Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008004.1 Corchorus capsularis cultivar CVL-1 contig08025, 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: 6361
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33


Found at i:757 original size:15 final size:15

Alignment explanation


    Indices: 708--753  Score: 51
    Period size: 14  Copynumber: 3.1  Consensus size: 15

        698 TTTTTTTCTA

                             
        708 ATTTACTT-ATTACCAT
          1 ATTTACTTAATTA--AT

                     *     
        724 ATTTACTTATTTAAT
          1 ATTTACTTAATTAAT

                           
        739 ATTTA-TTAATTAAT
          1 ATTTACTTAATTAAT

             
        753 A
          1 A

        754 ATTTCTTCAA


Statistics
Matches: 27,  Mismatches: 2, Indels: 4
        0.82            0.06        0.12

Matches are distributed among these distances:
  14    9  0.33
  15    7  0.26
  16    8  0.30
  17    3  0.11

ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54


Consensus pattern (15 bp):   
ATTTACTTAATTAAT

Found at i:4511 original size:6 final size:6

Alignment explanation


    Indices: 4500--4526  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

       4490 ATTAATCTGC

                                           
       4500 TTTAGA TTTAGA TTTAGA TTTAGA TTT
          1 TTTAGA TTTAGA TTTAGA TTTAGA TTT

       4527 GCTTTGCTTT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56


Consensus pattern (6 bp):   
TTTAGA

Found at i:4853 original size:22 final size:24

Alignment explanation


    Indices: 4828--4884  Score: 73
    Period size: 25  Copynumber: 2.4  Consensus size: 24

       4818 CGTTTTTTCT

                                   *
       4828 ATAAAAAAAAA-AG-TTTGCATCG
          1 ATAAAAAAAAATAGTTTTGCATCA

                        *            
       4850 ATAAAAAAAAATTGTTTTTGCATCA
          1 ATAAAAAAAAATAG-TTTTGCATCA

                      
       4875 ATAAAAAAAA
          1 ATAAAAAAAA

       4885 GTTTCTTTAT


Statistics
Matches: 30,  Mismatches: 2, Indels: 3
        0.86            0.06        0.09

Matches are distributed among these distances:
  22   11  0.37
  23    1  0.03
  25   18  0.60

ACGTcount: A:0.58, C:0.07, G:0.09, T:0.26


Consensus pattern (24 bp):   
ATAAAAAAAAATAGTTTTGCATCA

Done.