Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024612.1 Corchorus olitorius cultivar O-4 contig24645, 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: 11143
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33


Found at i:30 original size:21 final size:21

Alignment explanation


    Indices: 4--64  Score: 95
    Period size: 21  Copynumber: 2.9  Consensus size: 21

          1 AGC

                      *          
          4 AGGTTCCAAGTTCATTGGAGA
          1 AGGTTCCAAGATCATTGGAGA

                                 
         25 AGGTTCCAAGATCATTGGAGA
          1 AGGTTCCAAGATCATTGGAGA

                 *    *        
         46 AGGTTTCAAGCTCATTGGA
          1 AGGTTCCAAGATCATTGGA

         65 AATGCCTAAG


Statistics
Matches: 37,  Mismatches: 3, Indels: 0
        0.93            0.08        0.00

Matches are distributed among these distances:
  21   37  1.00

ACGTcount: A:0.30, C:0.15, G:0.28, T:0.28


Consensus pattern (21 bp):   
AGGTTCCAAGATCATTGGAGA

Found at i:2694 original size:22 final size:22

Alignment explanation


    Indices: 2669--2710  Score: 75
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       2659 TCGGCAGTGT

                                  
       2669 AAATTTTGGACTCCACAAGCGG
          1 AAATTTTGGACTCCACAAGCGG

                        *       
       2691 AAATTTTGGACTTCACAAGC
          1 AAATTTTGGACTCCACAAGC

       2711 AGGTTGTGGA


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.33, C:0.21, G:0.19, T:0.26


Consensus pattern (22 bp):   
AAATTTTGGACTCCACAAGCGG

Found at i:7920 original size:15 final size:15

Alignment explanation


    Indices: 7868--7920  Score: 52
    Period size: 15  Copynumber: 3.5  Consensus size: 15

       7858 AATAAAAATA

                           
       7868 AAAAAAATTTATTTT
          1 AAAAAAATTTATTTT

              * * *        
       7883 AATATATTTTATTTT
          1 AAAAAAATTTATTTT

             ***           
       7898 ATTGAAATTTATTTT
          1 AAAAAAATTTATTTT

                    
       7913 AAAAAAAT
          1 AAAAAAAT

       7921 AAAAAAGAAA


Statistics
Matches: 28,  Mismatches: 10, Indels: 0
        0.74            0.26        0.00

Matches are distributed among these distances:
  15   28  1.00

ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51


Consensus pattern (15 bp):   
AAAAAAATTTATTTT
Done.