Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008502.1 Kokia drynarioides strain JFW-HI SEQ_123178, 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: 26496
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:3778 original size:15 final size:15

Alignment explanation


    Indices: 3747--3789  Score: 52
    Period size: 15  Copynumber: 2.9  Consensus size: 15

       3737 AAGGTATAAC

                            
       3747 AAAAGCAAAAG-AATG
          1 AAAAG-AAAAGAAATG

               *    *      
       3762 AAAGGAAATGAAATG
          1 AAAAGAAAAGAAATG

                         
       3777 AAAAGAAAAGAAA
          1 AAAAGAAAAGAAA

       3790 ATATATGTAT


Statistics
Matches: 23,  Mismatches: 4, Indels: 2
        0.79            0.14        0.07

Matches are distributed among these distances:
  14    4  0.17
  15   19  0.83

ACGTcount: A:0.70, C:0.02, G:0.21, T:0.07


Consensus pattern (15 bp):   
AAAAGAAAAGAAATG

Found at i:9762 original size:2 final size:2

Alignment explanation


    Indices: 9757--9782  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       9747 AATTTTTTAA

                                                  
       9757 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

       9783 TTAAAAAAAT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:10279 original size:17 final size:18

Alignment explanation


    Indices: 10259--10305  Score: 51
    Period size: 19  Copynumber: 2.6  Consensus size: 18

      10249 TGTTAGTGGG

                              
      10259 TTTTATTAAAAAATA-TA
          1 TTTTATTAAAAAATATTA

                          *     
      10276 TTTTATTTATAAAAGTATTA
          1 TTTTA-TTA-AAAAATATTA

                 *    
      10296 TTTTAATAAA
          1 TTTTATTAAA

      10306 TATATTTCGT


Statistics
Matches: 25,  Mismatches: 2, Indels: 5
        0.78            0.06        0.16

Matches are distributed among these distances:
  17    5  0.20
  18    5  0.20
  19    8  0.32
  20    7  0.28

ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51


Consensus pattern (18 bp):   
TTTTATTAAAAAATATTA

Found at i:10311 original size:17 final size:17

Alignment explanation


    Indices: 10259--10312  Score: 58
    Period size: 17  Copynumber: 3.2  Consensus size: 17

      10249 TGTTAGTGGG

                     *       
      10259 TTTTATTAAAAAATATA
          1 TTTTATTAATAAATATA

                   *          
      10276 TTTTATTTATAAA-AGTA
          1 TTTTATTAATAAATA-TA

                              
      10293 TTATT-TTAATAAATATA
          1 TT-TTATTAATAAATATA

               
      10310 TTT
          1 TTT

      10313 CGTGTCAAAA


Statistics
Matches: 31,  Mismatches: 3, Indels: 7
        0.76            0.07        0.17

Matches are distributed among these distances:
  16    2  0.06
  17   26  0.84
  18    3  0.10

ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54


Consensus pattern (17 bp):   
TTTTATTAATAAATATA

Found at i:24824 original size:40 final size:40

Alignment explanation


    Indices: 24779--24859  Score: 153
    Period size: 40  Copynumber: 2.0  Consensus size: 40

      24769 AGACATAAAC

                        *                           
      24779 TTGTGTTCAGGTGTCTATACTTACTCAAGCCTGAGTAACA
          1 TTGTGTTCAGGTCTCTATACTTACTCAAGCCTGAGTAACA

                                                    
      24819 TTGTGTTCAGGTCTCTATACTTACTCAAGCCTGAGTAACA
          1 TTGTGTTCAGGTCTCTATACTTACTCAAGCCTGAGTAACA

             
      24859 T
          1 T

      24860 AGATTCCTAA


Statistics
Matches: 40,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  40   40  1.00

ACGTcount: A:0.25, C:0.21, G:0.19, T:0.36


Consensus pattern (40 bp):   
TTGTGTTCAGGTCTCTATACTTACTCAAGCCTGAGTAACA
Done.