Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009624.1 Corchorus olitorius cultivar O-4 contig09656, 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: 14248
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.29


Found at i:1876 original size:7 final size:7

Alignment explanation


    Indices: 1864--1909  Score: 85
    Period size: 7  Copynumber: 6.7  Consensus size: 7

       1854 GATTTTGCAA

                   
       1864 TTTAGGG
          1 TTTAGGG

                   
       1871 TTTAGGG
          1 TTTAGGG

                   
       1878 -TTAGGG
          1 TTTAGGG

                   
       1884 TTTAGGG
          1 TTTAGGG

                   
       1891 TTTAGGG
          1 TTTAGGG

                   
       1898 TTTAGGG
          1 TTTAGGG

                 
       1905 TTTAG
          1 TTTAG

       1910 TAGAAGATCT


Statistics
Matches: 38,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   6    6  0.16
   7   32  0.84

ACGTcount: A:0.15, C:0.00, G:0.41, T:0.43


Consensus pattern (7 bp):   
TTTAGGG

Found at i:1883 original size:13 final size:13

Alignment explanation


    Indices: 1865--1906  Score: 75
    Period size: 13  Copynumber: 3.2  Consensus size: 13

       1855 ATTTTGCAAT

                         
       1865 TTAGGGTTTAGGG
          1 TTAGGGTTTAGGG

                         
       1878 TTAGGGTTTAGGG
          1 TTAGGGTTTAGGG

                          
       1891 TTTAGGGTTTAGGG
          1 -TTAGGGTTTAGGG

              
       1905 TT
          1 TT

       1907 TAGTAGAAGA


Statistics
Matches: 28,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
  13   15  0.54
  14   13  0.46

ACGTcount: A:0.14, C:0.00, G:0.43, T:0.43


Consensus pattern (13 bp):   
TTAGGGTTTAGGG

Found at i:1889 original size:20 final size:21

Alignment explanation


    Indices: 1864--1909  Score: 85
    Period size: 20  Copynumber: 2.2  Consensus size: 21

       1854 GATTTTGCAA

                                 
       1864 TTTAGGGTTTAGGG-TTAGGG
          1 TTTAGGGTTTAGGGTTTAGGG

                                 
       1884 TTTAGGGTTTAGGGTTTAGGG
          1 TTTAGGGTTTAGGGTTTAGGG

                 
       1905 TTTAG
          1 TTTAG

       1910 TAGAAGATCT


Statistics
Matches: 25,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  20   14  0.56
  21   11  0.44

ACGTcount: A:0.15, C:0.00, G:0.41, T:0.43


Consensus pattern (21 bp):   
TTTAGGGTTTAGGGTTTAGGG

Found at i:9421 original size:23 final size:19

Alignment explanation


    Indices: 9377--9419  Score: 59
    Period size: 21  Copynumber: 2.2  Consensus size: 19

       9367 AGAAGGAAAA

                               
       9377 AGAAAATGAAAAAGAGAAG
          1 AGAAAATGAAAAAGAGAAG

                               * 
       9396 AGAAAGATGACAAAAGAGACG
          1 AGAAA-ATGA-AAAAGAGAAG

               
       9417 AGA
          1 AGA

       9420 GAGTGTTACG


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  19    5  0.24
  20    4  0.19
  21   12  0.57

ACGTcount: A:0.63, C:0.05, G:0.28, T:0.05


Consensus pattern (19 bp):   
AGAAAATGAAAAAGAGAAG

Found at i:12719 original size:18 final size:19

Alignment explanation


    Indices: 12686--12723  Score: 60
    Period size: 19  Copynumber: 2.1  Consensus size: 19

      12676 ATCATACTCC

                               
      12686 AAAAATAAAAATAATTATA
          1 AAAAATAAAAATAATTATA

                  *            
      12705 AAAAATTAAAA-AATTATA
          1 AAAAATAAAAATAATTATA

             
      12723 A
          1 A

      12724 CATCAATTTG


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  18    8  0.44
  19   10  0.56

ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26


Consensus pattern (19 bp):   
AAAAATAAAAATAATTATA

Found at i:13562 original size:2 final size:2

Alignment explanation


    Indices: 13555--13590  Score: 63
    Period size: 2  Copynumber: 18.0  Consensus size: 2

      13545 TTATAGTAGC

                        *                                        
      13555 AT AT AT AT TT 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

      13591 TTTTATATGT


Statistics
Matches: 32,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (2 bp):   
AT

Done.