Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014880.1 Kokia drynarioides strain JFW-HI SEQ_129923, 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: 6951
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31


Found at i:6296 original size:21 final size:21

Alignment explanation


    Indices: 6270--6408  Score: 84
    Period size: 23  Copynumber: 6.1  Consensus size: 21

       6260 ATACGGAACA

                              *  
       6270 AACAGAGAGTACCAAAGTACT
          1 AACAGAGAGTACCAAAGTGCT

                     *            
       6291 AACAGAGAGCA-CATAAGTGCT
          1 AACAGAGAGTACCA-AAGTGCT

                                *      
       6312 GGGCAACAGAGAGCTTA-CACAGTGCT
          1 ----AACAGAGAG--TACCAAAGTGCT

                 *              *  
       6338 AAACAAAGAGTACACAAAGTACT
          1 -AACAGAGAGTAC-CAAAGTGCT

                      *            
       6361 AATCAGAGAGCACACAAAGTGCT
          1 AA-CAGAGAGTAC-CAAAGTGCT

                            *      
       6384 AATCAGAGAGTACACACAGTGCT
          1 AA-CAGAGAGTAC-CAAAGTGCT

              
       6407 AA
          1 AA

       6409 TAACAGAGAG


Statistics
Matches: 95,  Mismatches: 13, Indels: 18
        0.75            0.10        0.14

Matches are distributed among these distances:
  20    2  0.02
  21   18  0.19
  22    2  0.02
  23   55  0.58
  25    9  0.09
  26    6  0.06
  27    3  0.03

ACGTcount: A:0.44, C:0.20, G:0.22, T:0.14


Consensus pattern (21 bp):   
AACAGAGAGTACCAAAGTGCT

Found at i:6342 original size:23 final size:22

Alignment explanation


    Indices: 6316--6442  Score: 85
    Period size: 23  Copynumber: 5.5  Consensus size: 22

       6306 AGTGCTGGGC

                       *           
       6316 AACAGAGAGCTTACACAGTGCTA
          1 AACAGAGAGC-CACACAGTGCTA

                *     *    *   *   
       6339 AACAAAGAGTACACAAAGTACTA
          1 AACAGAGAG-CCACACAGTGCTA

             *             *       
       6362 ATCAGAGAGCACACAAAGTGCTA
          1 AACAGAGAGC-CACACAGTGCTA

             *        *             
       6385 ATCAGAGAGTACACACAGTGCTAA
          1 AACAGAGAG-CCACACAGTGCT-A

                            *        
       6409 TAACAGAGAG-CACGAGACGTGCTA
          1 -AACAGAGAGCCAC-ACA-GTGCTA

                      
       6433 AACAGAGAGC
          1 AACAGAGAGC

       6443 GCGCTAGTGT


Statistics
Matches: 83,  Mismatches: 13, Indels: 15
        0.75            0.12        0.14

Matches are distributed among these distances:
  23   66  0.80
  24    4  0.05
  25   13  0.16

ACGTcount: A:0.44, C:0.20, G:0.22, T:0.13


Consensus pattern (22 bp):   
AACAGAGAGCCACACAGTGCTA

Found at i:6391 original size:69 final size:66

Alignment explanation


    Indices: 6269--6408  Score: 167
    Period size: 69  Copynumber: 2.0  Consensus size: 66

       6259 TATACGGAAC

                 *                             *                       *     
       6269 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTGGGCAACAGAGAGCT-TACACA
          1 AAACAAAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCT--G-AACAGAGAG-TACACACA

                 
       6333 GTGCT
         62 GTGCT

                                                                             
       6338 AAACAAAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT-AATCAGAGAGTACACACA
          1 AAACAAAGAGTAC-CAAAGTACTAA-CAGAGAGCACA-AAAGTGCTGAA-CAGAGAGTACACACA

                 
       6402 GTGCT
         62 GTGCT

              
       6407 AA
          1 AA

       6409 TAACAGAGAG


Statistics
Matches: 63,  Mismatches: 3, Indels: 10
        0.83            0.04        0.13

Matches are distributed among these distances:
  68    3  0.05
  69   31  0.49
  70   11  0.17
  71   11  0.17
  72    7  0.11

ACGTcount: A:0.44, C:0.20, G:0.21, T:0.14


Consensus pattern (66 bp):   
AAACAAAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCTGAACAGAGAGTACACACAGTGC
T

Found at i:6399 original size:25 final size:24

Alignment explanation


    Indices: 6332--6418  Score: 99
    Period size: 23  Copynumber: 3.7  Consensus size: 24

       6322 GAGCTTACAC

                    *  *            
       6332 AGTGCTAAACAAAGAGT-ACACAA
          1 AGTGCTAATCAGAGAGTCACACAA

               *                    
       6355 AGTACTAATCAGAGAG-CACACAA
          1 AGTGCTAATCAGAGAGTCACACAA

                                   *
       6378 AGTGCTAATCAGAGAGT-ACACAC
          1 AGTGCTAATCAGAGAGTCACACAA

                              
       6401 AGTGCTAATAACAGAGAG
          1 AGTGCTAAT--CAGAGAG

       6419 CACGAGACGT


Statistics
Matches: 55,  Mismatches: 5, Indels: 6
        0.83            0.08        0.09

Matches are distributed among these distances:
  23   48  0.87
  25    7  0.13

ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15


Consensus pattern (24 bp):   
AGTGCTAATCAGAGAGTCACACAA

Found at i:6431 original size:48 final size:46

Alignment explanation


    Indices: 6318--6441  Score: 133
    Period size: 46  Copynumber: 2.7  Consensus size: 46

       6308 TGCTGGGCAA

                    **   *           *                    
       6318 CAGAGAGCTTACACAGTGCTAAACAAAGAGTACACAAAGTACTAAT
          1 CAGAGAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACTAAT

                                  *             *   *     
       6364 CAGAGAGCACACAAAGTGCTAATCAGAGAGTACACACAGTGCTAAT
          1 CAGAGAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACTAAT

                           * *               
       6410 AACAGAGAGCACGA-GACGTGCTAAACAGAGAG
          1 --CAGAGAGCAC-ACAAAGTGCTAAACAGAGAG

       6442 CGCGCTAGTG


Statistics
Matches: 65,  Mismatches: 10, Indels: 4
        0.82            0.13        0.05

Matches are distributed among these distances:
  46   39  0.60
  48   25  0.38
  49    1  0.02

ACGTcount: A:0.44, C:0.20, G:0.23, T:0.14


Consensus pattern (46 bp):   
CAGAGAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACTAAT
Done.