Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003278.1 Kokia drynarioides strain JFW-HI SEQ_115939, 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, 785

Length: 1309
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29


Found at i:73 original size:4 final size:4

Alignment explanation


    Indices: 64--129  Score: 71
    Period size: 4  Copynumber: 16.2  Consensus size: 4

         54 AAATAAACGG

                                                 *      *     *          
         64 GAAA GAAA GAAA GGAAA GAAA GAAA GAAA GGAA GAAG GAGAG GAAA GAAA
          1 GAAA GAAA GAAA -GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA

                    *            
        114 G-AA GAAG GAAA GAAA G
          1 GAAA GAAA GAAA GAAA G

        130 GTAATGTGTT


Statistics
Matches: 53,  Mismatches: 6, Indels: 6
        0.82            0.09        0.09

Matches are distributed among these distances:
   3    3  0.06
   4   42  0.79
   5    8  0.15

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


Consensus pattern (4 bp):   
GAAA

Found at i:86 original size:17 final size:16

Alignment explanation


    Indices: 64--129  Score: 70
    Period size: 15  Copynumber: 4.3  Consensus size: 16

         54 AAATAAACGG

                             
         64 GAAAGAAAGAAAGGAAA
          1 GAAAG-AAGAAAGGAAA

                             
         81 GAAAGAAAGAAAGG-AA
          1 GAAAG-AAGAAAGGAAA

                     *      
         97 G-AAG--GAGAGGAAA
          1 GAAAGAAGAAAGGAAA

                            
        110 GAAAGAAG-AAGGAAA
          1 GAAAGAAGAAAGGAAA

                 
        125 GAAAG
          1 GAAAG

        130 GTAATGTGTT


Statistics
Matches: 43,  Mismatches: 2, Indels: 10
        0.78            0.04        0.18

Matches are distributed among these distances:
  12    5  0.12
  13    3  0.07
  14    3  0.07
  15   14  0.33
  16    4  0.09
  17   14  0.33

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


Consensus pattern (16 bp):   
GAAAGAAGAAAGGAAA

Found at i:130 original size:29 final size:31

Alignment explanation


    Indices: 63--130  Score: 92
    Period size: 29  Copynumber: 2.4  Consensus size: 31

         53 CAAATAAACG

                                           
         63 GGAAAGAAA-GAAAGGAAAGAAAGAAAGAAA
          1 GGAAAGAAAGGAAAGGAAAGAAAGAAAGAAA

                        *                  
         93 GG-AAG-AAGGAGAGGAAAGAAAG-AAG-AA
          1 GGAAAGAAAGGAAAGGAAAGAAAGAAAGAAA

                       
        120 GGAAAGAAAGG
          1 GGAAAGAAAGG

        131 TAATGTGTTT


Statistics
Matches: 34,  Mismatches: 1, Indels: 7
        0.81            0.02        0.17

Matches are distributed among these distances:
  27    4  0.12
  28    8  0.24
  29   20  0.59
  30    2  0.06

ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00


Consensus pattern (31 bp):   
GGAAAGAAAGGAAAGGAAAGAAAGAAAGAAA
Done.