Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002970.1 Kokia drynarioides strain JFW-HI SEQ_115449, 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: 6751
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.32


Found at i:60 original size:2 final size:2

Alignment explanation


    Indices: 48--84  Score: 65
    Period size: 2  Copynumber: 18.5  Consensus size: 2

         38 TCCACTAACT

                  *                                                
         48 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

         85 TAATAATAAT


Statistics
Matches: 33,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:6238 original size:37 final size:37

Alignment explanation


    Indices: 6183--6268  Score: 118
    Period size: 37  Copynumber: 2.3  Consensus size: 37

       6173 TTAGATCACT

                *        *                       
       6183 GGCATAAAGCCTATTAGGCACAAAGCCTGATAACACC
          1 GGCACAAAGCCTACTAGGCACAAAGCCTGATAACACC

                                *    *  *       *
       6220 GGCACAAAGCCTACTAGGCATAAAGTCTTATAACACT
          1 GGCACAAAGCCTACTAGGCACAAAGCCTGATAACACC

                        
       6257 GGCACAAAGCCT
          1 GGCACAAAGCCT

       6269 GATAACACCA


Statistics
Matches: 43,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  37   43  1.00

ACGTcount: A:0.37, C:0.27, G:0.19, T:0.17


Consensus pattern (37 bp):   
GGCACAAAGCCTACTAGGCACAAAGCCTGATAACACC

Found at i:6268 original size:58 final size:58

Alignment explanation


    Indices: 6199--6322  Score: 203
    Period size: 58  Copynumber: 2.1  Consensus size: 58

       6189 AAGCCTATTA

                                 *                   *    *  *       *
       6199 GGCACAAAGCCTGATAACACCGGCACAAAGCCTACTAGGCATAAAGTCTTATAACACT
          1 GGCACAAAGCCTGATAACACCAGCACAAAGCCTACTAGGCACAAAGCCTGATAACACC

                                                                      
       6257 GGCACAAAGCCTGATAACACCAGCACAAAGCCTACTAGGCACAAAGCCTGATAACACC
          1 GGCACAAAGCCTGATAACACCAGCACAAAGCCTACTAGGCACAAAGCCTGATAACACC

                    
       6315 GGCACAAA
          1 GGCACAAA

       6323 ACCTACTAGG


Statistics
Matches: 61,  Mismatches: 5, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  58   61  1.00

ACGTcount: A:0.40, C:0.30, G:0.18, T:0.13


Consensus pattern (58 bp):   
GGCACAAAGCCTGATAACACCAGCACAAAGCCTACTAGGCACAAAGCCTGATAACACC

Found at i:6298 original size:37 final size:37

Alignment explanation


    Indices: 6257--6377  Score: 206
    Period size: 37  Copynumber: 3.3  Consensus size: 37

       6247 TTATAACACT

                                 *               
       6257 GGCACAAAGCCTGATAACACCAGCACAAAGCCTACTA
          1 GGCACAAAGCCTGATAACACCGGCACAAAGCCTACTA

                                         *       
       6294 GGCACAAAGCCTGATAACACCGGCACAAAACCTACTA
          1 GGCACAAAGCCTGATAACACCGGCACAAAGCCTACTA

                *       *                        
       6331 GGCATAAAGCCTTATAACACCGGCACAAAGCCTACTA
          1 GGCACAAAGCCTGATAACACCGGCACAAAGCCTACTA

                      
       6368 GGCACAAAGC
          1 GGCACAAAGC

       6378 TTGGATTTGT


Statistics
Matches: 78,  Mismatches: 6, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  37   78  1.00

ACGTcount: A:0.40, C:0.31, G:0.17, T:0.12


Consensus pattern (37 bp):   
GGCACAAAGCCTGATAACACCGGCACAAAGCCTACTA

Found at i:6300 original size:16 final size:16

Alignment explanation


    Indices: 6279--6377  Score: 58
    Period size: 16  Copynumber: 5.6  Consensus size: 16

       6269 GATAACACCA

                            
       6279 GCACAAAGCCTACTAG
          1 GCACAAAGCCTACTAG

                                  
       6295 GCACAAAGCCTGA-TAACACCG
          1 GCACAAAGCCT-ACT---A--G

                   *        
       6316 GCACAAAACCTACTAG
          1 GCACAAAGCCTACTAG

               *                  
       6332 GCATAAAGCCTTA-TAACACCG
          1 GCACAAAGCC-TACT---A--G

                            
       6353 GCACAAAGCCTACTAG
          1 GCACAAAGCCTACTAG

                     
       6369 GCACAAAGC
          1 GCACAAAGC

       6378 TTGGATTTGT


Statistics
Matches: 65,  Mismatches: 4, Indels: 28
        0.67            0.04        0.29

Matches are distributed among these distances:
  16   32  0.49
  17    3  0.05
  18    2  0.03
  19    2  0.03
  20    3  0.05
  21   23  0.35

ACGTcount: A:0.39, C:0.31, G:0.17, T:0.12


Consensus pattern (16 bp):   
GCACAAAGCCTACTAG

Found at i:6356 original size:95 final size:95

Alignment explanation


    Indices: 6188--6363  Score: 316
    Period size: 95  Copynumber: 1.9  Consensus size: 95

       6178 TCACTGGCAT

                    *                               *                *       
       6188 AAAGCCTATTAGGCACAAAGCCTGATAACACCGGCACAAAGCCTACTAGGCATAAAGTCTTATAA
          1 AAAGCCTACTAGGCACAAAGCCTGATAACACCGGCACAAAACCTACTAGGCATAAAGCCTTATAA

               *                          
       6253 CACTGGCACAAAGCCTGATAACACCAGCAC
         66 CACCGGCACAAAGCCTGATAACACCAGCAC

                                                                             
       6283 AAAGCCTACTAGGCACAAAGCCTGATAACACCGGCACAAAACCTACTAGGCATAAAGCCTTATAA
          1 AAAGCCTACTAGGCACAAAGCCTGATAACACCGGCACAAAACCTACTAGGCATAAAGCCTTATAA

                            
       6348 CACCGGCACAAAGCCT
         66 CACCGGCACAAAGCCT

       6364 ACTAGGCACA


Statistics
Matches: 77,  Mismatches: 4, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  95   77  1.00

ACGTcount: A:0.39, C:0.30, G:0.16, T:0.15


Consensus pattern (95 bp):   
AAAGCCTACTAGGCACAAAGCCTGATAACACCGGCACAAAACCTACTAGGCATAAAGCCTTATAA
CACCGGCACAAAGCCTGATAACACCAGCAC
Done.