Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008757.1 Kokia drynarioides strain JFW-HI SEQ_123440, 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: 19446
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31


Found at i:160 original size:2 final size:2

Alignment explanation


    Indices: 153--179  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

        143 TTTTCTTTTA

                                                    
        153 AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT A

        180 CTAATGACAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:11873 original size:19 final size:19

Alignment explanation


    Indices: 11849--11900  Score: 54
    Period size: 19  Copynumber: 2.7  Consensus size: 19

      11839 GCCTAACAAA

                                
      11849 GAAAAA-GAAAAAACGAAAG
          1 GAAAAAGGAAAAAA-GAAAG

                             *  
      11868 GAAAAATGG-AAAAAGAGAG
          1 GAAAAA-GGAAAAAAGAAAG

            *             
      11887 AAAAAAGGAAAAAA
          1 GAAAAAGGAAAAAA

      11901 AACACAATAG


Statistics
Matches: 28,  Mismatches: 2, Indels: 6
        0.78            0.06        0.17

Matches are distributed among these distances:
  18    2  0.07
  19   20  0.71
  20    5  0.18
  21    1  0.04

ACGTcount: A:0.73, C:0.02, G:0.23, T:0.02


Consensus pattern (19 bp):   
GAAAAAGGAAAAAAGAAAG

Found at i:13222 original size:40 final size:40

Alignment explanation


    Indices: 13178--13286  Score: 112
    Period size: 40  Copynumber: 2.7  Consensus size: 40

      13168 AATATTTCTG

                   *                 *     * **      
      13178 AATAAATAAAAAGGTTGAAAATGG-TATTATCAGGAAGGAT
          1 AATAAATGAAAAGGTTGAAAA-GGAAATTATAAAAAAGGAT

                 *            *                     
      13218 AATAACTGAAAAGGTTGACAAGGAAATTATAAAAAAGGAT
          1 AATAAATGAAAAGGTTGAAAAGGAAATTATAAAAAAGGAT

                         * *             
      13258 AATAAATGAAAAGATCGAAAAGGTAAATT
          1 AATAAATGAAAAGGTTGAAAAGG-AAATT

      13287 TATTGAATTA


Statistics
Matches: 56,  Mismatches: 11, Indels: 3
        0.80            0.16        0.04

Matches are distributed among these distances:
  39    2  0.04
  40   49  0.88
  41    5  0.09

ACGTcount: A:0.54, C:0.04, G:0.20, T:0.22


Consensus pattern (40 bp):   
AATAAATGAAAAGGTTGAAAAGGAAATTATAAAAAAGGAT

Found at i:14400 original size:17 final size:18

Alignment explanation


    Indices: 14378--14414  Score: 58
    Period size: 17  Copynumber: 2.1  Consensus size: 18

      14368 GGCCAATAAC

                      *       
      14378 AATATAAACATG-AATTA
          1 AATATAAACAAGCAATTA

                              
      14395 AATATAAACAAGCAATTA
          1 AATATAAACAAGCAATTA

              
      14413 AA
          1 AA

      14415 CACAATAAAC


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  17   11  0.61
  18    7  0.39

ACGTcount: A:0.62, C:0.08, G:0.05, T:0.24


Consensus pattern (18 bp):   
AATATAAACAAGCAATTA

Done.