Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017336.1 Corchorus olitorius cultivar O-4 contig17369, 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: 22676
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:984 original size:3 final size:3

Alignment explanation


    Indices: 976--1042  Score: 134
    Period size: 3  Copynumber: 22.3  Consensus size: 3

        966 AAATAGTTTG

                                                                           
        976 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA

                                     
       1024 TAA TAA TAA TAA TAA TAA T
          1 TAA TAA TAA TAA TAA TAA T

       1043 GATGATGATG


Statistics
Matches: 64,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   64  1.00

ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34


Consensus pattern (3 bp):   
TAA

Found at i:1047 original size:3 final size:3

Alignment explanation


    Indices: 1041--1079  Score: 78
    Period size: 3  Copynumber: 13.0  Consensus size: 3

       1031 AATAATAATA

                                                               
       1041 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
          1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG

       1080 CTCAATATAA


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   36  1.00

ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33


Consensus pattern (3 bp):   
ATG

Found at i:5581 original size:12 final size:12

Alignment explanation


    Indices: 5559--5590  Score: 57
    Period size: 12  Copynumber: 2.8  Consensus size: 12

       5549 AAATACAATA

                        
       5559 ATATA-TATACT
          1 ATATATTATACT

                        
       5570 ATATATTATACT
          1 ATATATTATACT

                     
       5582 ATATATTAT
          1 ATATATTAT

       5591 TTTTAGTTAC


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  11    5  0.25
  12   15  0.75

ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50


Consensus pattern (12 bp):   
ATATATTATACT

Found at i:8180 original size:24 final size:23

Alignment explanation


    Indices: 8138--8182  Score: 63
    Period size: 24  Copynumber: 1.9  Consensus size: 23

       8128 TGCTTGTGAA

                          *        
       8138 AATTAATTTTAAAATTACAATAG
          1 AATTAATTTTAAAACTACAATAG

                 *                
       8161 AATTATTTTTAAAAACTACAAT
          1 AATTAATTTT-AAAACTACAAT

       8183 GATTTTGGTG


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  23    9  0.47
  24   10  0.53

ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40


Consensus pattern (23 bp):   
AATTAATTTTAAAACTACAATAG

Found at i:15893 original size:2 final size:2

Alignment explanation


    Indices: 15888--15919  Score: 55
    Period size: 2  Copynumber: 16.0  Consensus size: 2

      15878 GGCACAAATA

                                          *                
      15888 AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      15920 GTATTCTTGA


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

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:18605 original size:39 final size:39

Alignment explanation


    Indices: 18548--18622  Score: 123
    Period size: 39  Copynumber: 1.9  Consensus size: 39

      18538 ACTGATAAGT

                     *   *                         
      18548 TGGTTTATATTCTGTTGGTTCTTTTGGATGTGTTGTCGC
          1 TGGTTTATACTCTATTGGTTCTTTTGGATGTGTTGTCGC

                                       *        
      18587 TGGTTTATACTCTATTGGTTCTTTTGGTTGTGTTGT
          1 TGGTTTATACTCTATTGGTTCTTTTGGATGTGTTGT

      18623 TGTTGTAATG


Statistics
Matches: 33,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  39   33  1.00

ACGTcount: A:0.08, C:0.09, G:0.27, T:0.56


Consensus pattern (39 bp):   
TGGTTTATACTCTATTGGTTCTTTTGGATGTGTTGTCGC
Done.