Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016999.1 Corchorus olitorius cultivar O-4 contig17032, 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: 2549
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29


Found at i:2050 original size:3 final size:3

Alignment explanation


    Indices: 2032--2064  Score: 52
    Period size: 3  Copynumber: 11.7  Consensus size: 3

       2022 AAAAAAACAA

                                                          
       2032 AAG AA- AAG AA- AAG AAG AAG AAG AAG AAG AAG AA
          1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA

       2065 AGAGTGTGGG


Statistics
Matches: 28,  Mismatches: 0, Indels: 4
        0.88            0.00        0.12

Matches are distributed among these distances:
   2    4  0.14
   3   24  0.86

ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00


Consensus pattern (3 bp):   
AAG

Found at i:2127 original size:12 final size:12

Alignment explanation


    Indices: 2085--2144  Score: 56
    Period size: 12  Copynumber: 5.2  Consensus size: 12

       2075 CTTGGCCCAT

                  *     
       2085 AAGGAAGAAGAA
          1 AAGGAAAAAGAA

                         
       2097 GAA-GAAAAA-AA
          1 -AAGGAAAAAGAA

                        
       2108 AA-GAAAAAGAA
          1 AAGGAAAAAGAA

             *           
       2119 AGGGAAAAAGGAA
          1 AAGGAAAAA-GAA

                        
       2132 AAGG-AAAAGAA
          1 AAGGAAAAAGAA

              
       2143 AA
          1 AA

       2145 TAAAATTAAT


Statistics
Matches: 41,  Mismatches: 3, Indels: 8
        0.79            0.06        0.15

Matches are distributed among these distances:
  10    8  0.20
  11   10  0.24
  12   15  0.37
  13    8  0.20

ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00


Consensus pattern (12 bp):   
AAGGAAAAAGAA
Done.