Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000970.1 Kokia drynarioides strain JFW-HI SEQ_112153, 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: 9375
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35


Found at i:5082 original size:22 final size:23

Alignment explanation


    Indices: 5022--5084  Score: 74
    Period size: 23  Copynumber: 2.8  Consensus size: 23

       5012 TCAGGGGTCG

                                 * 
       5022 AAATTAAATTATAATTTTTACGA
          1 AAATTAAATTATAATTTTTACAA

            *   *   *              
       5045 TAATAAAAATATAATTTTTA-AA
          1 AAATTAAATTATAATTTTTACAA

                       *      
       5067 AAATTAAATTAAAATTTT
          1 AAATTAAATTATAATTTT

       5085 ATCACTTTTA


Statistics
Matches: 32,  Mismatches: 8, Indels: 1
        0.78            0.20        0.02

Matches are distributed among these distances:
  22   15  0.47
  23   17  0.53

ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43


Consensus pattern (23 bp):   
AAATTAAATTATAATTTTTACAA

Found at i:8665 original size:19 final size:19

Alignment explanation


    Indices: 8634--8672  Score: 62
    Period size: 20  Copynumber: 2.1  Consensus size: 19

       8624 ATAATTTTTT

                                
       8634 TAAAAAATATAATTCAAAAA
          1 TAAAAAATATAATT-AAAAA

                               
       8654 TAAAAAAT-TAATTAAAAA
          1 TAAAAAATATAATTAAAAA

             
       8672 T
          1 T

       8673 TTTAAAAAAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  18    6  0.32
  19    5  0.26
  20    8  0.42

ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28


Consensus pattern (19 bp):   
TAAAAAATATAATTAAAAA

Found at i:8678 original size:21 final size:22

Alignment explanation


    Indices: 8631--8684  Score: 71
    Period size: 21  Copynumber: 2.6  Consensus size: 22

       8621 TAAATAATTT

                                   
       8631 TTTTAAAAAATATAATTCAAAAA
          1 TTTTAAAAAAT-TAATTCAAAAA

                                  
       8654 ---TAAAAAATTAATT-AAAAA
          1 TTTTAAAAAATTAATTCAAAAA

                         
       8672 TTTTAAAAAATTA
          1 TTTTAAAAAATTA

       8685 CGCAATTTTT


Statistics
Matches: 28,  Mismatches: 0, Indels: 8
        0.78            0.00        0.22

Matches are distributed among these distances:
  18    5  0.18
  19    5  0.18
  20    8  0.29
  21   10  0.36

ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35


Consensus pattern (22 bp):   
TTTTAAAAAATTAATTCAAAAA

Found at i:9341 original size:2 final size:2

Alignment explanation


    Indices: 9334--9375  Score: 84
    Period size: 2  Copynumber: 21.0  Consensus size: 2

       9324 ATCTTTTTAC

                                                                          
       9334 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT


Statistics
Matches: 40,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   40  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.