Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005817.1 Corchorus capsularis cultivar CVL-1 contig05835, 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: 4449
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.30


Found at i:3618 original size:12 final size:12

Alignment explanation


    Indices: 3601--3644  Score: 51
    Period size: 12  Copynumber: 3.9  Consensus size: 12

       3591 AAAAGAAGGA

                        
       3601 GAAGAAAAGAAT
          1 GAAGAAAAGAAT

                         
       3613 GAAGAAAAGAATT
          1 GAAGAAAAGAA-T

                        
       3626 G-A-AAAAGAA-
          1 GAAGAAAAGAAT

                       
       3635 -AAGAAAAGAA
          1 GAAGAAAAGAA

       3645 AAGAAAGAAG


Statistics
Matches: 29,  Mismatches: 0, Indels: 8
        0.78            0.00        0.22

Matches are distributed among these distances:
   9    1  0.03
  10    7  0.24
  11    7  0.24
  12   12  0.41
  13    2  0.07

ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07


Consensus pattern (12 bp):   
GAAGAAAAGAAT

Found at i:3650 original size:21 final size:22

Alignment explanation


    Indices: 3605--3650  Score: 58
    Period size: 21  Copynumber: 2.1  Consensus size: 22

       3595 GAAGGAGAAG

                               **  
       3605 AAAAGAATGAAGAAAAGAATTGA
          1 AAAAGAA-GAAGAAAAGAAAAGA

                                  
       3628 AAAAGAA-AAGAAAAGAAAAGA
          1 AAAAGAAGAAGAAAAGAAAAGA

              
       3649 AA
          1 AA

       3651 GAAGTTGAAA


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  21   14  0.67
  23    7  0.33

ACGTcount: A:0.74, C:0.00, G:0.20, T:0.07


Consensus pattern (22 bp):   
AAAAGAAGAAGAAAAGAAAAGA

Found at i:3653 original size:4 final size:5

Alignment explanation


    Indices: 3602--3650  Score: 53
    Period size: 5  Copynumber: 9.2  Consensus size: 5

       3592 AAAGAAGGAG

                                      **                            
       3602 AAGAA AAGAA TGAAGAA AAGAA TTGAAA AAGAA AAGAA AAGAA AAGAA
          1 AAGAA AAGAA --AAGAA AAGAA AAG-AA AAGAA AAGAA AAGAA AAGAA

             
       3650 A
          1 A

       3651 GAAGTTGAAA


Statistics
Matches: 37,  Mismatches: 4, Indels: 6
        0.79            0.09        0.13

Matches are distributed among these distances:
   5   29  0.78
   6    3  0.08
   7    5  0.14

ACGTcount: A:0.73, C:0.00, G:0.20, T:0.06


Consensus pattern (5 bp):   
AAGAA

Found at i:3933 original size:36 final size:36

Alignment explanation


    Indices: 3850--3923  Score: 105
    Period size: 36  Copynumber: 2.1  Consensus size: 36

       3840 TGAAGAAGAT

                *        **         *           
       3850 TTTCTTCAAAGTGTGATCTTTTCACAAGAAAAAATG
          1 TTTCCTCAAAGTGCAATCTTTTCAAAAGAAAAAATG

                                                
       3886 TTTCCTCAAAGTGCAATCTTTTCAAAAG-AAAAATG
          1 TTTCCTCAAAGTGCAATCTTTTCAAAAGAAAAAATG

               
       3921 TTT
          1 TTT

       3924 TTCAAAAAGT


Statistics
Matches: 34,  Mismatches: 4, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  35   10  0.29
  36   24  0.71

ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36


Consensus pattern (36 bp):   
TTTCCTCAAAGTGCAATCTTTTCAAAAGAAAAAATG
Done.