Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002577.1 Kokia drynarioides strain JFW-HI SEQ_114778, 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: 8872
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.36


Found at i:2014 original size:17 final size:17

Alignment explanation


    Indices: 1992--2031  Score: 80
    Period size: 17  Copynumber: 2.4  Consensus size: 17

       1982 TATAAGATAC

                             
       1992 ACTCATTAAAGATTAGA
          1 ACTCATTAAAGATTAGA

                             
       2009 ACTCATTAAAGATTAGA
          1 ACTCATTAAAGATTAGA

                  
       2026 ACTCAT
          1 ACTCAT

       2032 AAAACTTTTG


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   23  1.00

ACGTcount: A:0.45, C:0.15, G:0.10, T:0.30


Consensus pattern (17 bp):   
ACTCATTAAAGATTAGA

Found at i:2113 original size:17 final size:19

Alignment explanation


    Indices: 2082--2119  Score: 53
    Period size: 17  Copynumber: 2.1  Consensus size: 19

       2072 TAACCTATAA

                               
       2082 TTCCTATATTGCACTGTGT
          1 TTCCTATATTGCACTGTGT

                           *   
       2101 TTCCTAT-TT-CACTTTGT
          1 TTCCTATATTGCACTGTGT

              
       2118 TT
          1 TT

       2120 TTAGAAAATC


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  17    9  0.50
  18    2  0.11
  19    7  0.39

ACGTcount: A:0.13, C:0.21, G:0.11, T:0.55


Consensus pattern (19 bp):   
TTCCTATATTGCACTGTGT

Found at i:3716 original size:23 final size:24

Alignment explanation


    Indices: 3660--3736  Score: 138
    Period size: 24  Copynumber: 3.2  Consensus size: 24

       3650 AGCCCTCACA

                  *                 
       3660 AGCCCATAATGGTTAGCTCTTACG
          1 AGCCCAGAATGGTTAGCTCTTACG

                                    
       3684 AGCCCAGAATGGTTAGCTCTTACG
          1 AGCCCAGAATGGTTAGCTCTTACG

                                    
       3708 A-CCCAGAATGGTTAGCTCTTACG
          1 AGCCCAGAATGGTTAGCTCTTACG

                  
       3731 AGCCCA
          1 AGCCCA

       3737 AACAGAGTTT


Statistics
Matches: 51,  Mismatches: 1, Indels: 2
        0.94            0.02        0.04

Matches are distributed among these distances:
  23   23  0.45
  24   28  0.55

ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25


Consensus pattern (24 bp):   
AGCCCAGAATGGTTAGCTCTTACG

Found at i:3923 original size:19 final size:16

Alignment explanation


    Indices: 3884--3915  Score: 64
    Period size: 16  Copynumber: 2.0  Consensus size: 16

       3874 ATTATCACGA

                            
       3884 ATGTTTAACATTCTTC
          1 ATGTTTAACATTCTTC

                            
       3900 ATGTTTAACATTCTTC
          1 ATGTTTAACATTCTTC

       3916 TAGTTGTTGT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.25, C:0.19, G:0.06, T:0.50


Consensus pattern (16 bp):   
ATGTTTAACATTCTTC
Done.