Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005369.1 Kokia drynarioides strain JFW-HI SEQ_119352, 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: 6425
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28


Found at i:5260 original size:42 final size:42

Alignment explanation


    Indices: 5201--5512  Score: 455
    Period size: 42  Copynumber: 7.6  Consensus size: 42

       5191 GCCGTAACAG

                                                **    
       5201 TGAAGACATCATCCAATCTCTTACCCCGATCATGGGATAGAT
          1 TGAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGAT

                                                      
       5243 TGAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGAT
          1 TGAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGAT

                                          *        *  
       5285 TGAAG-C--CATCCAATCTCTTACCCCGATTATGGGGCAAAT
          1 TGAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGAT

                                                      
       5324 TGAAGACATCATCCAATCTCTTA-CCCGATCATGGGGCAGAT
          1 TGAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGAT

                       *             *           *    
       5365 TGAAGACA--AACCAATCTCTTACCTCGATCATGGGGTAGAT
          1 TGAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGAT

                 *                                    
       5405 TGAAGTCATCATCCAATCTCTTACCCCGATCATGGGGCAGAT
          1 TGAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGAT

                                   *                   
       5447 TGAAG-C--CATCCAATCTCTTATCCCGATCATGGGGCA-AGT
          1 TGAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGA-T

                               *       
       5486 TGAAGACATCATCCAATCTTTTACCCC
          1 TGAAGACATCATCCAATCTCTTACCCC

       5513 TAAATTAAGA


Statistics
Matches: 244,  Mismatches: 16, Indels: 20
        0.87            0.06        0.07

Matches are distributed among these distances:
  38    1  0.00
  39   83  0.34
  40   25  0.10
  41   26  0.11
  42  109  0.45

ACGTcount: A:0.29, C:0.28, G:0.18, T:0.26


Consensus pattern (42 bp):   
TGAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGAT

Found at i:5345 original size:81 final size:81

Alignment explanation


    Indices: 5210--5512  Score: 473
    Period size: 81  Copynumber: 3.7  Consensus size: 81

       5200 GTGAAGACAT

                                       ** *                                  
       5210 CATCCAATCTCTTACCCCGATCATGGGATAGATTGAAGACATCATCCAATCTCTTACCCCGATCA
          1 CATCCAATCTCTTACCCCGATCATGGGGCAAATTGAAGACATCATCCAATCTCTTACCCCGATCA

                            
       5275 TGGGGCAGATTGAAGC
         66 TGGGGCAGATTGAAGC

                                 *                                           
       5291 CATCCAATCTCTTACCCCGATTATGGGGCAAATTGAAGACATCATCCAATCTCTTA-CCCGATCA
          1 CATCCAATCTCTTACCCCGATCATGGGGCAAATTGAAGACATCATCCAATCTCTTACCCCGATCA

                             
       5355 TGGGGCAGATTGAAGAC
         66 TGGGGCAGATTGAAG-C

            * *             *           * *       *                          
       5372 AAACCAATCTCTTACCTCGATCATGGGGTAGATTGAAGTCATCATCCAATCTCTTACCCCGATCA
          1 CATCCAATCTCTTACCCCGATCATGGGGCAAATTGAAGACATCATCCAATCTCTTACCCCGATCA

                            
       5437 TGGGGCAGATTGAAGC
         66 TGGGGCAGATTGAAGC

                          *                *                    *       
       5453 CATCCAATCTCTTATCCCGATCATGGGGCAAGTTGAAGACATCATCCAATCTTTTACCCC
          1 CATCCAATCTCTTACCCCGATCATGGGGCAAATTGAAGACATCATCCAATCTCTTACCCC

       5513 TAAATTAAGA


Statistics
Matches: 200,  Mismatches: 20, Indels: 4
        0.89            0.09        0.02

Matches are distributed among these distances:
  80   23  0.12
  81  154  0.77
  82   23  0.12

ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26


Consensus pattern (81 bp):   
CATCCAATCTCTTACCCCGATCATGGGGCAAATTGAAGACATCATCCAATCTCTTACCCCGATCA
TGGGGCAGATTGAAGC

Found at i:5481 original size:162 final size:162

Alignment explanation


    Indices: 5213--5511  Score: 535
    Period size: 162  Copynumber: 1.8  Consensus size: 162

       5203 AAGACATCAT

                                                                             
       5213 CCAATCTCTTACCCCGATCATGGGATAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGG
          1 CCAATCTCTTACCCCGATCATGGGATAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGG

                                              *                              
       5278 GGCAGATTGAAGCCATCCAATCTCTTACCCCGATTATGGGGCAAATTGAAGACATCATCCAATCT
         66 GGCAGATTGAAGCCATCCAATCTCTTACCCCGATCATGGGGCAAATTGAAGACATCATCCAATCT

                                            
       5343 CTTACCCGATCATGGGGCAGATTGAAGACAAA
        131 CTTACCCGATCATGGGGCAGATTGAAGACAAA

                         *          *          *                             
       5375 CCAATCTCTTACCTCGATCATGGGGTAGATTGAAGTCATCATCCAATCTCTTACCCCGATCATGG
          1 CCAATCTCTTACCCCGATCATGGGATAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGG

                                       *                *                    
       5440 GGCAGATTGAAGCCATCCAATCTCTTATCCCGATCATGGGGCAAGTTGAAGACATCATCCAATCT
         66 GGCAGATTGAAGCCATCCAATCTCTTACCCCGATCATGGGGCAAATTGAAGACATCATCCAATCT

            *      
       5505 TTTACCC
        131 CTTACCC

       5512 CTAAATTAAG


Statistics
Matches: 130,  Mismatches: 7, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
 162  130  1.00

ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26


Consensus pattern (162 bp):   
CCAATCTCTTACCCCGATCATGGGATAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGG
GGCAGATTGAAGCCATCCAATCTCTTACCCCGATCATGGGGCAAATTGAAGACATCATCCAATCT
CTTACCCGATCATGGGGCAGATTGAAGACAAA
Done.