Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012169.1 Kokia drynarioides strain JFW-HI SEQ_127170, 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, 610

Length: 1018
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28


Found at i:49 original size:4 final size:4

Alignment explanation


    Indices: 40--133  Score: 75
    Period size: 4  Copynumber: 23.2  Consensus size: 4

         30 AAATAAACGG

                            *      *     *                   *   *       
         40 GAAA GAAA GAAA GGAA GAAG GAGAG GAAA GAAA G-AA GAAG GAGA GAAAA
          1 GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA GAAA GAAA GAAA G-AAA

                       *      *     *                                
         89 GAAA GAAA GGAA GAAG GAGAG GAAA GAAA G-AA GAAA GAAA GAAA G
          1 GAAA GAAA GAAA GAAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA G

        134 GTAATATGTT


Statistics
Matches: 73,  Mismatches: 12, Indels: 10
        0.77            0.13        0.11

Matches are distributed among these distances:
   3    6  0.08
   4   56  0.77
   5   11  0.15

ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00


Consensus pattern (4 bp):   
GAAA

Found at i:68 original size:25 final size:25

Alignment explanation


    Indices: 39--120  Score: 120
    Period size: 25  Copynumber: 3.5  Consensus size: 25

         29 CAAATAAACG

                                     
         39 GGAAAGAAAGAAAGGAAGAAGGAGA
          1 GGAAAGAAAGAAAGGAAGAAGGAGA

                                     
         64 -G---GAAAGAAA-GAAGAAGGAGA
          1 GGAAAGAAAGAAAGGAAGAAGGAGA

             *                       
         84 GAAAAGAAAGAAAGGAAGAAGGAGA
          1 GGAAAGAAAGAAAGGAAGAAGGAGA

                        
        109 GGAAAGAAAGAA
          1 GGAAAGAAAGAA

        121 GAAAGAAAGA


Statistics
Matches: 50,  Mismatches: 2, Indels: 10
        0.81            0.03        0.16

Matches are distributed among these distances:
  20   11  0.22
  21    8  0.16
  24    9  0.18
  25   22  0.44

ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00


Consensus pattern (25 bp):   
GGAAAGAAAGAAAGGAAGAAGGAGA

Found at i:78 original size:20 final size:21

Alignment explanation


    Indices: 44--123  Score: 110
    Period size: 20  Copynumber: 3.7  Consensus size: 21

         34 AAACGGGAAA

                                 
         44 GAAAGAAAGGAAGAAGGAGAG
          1 GAAAGAAAGGAAGAAGGAGAG

                                 
         65 GAAAGAAA-GAAGAAGGAGAG
          1 GAAAGAAAGGAAGAAGGAGAG

                                     
         85 AAAAGAAAGAAAGGAAGAAGGAGAG
          1 ----GAAAGAAAGGAAGAAGGAGAG

                           
        110 GAAAGAAA-GAAGAA
          1 GAAAGAAAGGAAGAA

        124 AGAAAGAAAG


Statistics
Matches: 54,  Mismatches: 0, Indels: 11
        0.83            0.00        0.17

Matches are distributed among these distances:
  20   18  0.33
  21   16  0.30
  24    8  0.15
  25   12  0.22

ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00


Consensus pattern (21 bp):   
GAAAGAAAGGAAGAAGGAGAG

Found at i:90 original size:45 final size:45

Alignment explanation


    Indices: 41--132  Score: 166
    Period size: 45  Copynumber: 2.0  Consensus size: 45

         31 AATAAACGGG

                                                  *  *   
         41 AAAGAAAGAAAGGAAGAAGGAGAGGAAAGAAAGAAGAAGGAGAGA
          1 AAAGAAAGAAAGGAAGAAGGAGAGGAAAGAAAGAAGAAAGAAAGA

                                                         
         86 AAAGAAAGAAAGGAAGAAGGAGAGGAAAGAAAGAAGAAAGAAAGA
          1 AAAGAAAGAAAGGAAGAAGGAGAGGAAAGAAAGAAGAAAGAAAGA

              
        131 AA
          1 AA

        133 GGTAATATGT


Statistics
Matches: 45,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  45   45  1.00

ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00


Consensus pattern (45 bp):   
AAAGAAAGAAAGGAAGAAGGAGAGGAAAGAAAGAAGAAAGAAAGA
Done.