Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007605.1 Kokia drynarioides strain JFW-HI SEQ_122236, 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: 27413
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34


Found at i:17411 original size:23 final size:23

Alignment explanation


    Indices: 17385--17430  Score: 74
    Period size: 23  Copynumber: 2.0  Consensus size: 23

      17375 TCATTAACAT

                              *    
      17385 TGTTCGTGAACATGTTCGTTTAA
          1 TGTTCGTGAACATGTTCGATTAA

                       *           
      17408 TGTTCGTGAACTTGTTCGATTAA
          1 TGTTCGTGAACATGTTCGATTAA

      17431 GTTAAATAAA


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  23   21  1.00

ACGTcount: A:0.22, C:0.13, G:0.22, T:0.43


Consensus pattern (23 bp):   
TGTTCGTGAACATGTTCGATTAA

Found at i:27254 original size:4 final size:4

Alignment explanation


    Indices: 27245--27329  Score: 91
    Period size: 4  Copynumber: 20.8  Consensus size: 4

      27235 CAAATAAACG

                                                  *       *              
      27245 AGAA AGAA AGAAA AGAA AGAA AGAA AGAA AGGA AGAA GGAGA AGAA AGAA
          1 AGAA AGAA AG-AA AGAA AGAA AGAA AGAA AGAA AGAA AGA-A AGAA AGAA

                 *     *                   *            
      27295 AGAA GGAGA GGAA AGAA AG-A AGAA GGAA AGAA AGA
          1 AGAA AGA-A AGAA AGAA AGAA AGAA AGAA AGAA AGA

      27330 TAATGTGTTT


Statistics
Matches: 69,  Mismatches: 8, Indels: 8
        0.81            0.09        0.09

Matches are distributed among these distances:
   3    3  0.04
   4   55  0.80
   5   11  0.16

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


Consensus pattern (4 bp):   
AGAA

Found at i:27267 original size:17 final size:16

Alignment explanation


    Indices: 27245--27329  Score: 91
    Period size: 17  Copynumber: 5.2  Consensus size: 16

      27235 CAAATAAACG

                             
      27245 AGAAAGAAAGAAAAGAA
          1 AGAAAGAAAG-AAAGAA

                          * 
      27262 AGAAAGAAAGAAAGGA
          1 AGAAAGAAAGAAAGAA

                *            
      27278 AGAAGGAGAAGAAAGAA
          1 AGAAAGA-AAGAAAGAA

                *    *       
      27295 AGAAGGAGAGGAAAGAA
          1 AGAAAGA-AAGAAAGAA

                    *       
      27312 AG-AAGAAGGAAAGAA
          1 AGAAAGAAAGAAAGAA

               
      27327 AGA
          1 AGA

      27330 TAATGTGTTT


Statistics
Matches: 61,  Mismatches: 5, Indels: 5
        0.86            0.07        0.07

Matches are distributed among these distances:
  15   11  0.18
  16   14  0.23
  17   36  0.59

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


Consensus pattern (16 bp):   
AGAAAGAAAGAAAGAA

Found at i:27290 original size:29 final size:29

Alignment explanation


    Indices: 27246--27329  Score: 100
    Period size: 29  Copynumber: 2.9  Consensus size: 29

      27236 AAATAAACGA

                      *                   
      27246 GAAAGAAAGAAAAGAAAGAAAGAAAGAAAG
          1 GAAAG-AAGAGAAGAAAGAAAGAAAGAAAG

                                    *  *  
      27276 G-AAGAAGGAGAAGAAAGAAAGAAGGAGAG
          1 GAAAGAA-GAGAAGAAAGAAAGAAAGAAAG

                           *          
      27305 GAAAGAA-AGAAGAAGGAAAGAAAGA
          1 GAAAGAAGAGAAGAAAGAAAGAAAGA

      27330 TAATGTGTTT


Statistics
Matches: 47,  Mismatches: 5, Indels: 6
        0.81            0.09        0.10

Matches are distributed among these distances:
  28   18  0.38
  29   23  0.49
  30    6  0.13

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


Consensus pattern (29 bp):   
GAAAGAAGAGAAGAAAGAAAGAAAGAAAG
Done.