Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002026.1 Kokia drynarioides strain JFW-HI SEQ_113907, 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: 6630
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36


Found at i:1838 original size:30 final size:30

Alignment explanation


    Indices: 1804--1889  Score: 172
    Period size: 30  Copynumber: 2.9  Consensus size: 30

       1794 AAACAATTAT

                                          
       1804 CTCTAAAATAATAACAAAATTAACAAATGC
          1 CTCTAAAATAATAACAAAATTAACAAATGC

                                          
       1834 CTCTAAAATAATAACAAAATTAACAAATGC
          1 CTCTAAAATAATAACAAAATTAACAAATGC

                                      
       1864 CTCTAAAATAATAACAAAATTAACAA
          1 CTCTAAAATAATAACAAAATTAACAA

       1890 TAAAATAAGT


Statistics
Matches: 56,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  30   56  1.00

ACGTcount: A:0.58, C:0.16, G:0.02, T:0.23


Consensus pattern (30 bp):   
CTCTAAAATAATAACAAAATTAACAAATGC

Found at i:1985 original size:22 final size:23

Alignment explanation


    Indices: 1960--2010  Score: 61
    Period size: 22  Copynumber: 2.3  Consensus size: 23

       1950 AAATTGTAGC

                    *       *      
       1960 AAAATAGGGA-GAAAACAACAAA
          1 AAAATAGGCATGAAAAAAACAAA

                       *           
       1982 AAAATA-GCATTAAAAAAACAAA
          1 AAAATAGGCATGAAAAAAACAAA

                   
       2004 AAAATAG
          1 AAAATAG

       2011 CATATATATT


Statistics
Matches: 24,  Mismatches: 3, Indels: 3
        0.80            0.10        0.10

Matches are distributed among these distances:
  21    2  0.08
  22   22  0.92

ACGTcount: A:0.71, C:0.08, G:0.12, T:0.10


Consensus pattern (23 bp):   
AAAATAGGCATGAAAAAAACAAA

Found at i:2011 original size:22 final size:22

Alignment explanation


    Indices: 1971--2013  Score: 77
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       1961 AAATAGGGAG

                *                 
       1971 AAAACAACAAAAAAATAGCATT
          1 AAAAAAACAAAAAAATAGCATT

                                 
       1993 AAAAAAACAAAAAAATAGCAT
          1 AAAAAAACAAAAAAATAGCAT

       2014 ATATATTTTT


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  22   20  1.00

ACGTcount: A:0.72, C:0.12, G:0.05, T:0.12


Consensus pattern (22 bp):   
AAAAAAACAAAAAAATAGCATT

Found at i:5663 original size:20 final size:20

Alignment explanation


    Indices: 5638--5708  Score: 67
    Period size: 19  Copynumber: 3.6  Consensus size: 20

       5628 AAAATATAAG

                                
       5638 TTTTGAATTTTTTATAAATA
          1 TTTTGAATTTTTTATAAATA

                       **   **  
       5658 TTTTGAATTTTAAAT-GTTA
          1 TTTTGAATTTTTTATAAATA

                   *             
       5677 TTTTGAAATTTTTA-AAATTA
          1 TTTTGAATTTTTTATAAA-TA

                         
       5697 TTTT-AATTTTTT
          1 TTTTGAATTTTTT

       5709 TTTATAATTC


Statistics
Matches: 39,  Mismatches: 10, Indels: 5
        0.72            0.19        0.09

Matches are distributed among these distances:
  19   20  0.51
  20   19  0.49

ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62


Consensus pattern (20 bp):   
TTTTGAATTTTTTATAAATA

Found at i:5678 original size:19 final size:18

Alignment explanation


    Indices: 5647--5706  Score: 61
    Period size: 20  Copynumber: 3.2  Consensus size: 18

       5637 GTTTTGAATT

                               
       5647 TTTTATAAA-TATTTTGAA
          1 TTTTA-AAATTATTTTGAA

                    *           
       5665 TTTTAAATGTTATTTTGAAA
          1 TTTTAAA-ATTATTTTG-AA

                               
       5685 TTTTTAAAATTATTTT-AA
          1 -TTTTAAAATTATTTTGAA

                
       5703 TTTT
          1 TTTT

       5707 TTTTTATAAT


Statistics
Matches: 36,  Mismatches: 2, Indels: 9
        0.77            0.04        0.19

Matches are distributed among these distances:
  17    6  0.17
  18    7  0.19
  19    7  0.19
  20    9  0.25
  21    7  0.19

ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60


Consensus pattern (18 bp):   
TTTTAAAATTATTTTGAA
Done.