Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005321.1 Kokia drynarioides strain JFW-HI SEQ_119257, 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, 628

Length: 1047
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39


Found at i:731 original size:30 final size:30

Alignment explanation


    Indices: 695--886  Score: 173
    Period size: 29  Copynumber: 6.5  Consensus size: 30

        685 TATAAATCCC

                    * *                   
        695 ATTTTTAATCTCGAAACCTTCAAAAATTCT
          1 ATTTTTAACCCCGAAACCTTCAAAAATTCT

                   *                    *  
        725 ATTTTTATCCCCG-AA-CTTCTAAAAATCCT
          1 ATTTTTAACCCCGAAACCTTC-AAAAATTCT

                  *   *                   
        754 ATTTTTGACCTCGAAACCTTCAAAAATT-T
          1 ATTTTTAACCCCGAAACCTTCAAAAATTCT

                    *         *            
        783 CATTTTTACCCCCG-AACTTTCAAAAA-TCT
          1 -ATTTTTAACCCCGAAACCTTCAAAAATTCT

                         *    *            
        812 CATTTTTAACCCCAAAACTTTCAAAAATTCT
          1 -ATTTTTAACCCCGAAACCTTCAAAAATTCT

                   *                    *  
        843 ATTTTTACCCCCG-AA-CTTCTAAAAATCCT
          1 ATTTTTAACCCCGAAACCTTC-AAAAATTCT

                  *   *    
        872 ATTTTTGACCTCGAA
          1 ATTTTTAACCCCGAA

        887 TTTTTCCAAA


Statistics
Matches: 132,  Mismatches: 21, Indels: 18
        0.77            0.12        0.11

Matches are distributed among these distances:
  28    8  0.06
  29   65  0.49
  30   52  0.39
  31    7  0.05

ACGTcount: A:0.33, C:0.26, G:0.04, T:0.37


Consensus pattern (30 bp):   
ATTTTTAACCCCGAAACCTTCAAAAATTCT

Found at i:780 original size:59 final size:59

Alignment explanation


    Indices: 688--886  Score: 278
    Period size: 59  Copynumber: 3.4  Consensus size: 59

        678 TACATGATAT

                  *        *                            *              
        688 AAATCCCATTTTTAATCTCGAAACCTTCAAAAATTCTATTTTTATCCCCGAACTTCTAA
          1 AAATCCTATTTTTAACCTCGAAACCTTCAAAAATTCTATTTTTACCCCCGAACTTCTAA

                         *                                               
        747 AAATCCTATTTTTGACCTCGAAACCTTCAAAAATT-TCATTTTTACCCCCGAACTT-TCAA
          1 AAATCCTATTTTTAACCTCGAAACCTTCAAAAATTCT-ATTTTTACCCCCGAACTTCT-AA

                              * *    *                                  
        806 AAAT-CTCATTTTTAACCCCAAAACTTTCAAAAATTCTATTTTTACCCCCGAACTTCTAA
          1 AAATCCT-ATTTTTAACCTCGAAACCTTCAAAAATTCTATTTTTACCCCCGAACTTCTAA

                         *        
        865 AAATCCTATTTTTGACCTCGAA
          1 AAATCCTATTTTTAACCTCGAA

        887 TTTTTCCAAA


Statistics
Matches: 123,  Mismatches: 11, Indels: 12
        0.84            0.08        0.08

Matches are distributed among these distances:
  58    4  0.03
  59  115  0.93
  60    4  0.03

ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36


Consensus pattern (59 bp):   
AAATCCTATTTTTAACCTCGAAACCTTCAAAAATTCTATTTTTACCCCCGAACTTCTAA

Found at i:912 original size:59 final size:58

Alignment explanation


    Indices: 688--915  Score: 244
    Period size: 59  Copynumber: 3.9  Consensus size: 58

        678 TACATGATAT

                  *      * *        *            *      *              
        688 AAATCCCATTTTTAATCTCGAAACCTTCAAAAATTCTATTTTTATCCCCGAACTTCTAA
          1 AAATCCTATTTTTGACCTCGAAACTTTCAAAAATT-TCTTTTTACCCCCGAACTTCTAA

                                    *                                   
        747 AAATCCTATTTTTGACCTCGAAACCTTCAAAAATTTCATTTTTACCCCCGAACTT-TCAA
          1 AAATCCTATTTTTGACCTCGAAACTTTCAAAAATTTC-TTTTTACCCCCGAACTTCT-AA

                          *   * *                 *                     
        806 AAAT-CTCATTTTTAACCCCAAAACTTTCAAAAATTCTATTTTTACCCCCGAACTTCTAA
          1 AAATCCT-ATTTTTGACCTCGAAACTTTCAAAAATT-TCTTTTTACCCCCGAACTTCTAA

                                  **    *         *   *        
        865 AAATCCTATTTTTGACCTCGAATTTTTCCAAAATTATCGTTTCACCCCCGA
          1 AAATCCTATTTTTGACCTCGAAACTTTCAAAAATT-TCTTTTTACCCCCGA

        916 GAATCCAAAA


Statistics
Matches: 143,  Mismatches: 20, Indels: 12
        0.82            0.11        0.07

Matches are distributed among these distances:
  58    4  0.03
  59  135  0.94
  60    4  0.03

ACGTcount: A:0.32, C:0.27, G:0.04, T:0.36


Consensus pattern (58 bp):   
AAATCCTATTTTTGACCTCGAAACTTTCAAAAATTTCTTTTTACCCCCGAACTTCTAA

Found at i:912 original size:118 final size:118

Alignment explanation


    Indices: 688--915  Score: 332
    Period size: 118  Copynumber: 1.9  Consensus size: 118

        678 TACATGATAT

                           * * *                        *                    
        688 AAATCCCATTTTTAATCTCGAAACCTTCAAAAATTCTATTTTTATCCCCGAACTTCTAAAAATCC
          1 AAATCCCATTTTTAACCCCAAAACCTTCAAAAATTCTATTTTTACCCCCGAACTTCTAAAAATCC

                                            *   *                
        753 TATTTTTGACCTCGAAACCTTCAAAAATTTCATTTTTACCCCCGAACTTTCAA
         66 TATTTTTGACCTCGAAACCTTCAAAAATTTCAGTTTCACCCCCGAACTTTCAA

                 *                  *                                        
        806 AAATCTCATTTTTAACCCCAAAACTTTCAAAAATTCTATTTTTACCCCCGAACTTCTAAAAATCC
          1 AAATCCCATTTTTAACCCCAAAACCTTCAAAAATTCTATTTTTACCCCCGAACTTCTAAAAATCC

                            ***   *                       
        871 TATTTTTGACCTCGAATTTTTCCAAAATTATC-GTTTCACCCCCGA
         66 TATTTTTGACCTCGAAACCTTCAAAAATT-TCAGTTTCACCCCCGA

        916 GAATCCAAAA


Statistics
Matches: 97,  Mismatches: 12, Indels: 2
        0.87            0.11        0.02

Matches are distributed among these distances:
 118   95  0.98
 119    2  0.02

ACGTcount: A:0.32, C:0.27, G:0.04, T:0.36


Consensus pattern (118 bp):   
AAATCCCATTTTTAACCCCAAAACCTTCAAAAATTCTATTTTTACCCCCGAACTTCTAAAAATCC
TATTTTTGACCTCGAAACCTTCAAAAATTTCAGTTTCACCCCCGAACTTTCAA

Done.