Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008641.1 Kokia drynarioides strain JFW-HI SEQ_123321, 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: 21013
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33


Found at i:9322 original size:13 final size:13

Alignment explanation


    Indices: 9304--9328  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       9294 TTTAGTATTA

                         
       9304 TTTTAAAAAATAT
          1 TTTTAAAAAATAT

                        
       9317 TTTTAAAAAATA
          1 TTTTAAAAAATA

       9329 AAATATTTAT


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44


Consensus pattern (13 bp):   
TTTTAAAAAATAT

Found at i:11041 original size:23 final size:23

Alignment explanation


    Indices: 11015--11069  Score: 101
    Period size: 23  Copynumber: 2.4  Consensus size: 23

      11005 AATTAAATTG

                      *            
      11015 TAATTTTTACTATAATAAAAATA
          1 TAATTTTTACGATAATAAAAATA

                                   
      11038 TAATTTTTACGATAATAAAAATA
          1 TAATTTTTACGATAATAAAAATA

                     
      11061 TAATTTTTA
          1 TAATTTTTA

      11070 AAGAATTAAA


Statistics
Matches: 31,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  23   31  1.00

ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45


Consensus pattern (23 bp):   
TAATTTTTACGATAATAAAAATA

Found at i:11150 original size:10 final size:10

Alignment explanation


    Indices: 11135--11161  Score: 54
    Period size: 10  Copynumber: 2.7  Consensus size: 10

      11125 TTATTAATTT

                      
      11135 AAAATTTTAA
          1 AAAATTTTAA

                      
      11145 AAAATTTTAA
          1 AAAATTTTAA

                   
      11155 AAAATTT
          1 AAAATTT

      11162 AAATAAAAAA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   17  1.00

ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41


Consensus pattern (10 bp):   
AAAATTTTAA

Found at i:17056 original size:26 final size:26

Alignment explanation


    Indices: 17016--17083  Score: 113
    Period size: 26  Copynumber: 2.7  Consensus size: 26

      17006 CCACTTTAAT

                             *        
      17016 AAGCAC-CTC-TCTTCCTCCTTGTGG
          1 AAGCACACTCTTCTTCCACCTTGTGG

                                      
      17040 AAGCACACTCTTCTTCCACCTTGTGG
          1 AAGCACACTCTTCTTCCACCTTGTGG

                              
      17066 AAGCACACTCTTCTTCCA
          1 AAGCACACTCTTCTTCCA

      17084 AGTTTGAGGC


Statistics
Matches: 41,  Mismatches: 1, Indels: 2
        0.93            0.02        0.05

Matches are distributed among these distances:
  24    6  0.15
  25    3  0.07
  26   32  0.78

ACGTcount: A:0.19, C:0.37, G:0.13, T:0.31


Consensus pattern (26 bp):   
AAGCACACTCTTCTTCCACCTTGTGG

Found at i:19904 original size:17 final size:17

Alignment explanation


    Indices: 19873--19936  Score: 51
    Period size: 17  Copynumber: 3.8  Consensus size: 17

      19863 AAATAAACGG

                              
      19873 GAAAG-AAAGAGAGGAAA
          1 GAAAGAAAAGA-AGGAAA

                            *
      19890 GAAAGAAAAGAAGGAAG
          1 GAAAGAAAAGAAGGAAA

              *  *      *    
      19907 GAGAGGAAAGAAAG-AA
          1 GAAAGAAAAGAAGGAAA

               *     *    
      19923 GAAGGAAAAAAAGG
          1 GAAAGAAAAGAAGG

      19937 TAATATGTTT


Statistics
Matches: 36,  Mismatches: 10, Indels: 3
        0.73            0.20        0.06

Matches are distributed among these distances:
  16   10  0.28
  17   21  0.58
  18    5  0.14

ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00


Consensus pattern (17 bp):   
GAAAGAAAAGAAGGAAA

Found at i:19910 original size:26 final size:24

Alignment explanation


    Indices: 19881--19929  Score: 80
    Period size: 26  Copynumber: 2.0  Consensus size: 24

      19871 GGGAAAGAAA

                                      
      19881 GAGAGGAAAGAAAGAAAAGAAGGAAG
          1 GAGAGGAAAGAAAG--AAGAAGGAAG

                                   
      19907 GAGAGGAAAGAAAGAAGAAGGAA
          1 GAGAGGAAAGAAAGAAGAAGGAA

      19930 AAAAAGGTAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  24    9  0.39
  26   14  0.61

ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00


Consensus pattern (24 bp):   
GAGAGGAAAGAAAGAAGAAGGAAG
Done.