Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010719.1 Kokia drynarioides strain JFW-HI SEQ_125670, 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: 26268
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33

Warning! 19 characters in sequence are not A, C, G, or T


Found at i:12290 original size:23 final size:23

Alignment explanation


    Indices: 12251--12298  Score: 62
    Period size: 22  Copynumber: 2.1  Consensus size: 23

      12241 AGTCAATCCG

                        *          
      12251 AAAGTAAAGATTCAAT-CAAACA
          1 AAAGTAAAGATTAAATCCAAACA

                   *                
      12273 AAAGTAATGAATTAAATCCAAACA
          1 AAAGTAAAG-ATTAAATCCAAACA

              
      12297 AA
          1 AA

      12299 TTGATAAGTA


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  22    8  0.36
  23    6  0.27
  24    8  0.36

ACGTcount: A:0.60, C:0.12, G:0.08, T:0.19


Consensus pattern (23 bp):   
AAAGTAAAGATTAAATCCAAACA

Found at i:16197 original size:22 final size:22

Alignment explanation


    Indices: 16172--16213  Score: 57
    Period size: 22  Copynumber: 1.9  Consensus size: 22

      16162 ATTTTAATAT

                *    *     *      
      16172 AGTATATAATATATTTTTTTGG
          1 AGTACATAAAATATTATTTTGG

                                
      16194 AGTACATAAAATATTATTTT
          1 AGTACATAAAATATTATTTT

      16214 AAATTTTTAA


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  22   17  1.00

ACGTcount: A:0.38, C:0.02, G:0.10, T:0.50


Consensus pattern (22 bp):   
AGTACATAAAATATTATTTTGG

Found at i:16348 original size:2 final size:2

Alignment explanation


    Indices: 16341--16384  Score: 88
    Period size: 2  Copynumber: 22.0  Consensus size: 2

      16331 TACATTATCC

                                                                          
      16341 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

              
      16383 AT
          1 AT

      16385 TATTTTTTTT


Statistics
Matches: 42,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   42  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:22271 original size:17 final size:17

Alignment explanation


    Indices: 22249--22283  Score: 70
    Period size: 17  Copynumber: 2.1  Consensus size: 17

      22239 ATATGCATAG

                             
      22249 TATGATTACAAGTTTTA
          1 TATGATTACAAGTTTTA

                             
      22266 TATGATTACAAGTTTTA
          1 TATGATTACAAGTTTTA

             
      22283 T
          1 T

      22284 CCTTATATAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   18  1.00

ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49


Consensus pattern (17 bp):   
TATGATTACAAGTTTTA

Found at i:25217 original size:3 final size:3

Alignment explanation


    Indices: 25209--25262  Score: 99
    Period size: 3  Copynumber: 17.7  Consensus size: 3

      25199 AAAATTCCAA

                                                                        
      25209 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT

                      
      25255 AAT AAT AA
          1 AAT AAT AA

      25263 AAGAGAATAT


Statistics
Matches: 50,  Mismatches: 0, Indels: 2
        0.96            0.00        0.04

Matches are distributed among these distances:
   3   47  0.94
   4    3  0.06

ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31


Consensus pattern (3 bp):   
AAT

Found at i:25271 original size:13 final size:13

Alignment explanation


    Indices: 25209--25271  Score: 53
    Period size: 12  Copynumber: 5.1  Consensus size: 13

      25199 AAAATTCCAA

                     *   
      25209 AATAAT-AATAAT
          1 AATAATAAAGAAT

                     *   
      25221 AATAAT-AATAAT
          1 AATAATAAAGAAT

                     *   
      25233 AATAAT-AATAAT
          1 AATAATAAAGAAT

                     *   
      25245 AATAATAAATAAT
          1 AATAATAAAGAAT

                          
      25258 AATAA-AAGAGAAT
          1 AATAATAA-AGAAT

             
      25271 A
          1 A

      25272 TCATAAATTT


Statistics
Matches: 48,  Mismatches: 1, Indels: 3
        0.92            0.02        0.06

Matches are distributed among these distances:
  12   32  0.67
  13   16  0.33

ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29


Consensus pattern (13 bp):   
AATAATAAAGAAT

Found at i:25277 original size:25 final size:25

Alignment explanation


    Indices: 25209--25279  Score: 74
    Period size: 25  Copynumber: 2.9  Consensus size: 25

      25199 AAAATTCCAA

                 *  *                
      25209 AATAATAATAATAATAAT-AATAAT
          1 AATAAAAAGAATAATAATAAATAAT

                 *  *                
      25233 AATAATAATAATAATAATAAATAAT
          1 AATAAAAAGAATAATAATAAATAAT

                            *      
      25258 AATAAAAGAGAAT-ATCATAAAT
          1 AATAAAA-AGAATAATAATAAAT

      25280 TTTGCAACAA


Statistics
Matches: 42,  Mismatches: 3, Indels: 3
        0.88            0.06        0.06

Matches are distributed among these distances:
  24   18  0.43
  25   20  0.48
  26    4  0.10

ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30


Consensus pattern (25 bp):   
AATAAAAAGAATAATAATAAATAAT
Done.