Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013687.1 Kokia drynarioides strain JFW-HI SEQ_128715, 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: 5599
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31


Found at i:4212 original size:16 final size:16

Alignment explanation


    Indices: 4181--4217  Score: 58
    Period size: 16  Copynumber: 2.3  Consensus size: 16

       4171 ATGTGAAGAA

                            
       4181 TATTATTTAAAATTAT
          1 TATTATTTAAAATTAT

                             
       4197 TATT-TTTAAAATTTAT
          1 TATTATTTAAAA-TTAT

                 
       4213 TATTA
          1 TATTA

       4218 AAATAAAATT


Statistics
Matches: 19,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  15    7  0.37
  16   12  0.63

ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59


Consensus pattern (16 bp):   
TATTATTTAAAATTAT

Found at i:4239 original size:18 final size:18

Alignment explanation


    Indices: 4213--4257  Score: 54
    Period size: 18  Copynumber: 2.4  Consensus size: 18

       4203 TAAAATTTAT

                               
       4213 TATTAAAATAAAATTGAAA
          1 TATT-AAATAAAATTGAAA

                      **      
       4232 TATTAAATAATTTTGAAA
          1 TATTAAATAAAATTGAAA

              *     
       4250 TAATAAAT
          1 TATTAAAT

       4258 TATATTAATA


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  18   19  0.83
  19    4  0.17

ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38


Consensus pattern (18 bp):   
TATTAAATAAAATTGAAA

Found at i:4264 original size:28 final size:29

Alignment explanation


    Indices: 4231--4286  Score: 80
    Period size: 28  Copynumber: 2.0  Consensus size: 29

       4221 TAAAATTGAA

                                          
       4231 ATATTAAATAATTT-TGAAAT-AATAAATT
          1 ATATT-AATAATTTATGAAATGAATAAATT

                           *            
       4259 ATATTAATAATTTATTAAATGAATAAAT
          1 ATATTAATAATTTATGAAATGAATAAAT

       4287 ATAAATAATT


Statistics
Matches: 25,  Mismatches: 1, Indels: 3
        0.86            0.03        0.10

Matches are distributed among these distances:
  27    8  0.32
  28   10  0.40
  29    7  0.28

ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43


Consensus pattern (29 bp):   
ATATTAATAATTTATGAAATGAATAAATT

Found at i:4293 original size:26 final size:24

Alignment explanation


    Indices: 4229--4296  Score: 73
    Period size: 26  Copynumber: 2.6  Consensus size: 24

       4219 AATAAAATTG

                                     
       4229 AAATATTAAATAATTTTGAAATAAT
          1 AAATA-TAAATAATTTTGAAATAAT

                                *        
       4254 AAATTATATTAATAATTTATTAAATGAAT
          1 AAA-TATA--AATAATTT-TGAAAT-AAT

                          
       4283 AAATATAAATAATT
          1 AAATATAAATAATT

       4297 AAATATGTAT


Statistics
Matches: 37,  Mismatches: 1, Indels: 9
        0.79            0.02        0.19

Matches are distributed among these distances:
  25    5  0.14
  26    9  0.24
  27    8  0.22
  28    9  0.24
  29    6  0.16

ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41


Consensus pattern (24 bp):   
AAATATAAATAATTTTGAAATAAT

Found at i:4295 original size:29 final size:27

Alignment explanation


    Indices: 4237--4295  Score: 66
    Period size: 29  Copynumber: 2.1  Consensus size: 27

       4227 TGAAATATTA

                                     * 
       4237 AATAATTTTGAAATAATAAATTATATT
          1 AATAATTTTGAAATAATAAATTATAAT

                      *                   
       4264 AATAATTTATTAAATGAATAAA-TATAAAT
          1 AATAATTT-TGAAAT-AATAAATTAT-AAT

               
       4293 AAT
          1 AAT

       4296 TAAATATGTA


Statistics
Matches: 27,  Mismatches: 2, Indels: 4
        0.82            0.06        0.12

Matches are distributed among these distances:
  27    8  0.30
  28    8  0.30
  29   11  0.41

ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41


Consensus pattern (27 bp):   
AATAATTTTGAAATAATAAATTATAAT
Done.