Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012987.1 Corchorus capsularis cultivar CVL-1 contig13008, 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: 5661
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31


Found at i:2511 original size:12 final size:13

Alignment explanation


    Indices: 2494--2522  Score: 51
    Period size: 12  Copynumber: 2.3  Consensus size: 13

       2484 TTTTCCTTGC

                         
       2494 ATTGCTTTGATT-
          1 ATTGCTTTGATTG

                         
       2506 ATTGCTTTGATTG
          1 ATTGCTTTGATTG

                
       2519 ATTG
          1 ATTG

       2523 TCTATTCCTT


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  12   12  0.75
  13    4  0.25

ACGTcount: A:0.17, C:0.07, G:0.21, T:0.55


Consensus pattern (13 bp):   
ATTGCTTTGATTG

Found at i:4053 original size:11 final size:11

Alignment explanation


    Indices: 4037--4066  Score: 51
    Period size: 11  Copynumber: 2.7  Consensus size: 11

       4027 GAAGTTCGTG

                     * 
       4037 TTTGAAGATTA
          1 TTTGAAGATAA

                       
       4048 TTTGAAGATAA
          1 TTTGAAGATAA

                    
       4059 TTTGAAGA
          1 TTTGAAGA

       4067 ATTGAAGACA


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  11   18  1.00

ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40


Consensus pattern (11 bp):   
TTTGAAGATAA

Found at i:4065 original size:22 final size:22

Alignment explanation


    Indices: 4037--4096  Score: 65
    Period size: 22  Copynumber: 2.9  Consensus size: 22

       4027 GAAGTTCGTG

                               *  
       4037 TTTGAAGATTATTTGAAGATAA
          1 TTTGAAGATTATTTGAAGACAA

                                  
       4059 TTTGAAGA--A-TTGAAGACAA
          1 TTTGAAGATTATTTGAAGACAA

                           *    
       4078 -TTGAAGAATTATTTCAAGA
          1 TTTGAAG-ATTATTTGAAGA

       4097 AGCAAGAATT


Statistics
Matches: 32,  Mismatches: 2, Indels: 8
        0.76            0.05        0.19

Matches are distributed among these distances:
  18    6  0.19
  19   10  0.31
  20    1  0.03
  21    1  0.03
  22   14  0.44

ACGTcount: A:0.43, C:0.03, G:0.18, T:0.35


Consensus pattern (22 bp):   
TTTGAAGATTATTTGAAGACAA

Found at i:4083 original size:18 final size:19

Alignment explanation


    Indices: 4049--4087  Score: 62
    Period size: 18  Copynumber: 2.1  Consensus size: 19

       4039 TGAAGATTAT

                   *           
       4049 TTGAAGATAATTTGAAGAA
          1 TTGAAGACAATTTGAAGAA

                               
       4068 TTGAAGACAA-TTGAAGAA
          1 TTGAAGACAATTTGAAGAA

              
       4086 TT
          1 TT

       4088 ATTTCAAGAA


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  18   10  0.53
  19    9  0.47

ACGTcount: A:0.46, C:0.03, G:0.21, T:0.31


Consensus pattern (19 bp):   
TTGAAGACAATTTGAAGAA

Found at i:4489 original size:10 final size:10

Alignment explanation


    Indices: 4474--4499  Score: 52
    Period size: 10  Copynumber: 2.6  Consensus size: 10

       4464 ATTTGCTGCC

                      
       4474 AAATTCCAGA
          1 AAATTCCAGA

                      
       4484 AAATTCCAGA
          1 AAATTCCAGA

                  
       4494 AAATTC
          1 AAATTC

       4500 TAGAGTCCTC


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   16  1.00

ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23


Consensus pattern (10 bp):   
AAATTCCAGA
Done.