Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010030.1 Kokia drynarioides strain JFW-HI SEQ_124798, 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, 660

Length: 1100
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.30


Found at i:77 original size:4 final size:4

Alignment explanation


    Indices: 68--153  Score: 86
    Period size: 4  Copynumber: 21.2  Consensus size: 4

         58 AAATAAACGG

                                                 *          *            
         68 GAAA GAAA GAAA GGAAA GAAA GAAA GAAA GGAA GAAA GAGA GAAAA GAAA
          1 GAAA GAAA GAAA -GAAA GAAA GAAA GAAA GAAA GAAA GAAA G-AAA GAAA

                    *     *                   *            
        118 G-AA GAAG GAGAG GAAA GAAA G-AA GAAG GAAA GAAA G
          1 GAAA GAAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA G

        154 GTAATGTGTT


Statistics
Matches: 69,  Mismatches: 8, Indels: 10
        0.79            0.09        0.11

Matches are distributed among these distances:
   3    6  0.09
   4   52  0.75
   5   11  0.16

ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00


Consensus pattern (4 bp):   
GAAA

Found at i:106 original size:20 final size:19

Alignment explanation


    Indices: 68--153  Score: 95
    Period size: 20  Copynumber: 4.5  Consensus size: 19

         58 AAATAAACGG

                               
         68 GAAAGAAAGAAAG--GAAA
          1 GAAAGAAAGAAAGAAGAAA

                                
         85 GAAAGAAAGAAAGGAAGAAA
          1 GAAAGAAAGAAA-GAAGAAA

              *                *
        105 GAGAGAAAAGAAAGAAGAAG
          1 GAAAG-AAAGAAAGAAGAAA

                *              *
        125 GAGAGGAAAGAAAGAAGAAG
          1 GA-AAGAAAGAAAGAAGAAA

                     
        145 GAAAGAAAG
          1 GAAAGAAAG

        154 GTAATGTGTT


Statistics
Matches: 59,  Mismatches: 5, Indels: 8
        0.82            0.07        0.11

Matches are distributed among these distances:
  17   12  0.20
  18    1  0.02
  19    6  0.10
  20   32  0.54
  21    8  0.14

ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00


Consensus pattern (19 bp):   
GAAAGAAAGAAAGAAGAAA

Found at i:114 original size:29 final size:28

Alignment explanation


    Indices: 70--153  Score: 98
    Period size: 29  Copynumber: 2.9  Consensus size: 28

         60 ATAAACGGGA

                       *                 
         70 AAGAAAGAAAGGAAAGAAAGAAAGAAAGG
          1 AAGAAAGAAAGAAAAGAAAGAAAG-AAGG

                    *                   
         99 AAGAAAGAGAGAAAAGAAAG-AAGAAGG
          1 AAGAAAGAAAGAAAAGAAAGAAAGAAGG

                                        
        126 AGAGGAAAGAAAGAAGAAGGAAAGAAAG
          1 A-A-GAAAGAAAGAA-AA-GAAAGAAAG

        154 GTAATGTGTT


Statistics
Matches: 47,  Mismatches: 3, Indels: 7
        0.82            0.05        0.12

Matches are distributed among these distances:
  27    5  0.11
  28    4  0.09
  29   28  0.60
  30    2  0.04
  31    5  0.11
  32    3  0.06

ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00


Consensus pattern (28 bp):   
AAGAAAGAAAGAAAAGAAAGAAAGAAGG

Done.