Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008869.1 Kokia drynarioides strain JFW-HI SEQ_123555, 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, 769

Length: 1282
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36


Found at i:276 original size:41 final size:42

Alignment explanation


    Indices: 231--319  Score: 126
    Period size: 41  Copynumber: 2.1  Consensus size: 42

        221 AATTATTAAT

                         *           *   *            
        231 AAGACTCATATCTTGAGATGAGAATGAGATTATGATT-AAGG
          1 AAGACTCATATCTCGAGATGAGAATAAGAATATGATTAAAGG

                     *                        *       
        272 AAGACTCATGTCTCGAGATGAGAATAAGAATATGGTTAAAGG
          1 AAGACTCATATCTCGAGATGAGAATAAGAATATGATTAAAGG

                  
        314 AAGACT
          1 AAGACT

        320 TATGACTCGA


Statistics
Matches: 42,  Mismatches: 5, Indels: 1
        0.88            0.10        0.02

Matches are distributed among these distances:
  41   32  0.76
  42   10  0.24

ACGTcount: A:0.40, C:0.09, G:0.25, T:0.26


Consensus pattern (42 bp):   
AAGACTCATATCTCGAGATGAGAATAAGAATATGATTAAAGG

Found at i:329 original size:42 final size:41

Alignment explanation


    Indices: 231--329  Score: 119
    Period size: 41  Copynumber: 2.4  Consensus size: 41

        221 AATTATTAAT

                          *           *   *           
        231 AAGACTCAT-ATCTTGAGATGAGAATGAGATTATGATTAAGG
          1 AAGACTCATGA-CTCGAGATGAGAATAAGAATATGATTAAGG

                      *                       *       
        272 AAGACTCATGTCTCGAGATGAGAATAAGAATATGGTTAAAGG
          1 AAGACTCATGACTCGAGATGAGAATAAGAATATGATT-AAGG

                  *         
        314 AAGACTTATGACTCGA
          1 AAGACTCATGACTCGA

        330 TAGAGCATAA


Statistics
Matches: 49,  Mismatches: 7, Indels: 3
        0.83            0.12        0.05

Matches are distributed among these distances:
  41   31  0.63
  42   18  0.37

ACGTcount: A:0.39, C:0.10, G:0.24, T:0.26


Consensus pattern (41 bp):   
AAGACTCATGACTCGAGATGAGAATAAGAATATGATTAAGG

Found at i:924 original size:24 final size:24

Alignment explanation


    Indices: 890--948  Score: 91
    Period size: 24  Copynumber: 2.5  Consensus size: 24

        880 TGAAATTTAA

                                    
        890 GTTTCGGTAGTACTGAGAATATTT
          1 GTTTCGGTAGTACTGAGAATATTT

                  *          *      
        914 GTTTCGATAGTACTGAGCATATTT
          1 GTTTCGGTAGTACTGAGAATATTT

              *        
        938 GTATCGGTAGT
          1 GTTTCGGTAGT

        949 TAGAATGCTT


Statistics
Matches: 31,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  24   31  1.00

ACGTcount: A:0.24, C:0.10, G:0.25, T:0.41


Consensus pattern (24 bp):   
GTTTCGGTAGTACTGAGAATATTT
Done.