Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009838.1 Kokia drynarioides strain JFW-HI SEQ_124561, 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: 1936
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.39


Found at i:831 original size:6 final size:6

Alignment explanation


    Indices: 813--872  Score: 88
    Period size: 6  Copynumber: 10.3  Consensus size: 6

        803 ATTTAGTATA

                     *               *                             
        813 TTTATT TTCATT TTTATT TTTAGT TTTA-T TTTA-T TTTATT TTTATT
          1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT

                            
        859 TTTATT TTTATT TT
          1 TTTATT TTTATT TT

        873 AATTATGCAC


Statistics
Matches: 50,  Mismatches: 3, Indels: 2
        0.91            0.05        0.04

Matches are distributed among these distances:
   5   10  0.20
   6   40  0.80

ACGTcount: A:0.17, C:0.02, G:0.02, T:0.80


Consensus pattern (6 bp):   
TTTATT

Found at i:853 original size:28 final size:29

Alignment explanation


    Indices: 813--873  Score: 106
    Period size: 28  Copynumber: 2.1  Consensus size: 29

        803 ATTTAGTATA

                                         
        813 TTTATTTTCATTTTTATTTTTAGTTTTAT
          1 TTTATTTTCATTTTTATTTTTAGTTTTAT

                                  *      
        842 TTTATTTT-ATTTTTATTTTTATTTTTAT
          1 TTTATTTTCATTTTTATTTTTAGTTTTAT

                
        870 TTTA
          1 TTTA

        874 ATTATGCACT


Statistics
Matches: 31,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  28   23  0.74
  29    8  0.26

ACGTcount: A:0.18, C:0.02, G:0.02, T:0.79


Consensus pattern (29 bp):   
TTTATTTTCATTTTTATTTTTAGTTTTAT

Found at i:887 original size:34 final size:30

Alignment explanation


    Indices: 822--916  Score: 95
    Period size: 28  Copynumber: 3.1  Consensus size: 30

        812 ATTTATTTTC

                         *                
        822 ATTTTTATTTTTAGTTTTATTTT-ATT-TT
          1 ATTTTTATTTTTATTTTTATTTTAATTATT

                                              
        850 ATTTTTATTTTTATTTTTATTTTAATTATGCACT
          1 ATTTTTATTTTTATTTTTATTTTAATTAT----T

                     *         *     *     
        884 ATTTTTATTCTTATGTTTTTTTTTAGTTATT
          1 ATTTTTATTTTTAT-TTTTATTTTAATTATT

              
        915 AT
          1 AT

        917 CTCCTTCTCT


Statistics
Matches: 56,  Mismatches: 4, Indels: 11
        0.79            0.06        0.15

Matches are distributed among these distances:
  28   22  0.39
  29    3  0.05
  30    1  0.02
  31    3  0.05
  34   14  0.25
  35   13  0.23

ACGTcount: A:0.20, C:0.03, G:0.04, T:0.73


Consensus pattern (30 bp):   
ATTTTTATTTTTATTTTTATTTTAATTATT

Found at i:1826 original size:17 final size:17

Alignment explanation


    Indices: 1803--1836  Score: 59
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       1793 TATTATTTAA

                              
       1803 AAAAAAAGTCGAAAAAAT
          1 AAAAAAA-TCGAAAAAAT

                            
       1821 AAAAAAATCGAAAAAA
          1 AAAAAAATCGAAAAAA

       1837 AATTCAGAAA


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  17    9  0.56
  18    7  0.44

ACGTcount: A:0.76, C:0.06, G:0.09, T:0.09


Consensus pattern (17 bp):   
AAAAAAATCGAAAAAAT
Done.