Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020315.1 Corchorus olitorius cultivar O-4 contig20348, 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: 14226
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:9931 original size:2 final size:2

Alignment explanation


    Indices: 9924--9948  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       9914 AAATAAATAA

                                                 
       9924 AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT A

       9949 ACTTGTTCCC


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:12272 original size:56 final size:56

Alignment explanation


    Indices: 12200--12309  Score: 193
    Period size: 56  Copynumber: 2.0  Consensus size: 56

      12190 TTTATTTTGT

                  *              *                                  
      12200 AGAATAGTTAAGTAGAGATAGGGGGATATGATTTATTATAACATTTATTGTGTGGA
          1 AGAATAATTAAGTAGAGATAGAGGGATATGATTTATTATAACATTTATTGTGTGGA

                                                     *            
      12256 AGAATAATTAAGTAGAGATAGAGGGATATGATTTATTATAATATTTATTGTGTG
          1 AGAATAATTAAGTAGAGATAGAGGGATATGATTTATTATAACATTTATTGTGTG

      12310 AAAGGAAAAG


Statistics
Matches: 51,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  56   51  1.00

ACGTcount: A:0.37, C:0.01, G:0.25, T:0.37


Consensus pattern (56 bp):   
AGAATAATTAAGTAGAGATAGAGGGATATGATTTATTATAACATTTATTGTGTGGA

Found at i:12755 original size:27 final size:27

Alignment explanation


    Indices: 12696--12768  Score: 74
    Period size: 27  Copynumber: 2.7  Consensus size: 27

      12686 AGGGTCACCT

                          **          *
      12696 AGGGGCATTTTGGTTTTTTACACATTT
          1 AGGGGCATTTTGGTCATTTACACATTC

             *                 *  *    
      12723 AAGGGCATTTTGGTCATTTGCATATTC
          1 AGGGGCATTTTGGTCATTTACACATTC

                   **          
      12750 AGGGGCACGTTGGTCATTT
          1 AGGGGCATTTTGGTCATTT

      12769 TAAGTCCACA


Statistics
Matches: 37,  Mismatches: 9, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
  27   37  1.00

ACGTcount: A:0.19, C:0.14, G:0.26, T:0.41


Consensus pattern (27 bp):   
AGGGGCATTTTGGTCATTTACACATTC
Done.