Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002465.1 Kokia drynarioides strain JFW-HI SEQ_114596, 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: 13037
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35


Found at i:3766 original size:23 final size:23

Alignment explanation


    Indices: 3737--3838  Score: 100
    Period size: 23  Copynumber: 4.4  Consensus size: 23

       3727 ATCTTCAATT

                               **   
       3737 ACATGTTCGTTTAATGTT-CGTGA
          1 ACATGTTCGTTTAA-GTTAAATGA

                   * *             
       3760 ACATGTTTGATTAAGTTAAATGA
          1 ACATGTTCGTTTAAGTTAAATGA

                   *           **   
       3783 ACATGTTGGTTTAATGTT-CGTGA
          1 ACATGTTCGTTTAA-GTTAAATGA

                     *             
       3806 ACATGTTCGATTAAGTTAAATGA
          1 ACATGTTCGTTTAAGTTAAATGA

                      
       3829 ACATGTTCGT
          1 ACATGTTCGT

       3839 GAACATTAAA


Statistics
Matches: 63,  Mismatches: 13, Indels: 6
        0.77            0.16        0.07

Matches are distributed among these distances:
  22    6  0.10
  23   54  0.86
  24    3  0.05

ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40


Consensus pattern (23 bp):   
ACATGTTCGTTTAAGTTAAATGA

Found at i:3795 original size:46 final size:46

Alignment explanation


    Indices: 3737--3838  Score: 186
    Period size: 46  Copynumber: 2.2  Consensus size: 46

       3727 ATCTTCAATT

                                          *               
       3737 ACATGTTCGTTTAATGTTCGTGAACATGTTTGATTAAGTTAAATGA
          1 ACATGTTCGTTTAATGTTCGTGAACATGTTCGATTAAGTTAAATGA

                   *                                      
       3783 ACATGTTGGTTTAATGTTCGTGAACATGTTCGATTAAGTTAAATGA
          1 ACATGTTCGTTTAATGTTCGTGAACATGTTCGATTAAGTTAAATGA

                      
       3829 ACATGTTCGT
          1 ACATGTTCGT

       3839 GAACATTAAA


Statistics
Matches: 53,  Mismatches: 3, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  46   53  1.00

ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40


Consensus pattern (46 bp):   
ACATGTTCGTTTAATGTTCGTGAACATGTTCGATTAAGTTAAATGA

Found at i:3847 original size:23 final size:23

Alignment explanation


    Indices: 3803--3848  Score: 58
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       3793 TTAATGTTCG

                          *  *     
       3803 TGAACATGTTCGATTAAGTTAAA
          1 TGAACATGTTCGATGAAATTAAA

                                    
       3826 TGAACATGTTCG-TGAACATTAAA
          1 TGAACATGTTCGATGAA-ATTAAA

       3849 CAAACGAATA


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  22    3  0.15
  23   17  0.85

ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33


Consensus pattern (23 bp):   
TGAACATGTTCGATGAAATTAAA
Done.