Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015301.1 Corchorus olitorius cultivar O-4 contig15334, 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: 4785
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30


Found at i:229 original size:12 final size:11

Alignment explanation


    Indices: 212--259  Score: 78
    Period size: 12  Copynumber: 4.2  Consensus size: 11

        202 TTAATTCGCT

                       
        212 TTTGATTTGAA
          1 TTTGATTTGAA

                        
        223 CTTTGATTTGAA
          1 -TTTGATTTGAA

                        
        235 TTTCGATTTGAA
          1 TTT-GATTTGAA

                       
        247 TTTGATTTGAA
          1 TTTGATTTGAA

              
        258 TT
          1 TT

        260 ACTTAACGAA


Statistics
Matches: 35,  Mismatches: 0, Indels: 3
        0.92            0.00        0.08

Matches are distributed among these distances:
  11   13  0.37
  12   22  0.63

ACGTcount: A:0.25, C:0.04, G:0.17, T:0.54


Consensus pattern (11 bp):   
TTTGATTTGAA

Found at i:254 original size:23 final size:24

Alignment explanation


    Indices: 215--259  Score: 83
    Period size: 23  Copynumber: 1.9  Consensus size: 24

        205 ATTCGCTTTT

                                    
        215 GATTTGAACTTTGATTTGAATTTC
          1 GATTTGAACTTTGATTTGAATTTC

                                  
        239 GATTTGAA-TTTGATTTGAATT
          1 GATTTGAACTTTGATTTGAATT

        260 ACTTAACGAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  23   13  0.62
  24    8  0.38

ACGTcount: A:0.27, C:0.04, G:0.18, T:0.51


Consensus pattern (24 bp):   
GATTTGAACTTTGATTTGAATTTC

Found at i:569 original size:14 final size:13

Alignment explanation


    Indices: 544--602  Score: 66
    Period size: 14  Copynumber: 4.3  Consensus size: 13

        534 TAAAAGACTC

                         
        544 AAAACC-TTTTTG
          1 AAAACCTTTTTTG

                          
        556 AAAACCTATTTTTG
          1 AAAACCT-TTTTTG

                          
        570 AAAACCTTTTCTTG
          1 AAAACCTTTT-TTG

                  *        
        584 AAAACAATTTTCTTG
          1 AAAAC-CTTTT-TTG

                
        599 AAAA
          1 AAAA

        603 ACGTGTCTTG


Statistics
Matches: 42,  Mismatches: 1, Indels: 5
        0.88            0.02        0.10

Matches are distributed among these distances:
  12    6  0.14
  13    3  0.07
  14   21  0.50
  15   12  0.29

ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39


Consensus pattern (13 bp):   
AAAACCTTTTTTG

Done.