Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000939.1 Corchorus capsularis cultivar CVL-1 contig00939, 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: 20096
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32


Found at i:16210 original size:14 final size:15

Alignment explanation


    Indices: 16192--16230  Score: 53
    Period size: 15  Copynumber: 2.6  Consensus size: 15

      16182 TAAAATAAAC

                      *    
      16192 TTTTTAAAACTTATA
          1 TTTTTAAAACATATA

                            
      16207 TTTTTCAAAACATAT-
          1 TTTTT-AAAACATATA

                     
      16222 TTTTTAAAA
          1 TTTTTAAAA

      16231 TTTTAATTAT


Statistics
Matches: 22,  Mismatches: 1, Indels: 3
        0.85            0.04        0.12

Matches are distributed among these distances:
  14    4  0.18
  15   10  0.45
  16    8  0.36

ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51


Consensus pattern (15 bp):   
TTTTTAAAACATATA

Found at i:16211 original size:16 final size:14

Alignment explanation


    Indices: 16177--16230  Score: 54
    Period size: 14  Copynumber: 3.7  Consensus size: 14

      16167 TTTTTTTAAT

                      * * 
      16177 TTTTTTAAAATAAA
          1 TTTTTTAAAACATA

            *               
      16191 CTTTTTAAAACTTATA
          1 TTTTTTAAAAC--ATA

                 *        
      16207 TTTTTCAAAACATA
          1 TTTTTTAAAACATA

                      
      16221 TTTTTTAAAA
          1 TTTTTTAAAA

      16231 TTTTAATTAT


Statistics
Matches: 32,  Mismatches: 6, Indels: 4
        0.76            0.14        0.10

Matches are distributed among these distances:
  14   21  0.66
  16   11  0.34

ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50


Consensus pattern (14 bp):   
TTTTTTAAAACATA

Found at i:20034 original size:2 final size:2

Alignment explanation


    Indices: 20027--20056  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

      20017 ATTATTAAAT

                                                        
      20027 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
          1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA

      20057 TCATATATAT


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

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


Consensus pattern (2 bp):   
CA

Found at i:20064 original size:2 final size:2

Alignment explanation


    Indices: 20059--20096  Score: 76
    Period size: 2  Copynumber: 19.0  Consensus size: 2

      20049 CACACACATC

                                                                    
      20059 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


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

Matches are distributed among these distances:
   2   36  1.00

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


Consensus pattern (2 bp):   
AT

Done.