Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006167.1 Kokia drynarioides strain JFW-HI SEQ_120725, 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: 8270
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.30


Found at i:6313 original size:88 final size:84

Alignment explanation


    Indices: 6209--6441  Score: 305
    Period size: 88  Copynumber: 2.8  Consensus size: 84

       6199 CAATGCCATA

                                     *                                       
       6209 CATATATATACACATAAGTATTTGCCATTCATCTTTGCTTAAACTACCGTGCAACCTTAACATCT
          1 CATATATATACACATAAGTATTTGCAATTCATCTTTGCTTAAACTACCGTGCAA-CTTAACATC-

                      *            
       6274 TCTGTTATAATACATAACAATGC
         64 -C-GTTATAACACATAACAATGC

                                                      * *                    
       6297 CATATATATACACATAAGTATTTGCAATTCATCTTTGCTTAACCAACCGTGCAAC----C-TCCG
          1 CATATATATACACATAAGTATTTGCAATTCATCTTTGCTTAAACTACCGTGCAACTTAACATCCG

                               
       6357 TTATAACACATAACAATGC
         66 TTATAACACATAACAATGC

                      *                       *               *              
       6376 CATATATACACACACATAAGTATTTGCAATTCATTTTTGCTTAAACTACCATGCAATCTTAACAT
          1 CATATAT--ATACACATAAGTATTTGCAATTCATCTTTGCTTAAACTACCGTGCAA-CTTAACAT

             
       6441 C
         63 C

       6442 ATCAAGAAGA


Statistics
Matches: 128,  Mismatches: 9, Indels: 17
        0.83            0.06        0.11

Matches are distributed among these distances:
  79   26  0.20
  80    1  0.01
  81   42  0.33
  82    3  0.02
  83    1  0.01
  86    1  0.01
  87    3  0.02
  88   51  0.40

ACGTcount: A:0.35, C:0.24, G:0.08, T:0.33


Consensus pattern (84 bp):   
CATATATATACACATAAGTATTTGCAATTCATCTTTGCTTAAACTACCGTGCAACTTAACATCCG
TTATAACACATAACAATGC

Found at i:6431 original size:81 final size:79

Alignment explanation


    Indices: 6277--6431  Score: 238
    Period size: 81  Copynumber: 1.9  Consensus size: 79

       6267 AACATCTTCT

                   *                    *                                 *  
       6277 GTTATAATACATAACAATGCCATATATATACACATAAGTATTTGCAATTCATCTTTGCTTAACCA
          1 GTTATAACACATAACAATGCCATATATACACACATAAGTATTTGCAATTCATCTTTGCTTAAACA

               *          
       6342 ACCGTGCAACCTCC
         66 ACCATGCAACCTCC

                                                                  *          
       6356 GTTATAACACATAACAATGCCATATATACACACACATAAGTATTTGCAATTCATTTTTGCTTAAA
          1 GTTATAACACATAACAATGCCATATAT--ACACACATAAGTATTTGCAATTCATCTTTGCTTAAA

             *         
       6421 CTACCATGCAA
         64 CAACCATGCAA

       6432 TCTTAACATC


Statistics
Matches: 68,  Mismatches: 6, Indels: 2
        0.89            0.08        0.03

Matches are distributed among these distances:
  79   26  0.38
  81   42  0.62

ACGTcount: A:0.37, C:0.23, G:0.08, T:0.32


Consensus pattern (79 bp):   
GTTATAACACATAACAATGCCATATATACACACATAAGTATTTGCAATTCATCTTTGCTTAAACA
ACCATGCAACCTCC

Found at i:7213 original size:13 final size:13

Alignment explanation


    Indices: 7195--7219  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       7185 GCTAGAAACT

                         
       7195 TATAGAACAATAA
          1 TATAGAACAATAA

                        
       7208 TATAGAACAATA
          1 TATAGAACAATA

       7220 TGTAGATTTA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.60, C:0.08, G:0.08, T:0.24


Consensus pattern (13 bp):   
TATAGAACAATAA
Done.