Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021209.1 Corchorus olitorius cultivar O-4 contig21242, 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: 5703
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--52  Score: 104
    Period size: 2  Copynumber: 26.0  Consensus size: 2

                                                                          
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC

                          
         43 TC TC TC TC TC
          1 TC TC TC TC TC

         53 ATCCTTCTAT


Statistics
Matches: 50,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   50  1.00

ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50


Consensus pattern (2 bp):   
TC

Found at i:3111 original size:10 final size:10

Alignment explanation


    Indices: 3092--3137  Score: 65
    Period size: 10  Copynumber: 4.6  Consensus size: 10

       3082 ATACCTCGAT

                      
       3092 ATATCCGTAA
          1 ATATCCGTAA

                 *    
       3102 ATATCTGTAA
          1 ATATCCGTAA

                  *   
       3112 ATATCCATAA
          1 ATATCCGTAA

                 *    
       3122 ATATCTGTAA
          1 ATATCCGTAA

                  
       3132 ATATCC
          1 ATATCC

       3138 ATATTAAATT


Statistics
Matches: 30,  Mismatches: 6, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  10   30  1.00

ACGTcount: A:0.41, C:0.17, G:0.07, T:0.35


Consensus pattern (10 bp):   
ATATCCGTAA

Found at i:3117 original size:20 final size:20

Alignment explanation


    Indices: 3092--3140  Score: 89
    Period size: 20  Copynumber: 2.5  Consensus size: 20

       3082 ATACCTCGAT

                  *             
       3092 ATATCCGTAAATATCTGTAA
          1 ATATCCATAAATATCTGTAA

                                
       3112 ATATCCATAAATATCTGTAA
          1 ATATCCATAAATATCTGTAA

                     
       3132 ATATCCATA
          1 ATATCCATA

       3141 TTAAATTAAA


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  20   28  1.00

ACGTcount: A:0.43, C:0.16, G:0.06, T:0.35


Consensus pattern (20 bp):   
ATATCCATAAATATCTGTAA
Done.