Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005506.1 Corchorus capsularis cultivar CVL-1 contig05524, 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: 3431
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35


Found at i:2925 original size:39 final size:39

Alignment explanation


    Indices: 2882--2977  Score: 156
    Period size: 39  Copynumber: 2.5  Consensus size: 39

       2872 GGTGCCGAGA

                                        **      *  
       2882 ATGTTTGTGAAGATGGGGGTGAATTATTTGGTGTTGGGG
          1 ATGTTTGTGAAGATGGGGGTGAATTATTCAGTGTTGAGG

                          *                        
       2921 ATGTTTGTGAAGATAGGGGTGAATTATTCAGTGTTGAGG
          1 ATGTTTGTGAAGATGGGGGTGAATTATTCAGTGTTGAGG

                              
       2960 ATGTTTGTGAAGATGGGG
          1 ATGTTTGTGAAGATGGGG

       2978 ATTTCAAATT


Statistics
Matches: 52,  Mismatches: 5, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  39   52  1.00

ACGTcount: A:0.22, C:0.01, G:0.41, T:0.36


Consensus pattern (39 bp):   
ATGTTTGTGAAGATGGGGGTGAATTATTCAGTGTTGAGG

Found at i:3326 original size:15 final size:15

Alignment explanation


    Indices: 3306--3335  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       3296 CTACTTTTTG

                           
       3306 GTCTATACTTAAACA
          1 GTCTATACTTAAACA

                      *    
       3321 GTCTATACTTGAACA
          1 GTCTATACTTAAACA

       3336 TAAAGATTCT


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.37, C:0.20, G:0.10, T:0.33


Consensus pattern (15 bp):   
GTCTATACTTAAACA
Done.