Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001113.1 Kokia drynarioides strain JFW-HI SEQ_112394, 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: 7137
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.36


Found at i:1631 original size:25 final size:22

Alignment explanation


    Indices: 1588--1632  Score: 63
    Period size: 23  Copynumber: 1.9  Consensus size: 22

       1578 AATTATATTT

                                  
       1588 TATATATTATTTAAATATGTCA
          1 TATATATTATTTAAATATGTCA

                                   
       1610 TATATTATTATATTAAATTATGT
          1 TATA-TATTAT-TTAAA-TATGT

       1633 AAACATTACA


Statistics
Matches: 20,  Mismatches: 0, Indels: 3
        0.87            0.00        0.13

Matches are distributed among these distances:
  22    4  0.20
  23    6  0.30
  24    5  0.25
  25    5  0.25

ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53


Consensus pattern (22 bp):   
TATATATTATTTAAATATGTCA

Found at i:5630 original size:18 final size:18

Alignment explanation


    Indices: 5603--5640  Score: 51
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       5593 AATTTTATGA

                               
       5603 AATTTATAT-AATTGTTTT
          1 AATTTATATAAATT-TTTT

                 *            
       5621 AATTTTTATAAATTTTTT
          1 AATTTATATAAATTTTTT

              
       5639 AA
          1 AA

       5641 AAAACTTTTA


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

Matches are distributed among these distances:
  18   14  0.78
  19    4  0.22

ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61


Consensus pattern (18 bp):   
AATTTATATAAATTTTTT

Found at i:6042 original size:21 final size:22

Alignment explanation


    Indices: 6018--6059  Score: 59
    Period size: 21  Copynumber: 2.0  Consensus size: 22

       6008 TTTATTTTAA

                                  
       6018 AAATATTAAAATATT-AATATC
          1 AAATATTAAAATATTCAATATC

                   *    *        
       6039 AAATATTGAAATTTTCAATAT
          1 AAATATTAAAATATTCAATAT

       6060 TATTGAATAT


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

Matches are distributed among these distances:
  21   13  0.72
  22    5  0.28

ACGTcount: A:0.52, C:0.05, G:0.02, T:0.40


Consensus pattern (22 bp):   
AAATATTAAAATATTCAATATC

Found at i:6273 original size:17 final size:17

Alignment explanation


    Indices: 6207--6278  Score: 51
    Period size: 19  Copynumber: 4.2  Consensus size: 17

       6197 TATTATTGAA

                               
       6207 AAATATTTATATTAATAAT
          1 AAATATTT-TA-TAATAAT

                    *   *   *  
       6226 AAATGTATATTACAATTAT
          1 AAA--TATTTTATAATAAT

                   *         
       6245 AAATA-TAT-TAATAAT
          1 AAATATTTTATAATAAT

                             
       6260 AAATATTTTATAAT-AT
          1 AAATATTTTATAATAAT

               
       6276 AAA
          1 AAA

       6279 GATTAGGATA


Statistics
Matches: 41,  Mismatches: 8, Indels: 11
        0.68            0.13        0.18

Matches are distributed among these distances:
  15   10  0.24
  16    8  0.20
  17    6  0.15
  19   11  0.27
  20    2  0.05
  21    4  0.10

ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43


Consensus pattern (17 bp):   
AAATATTTTATAATAAT

Found at i:6274 original size:14 final size:15

Alignment explanation


    Indices: 6214--6274  Score: 61
    Period size: 17  Copynumber: 3.9  Consensus size: 15

       6204 GAAAAATATT

                           
       6214 TATATTAATAATAAA
          1 TATATTAATAATAAA

                         *     
       6229 TGTATATTACAATTATAAA
          1 --TATATT--AATAATAAA

                           
       6248 TATATTAATAATAAA
          1 TATATTAATAATAAA

                  *      
       6263 TAT-TTTATAATA
          1 TATATTAATAATA

       6275 TAAAGATTAG


Statistics
Matches: 39,  Mismatches: 3, Indels: 7
        0.80            0.06        0.14

Matches are distributed among these distances:
  14    8  0.21
  15   11  0.28
  17   12  0.31
  19    8  0.21

ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44


Consensus pattern (15 bp):   
TATATTAATAATAAA
Done.