Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01015013.1 Kokia drynarioides strain JFW-HI SEQ_130057, 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: 46763
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.31

Warning! 202 characters in sequence are not A, C, G, or T


Found at i:16640 original size:3 final size:3

Alignment explanation


    Indices: 16632--16658  Score: 54
    Period size: 3  Copynumber: 9.0  Consensus size: 3

      16622 CAATATATTC

                                               
      16632 AAT AAT AAT AAT AAT AAT AAT AAT AAT
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT

      16659 GTTTATAACC


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

Matches are distributed among these distances:
   3   24  1.00

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


Consensus pattern (3 bp):   
AAT

Found at i:31473 original size:22 final size:22

Alignment explanation


    Indices: 31448--31498  Score: 93
    Period size: 22  Copynumber: 2.3  Consensus size: 22

      31438 GAACACTTGG

                                  
      31448 ACCAACATTTTCATATAGTTGC
          1 ACCAACATTTTCATATAGTTGC

                            *     
      31470 ACCAACATTTTCATATGGTTGC
          1 ACCAACATTTTCATATAGTTGC

                   
      31492 ACCAACA
          1 ACCAACA

      31499 AGCCCAATGT


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  22   28  1.00

ACGTcount: A:0.33, C:0.25, G:0.10, T:0.31


Consensus pattern (22 bp):   
ACCAACATTTTCATATAGTTGC

Found at i:40355 original size:29 final size:29

Alignment explanation


    Indices: 40285--40345  Score: 113
    Period size: 29  Copynumber: 2.1  Consensus size: 29

      40275 GTGTATACAT

                  *                      
      40285 TTTATACAATTTTAACTCTATATCTCTTC
          1 TTTATAAAATTTTAACTCTATATCTCTTC

                                         
      40314 TTTATAAAATTTTAACTCTATATCTCTTC
          1 TTTATAAAATTTTAACTCTATATCTCTTC

               
      40343 TTT
          1 TTT

      40346 GATTTTTTTT


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

Matches are distributed among these distances:
  29   31  1.00

ACGTcount: A:0.28, C:0.18, G:0.00, T:0.54


Consensus pattern (29 bp):   
TTTATAAAATTTTAACTCTATATCTCTTC

Found at i:40845 original size:38 final size:38

Alignment explanation


    Indices: 40778--40867  Score: 96
    Period size: 38  Copynumber: 2.4  Consensus size: 38

      40768 TCATCAAATG

                               *  *  *              
      40778 TATTTTTATTTTTAA-ATTTTATTTTATTCA-GAAATTAT
          1 TATTTTTA-TTTTAATATTATACTTAATTCATG-AATTAT

                                             *    
      40816 TATTTTTATTTTAATATTATACTTAATTCATGAGTTAT
          1 TATTTTTATTTTAATATTATACTTAATTCATGAATTAT

               *           
      40854 TATGTTT-TTTTAAT
          1 TATTTTTATTTTAAT

      40868 CTTAAATCAT


Statistics
Matches: 45,  Mismatches: 5, Indels: 5
        0.82            0.09        0.09

Matches are distributed among these distances:
  37   13  0.29
  38   31  0.69
  39    1  0.02

ACGTcount: A:0.30, C:0.03, G:0.04, T:0.62


Consensus pattern (38 bp):   
TATTTTTATTTTAATATTATACTTAATTCATGAATTAT

Found at i:43768 original size:22 final size:25

Alignment explanation


    Indices: 43743--43794  Score: 74
    Period size: 22  Copynumber: 2.2  Consensus size: 25

      43733 TTATTTTAAA

                    *                
      43743 ATTTATATTTACAT-A-T-AAATAT
          1 ATTTATATATACATAATTGAAATAT

                                     
      43765 ATTTATATATACATAATTGAAATAT
          1 ATTTATATATACATAATTGAAATAT

                 
      43790 ATTTA
          1 ATTTA

      43795 CACGTTTATA


Statistics
Matches: 26,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  22   13  0.50
  23    1  0.04
  24    1  0.04
  25   11  0.42

ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48


Consensus pattern (25 bp):   
ATTTATATATACATAATTGAAATAT

Found at i:46703 original size:19 final size:18

Alignment explanation


    Indices: 46674--46727  Score: 65
    Period size: 18  Copynumber: 3.0  Consensus size: 18

      46664 AATGTTTTTT

                *              
      46674 AAAAGTATTTTT-AATATA
          1 AAAAATATTTTTAAATA-A

                              
      46692 AAAAATATTTTTAAATAA
          1 AAAAATATTTTTAAATAA

                   * *        
      46710 AAAAATAATATTAAATAA
          1 AAAAATATTTTTAAATAA

      46728 GTAATTTTTG


Statistics
Matches: 32,  Mismatches: 3, Indels: 2
        0.86            0.08        0.05

Matches are distributed among these distances:
  18   28  0.88
  19    4  0.12

ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37


Consensus pattern (18 bp):   
AAAAATATTTTTAAATAA
Done.