Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000485.1 Kokia drynarioides strain JFW-HI SEQ_111360, 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: 5378
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31


Found at i:5251 original size:20 final size:20

Alignment explanation


    Indices: 5226--5263  Score: 58
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       5216 ATTCTAAAGT

                                
       5226 TTAAGGTTCAAAATTTTAGA
          1 TTAAGGTTCAAAATTTTAGA

                    * *       
       5246 TTAAGGTTTAGAATTTTA
          1 TTAAGGTTCAAAATTTTA

       5264 AATTTTGAAT


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   16  1.00

ACGTcount: A:0.37, C:0.03, G:0.16, T:0.45


Consensus pattern (20 bp):   
TTAAGGTTCAAAATTTTAGA

Found at i:5304 original size:15 final size:15

Alignment explanation


    Indices: 5273--5331  Score: 52
    Period size: 15  Copynumber: 4.1  Consensus size: 15

       5263 AAATTTTGAA

                       *   
       5273 TTCGAAATTTAAAAT
          1 TTCGAAATTTAGAAT

              *       *     
       5288 TTAG-AATTTCGAAAT
          1 TTCGAAATTTAG-AAT

               *           
       5303 TT-AAAATTTAGAAT
          1 TTCGAAATTTAGAAT

                           
       5317 TTCGAAATTTA-AAT
          1 TTCGAAATTTAGAAT

             
       5331 T
          1 T

       5332 CAGAATTTAC


Statistics
Matches: 35,  Mismatches: 6, Indels: 7
        0.73            0.12        0.15

Matches are distributed among these distances:
  14   14  0.40
  15   21  0.60

ACGTcount: A:0.44, C:0.05, G:0.08, T:0.42


Consensus pattern (15 bp):   
TTCGAAATTTAGAAT

Found at i:5312 original size:7 final size:7

Alignment explanation


    Indices: 5277--5329  Score: 52
    Period size: 7  Copynumber: 7.3  Consensus size: 7

       5267 TTTGAATTCG

                   
       5277 AAATTTA
          1 AAATTTA

                   
       5284 AAATTTA
          1 AAATTTA

            *      *
       5291 GAATTTCG
          1 AAATTT-A

                   
       5299 AAATTTA
          1 AAATTTA

                   
       5306 AAATTTA
          1 AAATTTA

            *      *
       5313 GAATTTCG
          1 AAATTT-A

                   
       5321 AAATTTA
          1 AAATTTA

              
       5328 AA
          1 AA

       5330 TTCAGAATTT


Statistics
Matches: 36,  Mismatches: 8, Indels: 4
        0.75            0.17        0.08

Matches are distributed among these distances:
   7   26  0.72
   8   10  0.28

ACGTcount: A:0.49, C:0.04, G:0.08, T:0.40


Consensus pattern (7 bp):   
AAATTTA

Found at i:5336 original size:21 final size:22

Alignment explanation


    Indices: 5257--5339  Score: 125
    Period size: 22  Copynumber: 3.9  Consensus size: 22

       5247 TAAGGTTTAG

                 *      *         
       5257 AATTTTAAATTTTGAA-TTCGA
          1 AATTTAAAATTTAGAATTTCGA

                                  
       5278 AATTTAAAATTTAGAATTTCGA
          1 AATTTAAAATTTAGAATTTCGA

                                  
       5300 AATTTAAAATTTAGAATTTCGA
          1 AATTTAAAATTTAGAATTTCGA

                       *       
       5322 AATTT-AAATTCAGAATTT
          1 AATTTAAAATTTAGAATTT

       5340 ACAGTAAAAG


Statistics
Matches: 58,  Mismatches: 3, Indels: 2
        0.92            0.05        0.03

Matches are distributed among these distances:
  21   26  0.45
  22   32  0.55

ACGTcount: A:0.43, C:0.05, G:0.08, T:0.43


Consensus pattern (22 bp):   
AATTTAAAATTTAGAATTTCGA
Done.