Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019306.1 Corchorus olitorius cultivar O-4 contig19339, 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: 9128
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35


Found at i:3652 original size:29 final size:30

Alignment explanation


    Indices: 3600--3659  Score: 86
    Period size: 29  Copynumber: 2.0  Consensus size: 30

       3590 GAAGTTCATG

                               *      *    
       3600 TTTGAAGACTCATTGAAGACTTATTTGAAGA
          1 TTTGAAGACT-ATTGAAGAATTATTTCAAGA

                                          
       3631 TTTGAAGACT-TTGAAGAATTATTTCAAGA
          1 TTTGAAGACTATTGAAGAATTATTTCAAGA

       3660 GCCAGAATTG


Statistics
Matches: 27,  Mismatches: 2, Indels: 2
        0.87            0.06        0.06

Matches are distributed among these distances:
  29   17  0.63
  31   10  0.37

ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37


Consensus pattern (30 bp):   
TTTGAAGACTATTGAAGAATTATTTCAAGA

Found at i:5049 original size:15 final size:16

Alignment explanation


    Indices: 5018--5052  Score: 54
    Period size: 15  Copynumber: 2.2  Consensus size: 16

       5008 TTGCTTTGCT

                            
       5018 TTGTTTTCTAGTTTAA
          1 TTGTTTTCTAGTTTAA

                      *     
       5034 TTGTTTTCT-TTTTAA
          1 TTGTTTTCTAGTTTAA

                
       5049 TTGT
          1 TTGT

       5053 GATTTTTAAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  15    9  0.50
  16    9  0.50

ACGTcount: A:0.14, C:0.06, G:0.11, T:0.69


Consensus pattern (16 bp):   
TTGTTTTCTAGTTTAA

Found at i:5829 original size:11 final size:10

Alignment explanation


    Indices: 5804--5842  Score: 51
    Period size: 11  Copynumber: 3.7  Consensus size: 10

       5794 TTGAAATTAT

                    * 
       5804 TCTTCAATGG
          1 TCTTCAATAG

                       
       5814 TCTTCAAATAG
          1 TCTTC-AATAG

                       
       5825 TCTTCAATAAG
          1 TCTTCAAT-AG

                   
       5836 TCTTCAA
          1 TCTTCAA

       5843 ACACGAACTT


Statistics
Matches: 26,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  10    8  0.31
  11   18  0.69

ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38


Consensus pattern (10 bp):   
TCTTCAATAG

Found at i:6637 original size:21 final size:21

Alignment explanation


    Indices: 6611--6702  Score: 132
    Period size: 21  Copynumber: 4.4  Consensus size: 21

       6601 TGCTAGAAGT

                                  
       6611 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                     *          *
       6632 TCATTGGAGCAGGTTCCAAGT
          1 TCATTGGAGAAGGTTCCAAGC

                                *
       6653 TCATTGGAGAAGGTTCCAAGA
          1 TCATTGGAGAAGGTTCCAAGC

                           *     
       6674 TCATTGGAGAAGGTTTCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                    
       6695 TCATTGGA
          1 TCATTGGA

       6703 AATGCCTAAG


Statistics
Matches: 64,  Mismatches: 6, Indels: 2
        0.89            0.08        0.03

Matches are distributed among these distances:
  20    1  0.02
  21   63  0.98

ACGTcount: A:0.28, C:0.17, G:0.27, T:0.27


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTCCAAGC

Found at i:7769 original size:9 final size:10

Alignment explanation


    Indices: 7750--7775  Score: 52
    Period size: 10  Copynumber: 2.6  Consensus size: 10

       7740 AAAATATTTC

                      
       7750 AAAAATAAAA
          1 AAAAATAAAA

                      
       7760 AAAAATAAAA
          1 AAAAATAAAA

                  
       7770 AAAAAT
          1 AAAAAT

       7776 TTCGACCAGA


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:0.88, C:0.00, G:0.00, T:0.12


Consensus pattern (10 bp):   
AAAAATAAAA
Done.