Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000983.1 Kokia drynarioides strain JFW-HI SEQ_112174, 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: 5327
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33


Found at i:2392 original size:22 final size:23

Alignment explanation


    Indices: 2350--2422  Score: 103
    Period size: 24  Copynumber: 3.1  Consensus size: 23

       2340 AGTTTGACTC

                                    
       2350 AAACAAATAAACAGAGTTTAATTG
          1 AAACAAATAAACA-AGTTTAATTG

                                   
       2374 AAACAAATAAAC-AGTTTAATTG
          1 AAACAAATAAACAAGTTTAATTG

                  *              *  
       2396 AAACAATTAAACAAAGTTTAACTG
          1 AAACAAATAAAC-AAGTTTAATTG

               
       2420 AAA
          1 AAA

       2423 GATTATTTCT


Statistics
Matches: 45,  Mismatches: 2, Indels: 4
        0.88            0.04        0.08

Matches are distributed among these distances:
  22   21  0.47
  24   24  0.53

ACGTcount: A:0.56, C:0.10, G:0.10, T:0.25


Consensus pattern (23 bp):   
AAACAAATAAACAAGTTTAATTG

Found at i:2421 original size:24 final size:23

Alignment explanation


    Indices: 2340--2422  Score: 96
    Period size: 24  Copynumber: 3.6  Consensus size: 23

       2330 GACTAATAAG

                 *   *             
       2340 AGTTTGACTCAAACAAATAAACA
          1 AGTTTAACTGAAACAAATAAACA

                    *               
       2363 GAGTTTAATTGAAACAAATAAAC-
          1 -AGTTTAACTGAAACAAATAAACA

                   *        *       
       2386 AGTTTAATTGAAACAATTAAACAA
          1 AGTTTAACTGAAACAAATAAAC-A

                         
       2410 AGTTTAACTGAAA
          1 AGTTTAACTGAAA

       2423 GATTATTTCT


Statistics
Matches: 52,  Mismatches: 5, Indels: 4
        0.85            0.08        0.07

Matches are distributed among these distances:
  22   21  0.40
  24   31  0.60

ACGTcount: A:0.52, C:0.11, G:0.11, T:0.27


Consensus pattern (23 bp):   
AGTTTAACTGAAACAAATAAACA

Found at i:4392 original size:24 final size:24

Alignment explanation


    Indices: 4362--4417  Score: 85
    Period size: 24  Copynumber: 2.3  Consensus size: 24

       4352 AAATAAATAA

                                    
       4362 AATTGAAACAAATAAATAAAGTTT
          1 AATTGAAACAAATAAATAAAGTTT

                       *      *     
       4386 AATTGAAACAATTAAATAGAGTTT
          1 AATTGAAACAAATAAATAAAGTTT

              *     
       4410 AACTGAAA
          1 AATTGAAA

       4418 GGTTATTTCT


Statistics
Matches: 29,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  24   29  1.00

ACGTcount: A:0.55, C:0.05, G:0.11, T:0.29


Consensus pattern (24 bp):   
AATTGAAACAAATAAATAAAGTTT

Found at i:4691 original size:22 final size:22

Alignment explanation


    Indices: 4663--4706  Score: 88
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       4653 GACTGTTTGT

                                  
       4663 GCCAAAAAATAATAAAATAATA
          1 GCCAAAAAATAATAAAATAATA

                                  
       4685 GCCAAAAAATAATAAAATAATA
          1 GCCAAAAAATAATAAAATAATA

       4707 AAGATATAAT


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   22  1.00

ACGTcount: A:0.68, C:0.09, G:0.05, T:0.18


Consensus pattern (22 bp):   
GCCAAAAAATAATAAAATAATA
Done.