985  Score: 90
    Period size: 32  Copynumber: 2.0  Consensus size: 32

       4914 CAAGTAAGCC

                    *                       
       4924 CCAAATAAGA-CATTGAATTCGCCAATTTTAG
          1 CCAAATAAAACCATTGAATTCGCCAATTTTAG

                        *       *          
       4955 CCAAATAAAACCCTTGAATTGGCCAATTTTA
          1 CCAAATAAAACCATTGAATTCGCCAATTTTA

       4986 ATAAATTAAC


Statistics
Matches: 27,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  31    9  0.33
  32   18  0.67

ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29


Consensus pattern (32 bp):   
CCAAATAAAACCATTGAATTCGCCAATTTTAG

Found at i:8431 original size:55 final size:55

Alignment explanation


    Indices: 8369--8473  Score: 158
    Period size: 55  Copynumber: 1.9  Consensus size: 55

       8359 GCAGTTTAAC

                             *                   **                 
       8369 TCCGGATT-TGTCCAGATCCAATATGACTACTGAATATTGCTTTCCAGTTTAATAT
          1 TCCGGATTAT-TCCAGACCCAATATGACTACTGAATACCGCTTTCCAGTTTAATAT

                       *                                      
       8424 TCCGGATTATTTCAGACCCAATATGACTACTGAATACCGCTTTCCAGTTT
          1 TCCGGATTATTCCAGACCCAATATGACTACTGAATACCGCTTTCCAGTTT

       8474 TCGCCAATTA


Statistics
Matches: 45,  Mismatches: 4, Indels: 2
        0.88            0.08        0.04

Matches are distributed among these distances:
  55   44  0.98
  56    1  0.02

ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36


Consensus pattern (55 bp):   
TCCGGATTATTCCAGACCCAATATGACTACTGAATACCGCTTTCCAGTTTAATAT

Found at i:12581 original size:14 final size:14

Alignment explanation


    Indices: 12562--12589  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

      12552 AAACTCTCCA

                          
      12562 TGATTTCAATTTTT
          1 TGATTTCAATTTTT

                          
      12576 TGATTTCAATTTTT
          1 TGATTTCAATTTTT

      12590 CAATAGGAAC


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.21, C:0.07, G:0.07, T:0.64


Consensus pattern (14 bp):   
TGATTTCAATTTTT

Found at i:16425 original size:11 final size:11

Alignment explanation


    Indices: 16409--16443  Score: 52
    Period size: 11  Copynumber: 3.2  Consensus size: 11

      16399 TTGACAGCGT

                       
      16409 AACAAAAATAA
          1 AACAAAAATAA

                     * 
      16420 AACAAAAATGA
          1 AACAAAAATAA

                    *  
      16431 AACAAAAACAA
          1 AACAAAAATAA

              
      16442 AA
          1 AA

      16444 AACAGAAAAA


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  11   21  1.00

ACGTcount: A:0.80, C:0.11, G:0.03, T:0.06


Consensus pattern (11 bp):   
AACAAAAATAA
Done.