Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009862.1 Corchorus olitorius cultivar O-4 contig09894, 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: 16441
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31


Found at i:919 original size:19 final size:18

Alignment explanation


    Indices: 897--935  Score: 60
    Period size: 19  Copynumber: 2.1  Consensus size: 18

        887 AATAATAGTT

                               
        897 AAGAGAGTAAATAGGGAGA
          1 AAGAGAGTAAATAGGG-GA

                      *       
        916 AAGAGAGTAAGTAGGGGA
          1 AAGAGAGTAAATAGGGGA

              
        934 AA
          1 AA

        936 AAGAATATGG


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  18    4  0.21
  19   15  0.79

ACGTcount: A:0.51, C:0.00, G:0.38, T:0.10


Consensus pattern (18 bp):   
AAGAGAGTAAATAGGGGA

Found at i:14106 original size:21 final size:21

Alignment explanation


    Indices: 14081--14120  Score: 80
    Period size: 21  Copynumber: 1.9  Consensus size: 21

      14071 AGATTTTTGG

                                 
      14081 TCCGACTAAATTTGGATTTAC
          1 TCCGACTAAATTTGGATTTAC

                               
      14102 TCCGACTAAATTTGGATTT
          1 TCCGACTAAATTTGGATTT

      14121 TTTTTTCGAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40


Consensus pattern (21 bp):   
TCCGACTAAATTTGGATTTAC

Found at i:14960 original size:21 final size:21

Alignment explanation


    Indices: 14934--14980  Score: 78
    Period size: 21  Copynumber: 2.2  Consensus size: 21

      14924 AGGCAATTAT

                                  
      14934 AATGAGCTTGGAACCTT-CTCC
          1 AATGAGCTTGGAA-CTTGCTCC

                                 
      14955 AATGAGCTTGGAACTTGCTCC
          1 AATGAGCTTGGAACTTGCTCC

                 
      14976 AATGA
          1 AATGA

      14981 TCTCCTAGAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
  20    3  0.12
  21   22  0.88

ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28


Consensus pattern (21 bp):   
AATGAGCTTGGAACTTGCTCC
Done.