Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004535.1 Corchorus capsularis cultivar CVL-1 contig04546, 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, 606

Length: 1010
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35


Found at i:208 original size:11 final size:11

Alignment explanation


    Indices: 178--237  Score: 63
    Period size: 10  Copynumber: 5.6  Consensus size: 11

        168 TTGATTTAAT

                      *
        178 ATTTAAAT-GG
          1 ATTTAAATAGA

                       
        188 ATTT-AATAGA
          1 ATTTAAATAGA

                       
        198 ATTTAAATAGA
          1 ATTTAAATAGA

                      **
        209 ATTTTAAAT-TT
          1 A-TTTAAATAGA

                       
        220 ATTTAAATAGA
          1 ATTTAAATAGA

                   
        231 ATTTAAA
          1 ATTTAAA

        238 ATTTAATAAA


Statistics
Matches: 41,  Mismatches: 5, Indels: 7
        0.77            0.09        0.13

Matches are distributed among these distances:
   9    3  0.07
  10   16  0.39
  11   15  0.37
  12    7  0.17

ACGTcount: A:0.48, C:0.00, G:0.08, T:0.43


Consensus pattern (11 bp):   
ATTTAAATAGA

Found at i:220 original size:18 final size:19

Alignment explanation


    Indices: 178--243  Score: 55
    Period size: 22  Copynumber: 3.3  Consensus size: 19

        168 TTGATTTAAT

                      *          
        178 ATTTAAAT-GGATTTAATAGA
          1 ATTTAAATAGAATTTAA-A-A

                                 *
        198 ATTTAAATAGAATTTTAAATTT
          1 ATTTAAATAGAA-TTTAAA--A

                               
        220 ATTTAAATAGAATTT-AAA
          1 ATTTAAATAGAATTTAAAA

                  
        238 ATTTAA
          1 ATTTAA

        244 TAAAAATAAA


Statistics
Matches: 39,  Mismatches: 4, Indels: 8
        0.76            0.08        0.16

Matches are distributed among these distances:
  18    6  0.15
  20   10  0.26
  21    6  0.15
  22   17  0.44

ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44


Consensus pattern (19 bp):   
ATTTAAATAGAATTTAAAA

Found at i:223 original size:22 final size:22

Alignment explanation


    Indices: 198--242  Score: 81
    Period size: 22  Copynumber: 2.0  Consensus size: 22

        188 ATTTAATAGA

                           *      
        198 ATTTAAATAGAATTTTAAATTT
          1 ATTTAAATAGAATTTAAAATTT

                                  
        220 ATTTAAATAGAATTTAAAATTT
          1 ATTTAAATAGAATTTAAAATTT

             
        242 A
          1 A

        243 ATAAAAATAA


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  22   22  1.00

ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47


Consensus pattern (22 bp):   
ATTTAAATAGAATTTAAAATTT

Found at i:247 original size:21 final size:22

Alignment explanation


    Indices: 201--247  Score: 69
    Period size: 22  Copynumber: 2.2  Consensus size: 22

        191 TAATAGAATT

                        *        *
        201 TAAATAGAATTTTAAATTTATT
          1 TAAATAGAATTTAAAATTTATA

                                  
        223 TAAATAGAATTTAAAATTTA-A
          1 TAAATAGAATTTAAAATTTATA

                
        244 TAAA
          1 TAAA

        248 AATAAAAAAA


Statistics
Matches: 23,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  21    4  0.17
  22   19  0.83

ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43


Consensus pattern (22 bp):   
TAAATAGAATTTAAAATTTATA
Done.