Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011887.1 Kokia drynarioides strain JFW-HI SEQ_126884, 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: 4362
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.25


Found at i:3537 original size:17 final size:17

Alignment explanation


    Indices: 3513--3586  Score: 103
    Period size: 17  Copynumber: 4.4  Consensus size: 17

       3503 TTGGAAATTG

                             
       3513 AATTTATTTTAAATTTA
          1 AATTTATTTTAAATTTA

             *               
       3530 AGTTTATTTTAAATTTA
          1 AATTTATTTTAAATTTA

             *       *       
       3547 AGTTTATTTGAAATTTA
          1 AATTTATTTTAAATTTA

                    *    *   
       3564 AATTTATTATAAAATTA
          1 AATTTATTTTAAATTTA

                  
       3581 AATTTA
          1 AATTTA

       3587 GAAAAGTCCA


Statistics
Matches: 51,  Mismatches: 6, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  17   51  1.00

ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54


Consensus pattern (17 bp):   
AATTTATTTTAAATTTA

Found at i:4240 original size:24 final size:23

Alignment explanation


    Indices: 4201--4247  Score: 69
    Period size: 24  Copynumber: 2.0  Consensus size: 23

       4191 AATGATCATT

                                   
       4201 AATAATAATTGGTTAATAACAAG
          1 AATAATAATTGGTTAATAACAAG

                                     
       4224 AATAATAA-TGGCATTAATAACAAG
          1 AATAATAATTGG--TTAATAACAAG

       4248 TGGGCGGTTT


Statistics
Matches: 22,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  22    3  0.14
  23    8  0.36
  24   11  0.50

ACGTcount: A:0.53, C:0.06, G:0.13, T:0.28


Consensus pattern (23 bp):   
AATAATAATTGGTTAATAACAAG

Found at i:4310 original size:31 final size:31

Alignment explanation


    Indices: 4261--4342  Score: 105
    Period size: 31  Copynumber: 2.6  Consensus size: 31

       4251 GCGGTTTTTC

                  * *              *       
       4261 AAAATATTTATTAATAATAAT-TTTTTTAAA
          1 AAAATAATAATTAATAATAATATCTTTTAAA

                                             
       4291 CAATAATAATAA-TAATAATAATATCTTTTAAA
          1 -AA-AATAATAATTAATAATAATATCTTTTAAA

                                
       4323 AAAATAATAATTAATAATAA
          1 AAAATAATAATTAATAATAA

       4343 AAAAGGCATT


Statistics
Matches: 45,  Mismatches: 3, Indels: 6
        0.83            0.06        0.11

Matches are distributed among these distances:
  30    8  0.18
  31   23  0.51
  32   14  0.31

ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40


Consensus pattern (31 bp):   
AAAATAATAATTAATAATAATATCTTTTAAA

Found at i:4310 original size:34 final size:34

Alignment explanation


    Indices: 4263--4342  Score: 103
    Period size: 33  Copynumber: 2.4  Consensus size: 34

       4253 GGTTTTTCAA

                *   *                 *   *   
       4263 AATATTTATTAATAATAAT-T-TTTTTAAACAAT
          1 AATAATTAATAATAATAATATCTTTTAAAAAAAT

                                              
       4295 AATAA-TAATAATAATAATATCTTTTAAAAAAAT
          1 AATAATTAATAATAATAATATCTTTTAAAAAAAT

                           
       4328 AATAATTAATAATAA
          1 AATAATTAATAATAA

       4343 AAAAGGCATT


Statistics
Matches: 41,  Mismatches: 4, Indels: 4
        0.84            0.08        0.08

Matches are distributed among these distances:
  31   12  0.29
  32    5  0.12
  33   15  0.37
  34    9  0.22

ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41


Consensus pattern (34 bp):   
AATAATTAATAATAATAATATCTTTTAAAAAAAT
Done.