Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012978.1 Kokia drynarioides strain JFW-HI SEQ_127996, 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: 31175
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:22174 original size:24 final size:24

Alignment explanation


    Indices: 22156--22229  Score: 139
    Period size: 24  Copynumber: 3.1  Consensus size: 24

      22146 AGTTTGACTT

                         *          
      22156 AAACAAATAAACAAAGTTTAATTG
          1 AAACAAATAAACAGAGTTTAATTG

                                    
      22180 AAACAAATAAACAGAGTTTAATTG
          1 AAACAAATAAACAGAGTTTAATTG

                                    
      22204 AAACAAATAAACAGAGTTTAATTG
          1 AAACAAATAAACAGAGTTTAATTG

              
      22228 AA
          1 AA

      22230 TTTAATTGAA


Statistics
Matches: 49,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  24   49  1.00

ACGTcount: A:0.57, C:0.08, G:0.11, T:0.24


Consensus pattern (24 bp):   
AAACAAATAAACAGAGTTTAATTG

Found at i:24212 original size:24 final size:24

Alignment explanation


    Indices: 24184--24236  Score: 88
    Period size: 24  Copynumber: 2.2  Consensus size: 24

      24174 CTAATAACAA

                                    
      24184 TTTAACTCAAACAAATAAACAGAG
          1 TTTAACTCAAACAAATAAACAGAG

                 * *                
      24208 TTTAATTGAAACAAATAAACAGAG
          1 TTTAACTCAAACAAATAAACAGAG

                 
      24232 TTTAA
          1 TTTAA

      24237 TTGCATCAGT


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  24   27  1.00

ACGTcount: A:0.53, C:0.11, G:0.09, T:0.26


Consensus pattern (24 bp):   
TTTAACTCAAACAAATAAACAGAG

Found at i:24250 original size:24 final size:24

Alignment explanation


    Indices: 24192--24239  Score: 96
    Period size: 24  Copynumber: 2.0  Consensus size: 24

      24182 AATTTAACTC

                                    
      24192 AAACAAATAAACAGAGTTTAATTG
          1 AAACAAATAAACAGAGTTTAATTG

                                    
      24216 AAACAAATAAACAGAGTTTAATTG
          1 AAACAAATAAACAGAGTTTAATTG

      24240 CATCAGTTAA


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

Matches are distributed among these distances:
  24   24  1.00

ACGTcount: A:0.54, C:0.08, G:0.12, T:0.25


Consensus pattern (24 bp):   
AAACAAATAAACAGAGTTTAATTG

Found at i:29720 original size:18 final size:18

Alignment explanation


    Indices: 29690--29743  Score: 65
    Period size: 18  Copynumber: 3.0  Consensus size: 18

      29680 ATAAATTTGA

                    *         
      29690 AAAAATATCAAAATTTTT
          1 AAAAATATAAAAATTTTT

                         **   
      29708 AAAAATATAAAAAAATTT
          1 AAAAATATAAAAATTTTT

                               
      29726 AAAAAT-TCAAAAATTTTT
          1 AAAAATAT-AAAAATTTTT

      29744 TTTTTTTTTT


Statistics
Matches: 30,  Mismatches: 5, Indels: 2
        0.81            0.14        0.05

Matches are distributed among these distances:
  17    1  0.03
  18   29  0.97

ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35


Consensus pattern (18 bp):   
AAAAATATAAAAATTTTT

Found at i:29884 original size:21 final size:20

Alignment explanation


    Indices: 29858--29898  Score: 64
    Period size: 21  Copynumber: 2.0  Consensus size: 20

      29848 GTTAAATTTT

                  *              
      29858 AAAAATTATAAAAATATAAAA
          1 AAAAATAATAAAAATA-AAAA

                                
      29879 AAAAATAATAAAAATAAAAA
          1 AAAAATAATAAAAATAAAAA

      29899 TTTTAAAAAC


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  20    4  0.21
  21   15  0.79

ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20


Consensus pattern (20 bp):   
AAAAATAATAAAAATAAAAA
Done.