Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012017.1 Kokia drynarioides strain JFW-HI SEQ_127015, 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: 2917
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37


Found at i:71 original size:36 final size:36

Alignment explanation


    Indices: 16--84  Score: 93
    Period size: 36  Copynumber: 1.9  Consensus size: 36

          6 CACGCGCTAC

                      *   *                     
         16 ATTAAAATATGTTATGTGTAAAAATTTTATATACGT
          1 ATTAAAATATATTACGTGTAAAAATTTTATATACGT

                  *               *     *    
         52 ATTAAATTATATTACGTGTAAATATTTTTTATA
          1 ATTAAAATATATTACGTGTAAAAATTTTATATA

         85 TAAAAATATG


Statistics
Matches: 28,  Mismatches: 5, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  36   28  1.00

ACGTcount: A:0.41, C:0.03, G:0.09, T:0.48


Consensus pattern (36 bp):   
ATTAAAATATATTACGTGTAAAAATTTTATATACGT

Found at i:673 original size:29 final size:28

Alignment explanation


    Indices: 627--901  Score: 218
    Period size: 29  Copynumber: 9.5  Consensus size: 28

        617 AATCTGTCCA

                       *                
        627 AAAAATT-CATATTTACCCCGAACTTCC
          1 AAAAATTCCATTTTTACCCCGAACTTCC

                                *        *
        654 AAAAATTCCATTTTTGACCCTGAAACTTCT
          1 AAAAATTCCATTTTT-ACCCCG-AACTTCC

                                     *   
        684 AAAAATTCCATTTTTACCCTCGAACCTCC
          1 AAAAATTCCATTTTTACCC-CGAACTTCC

                               *         
        713 AAAAATTCCATTTTTAACCTC-AACTTCC
          1 AAAAATTCCATTTTT-ACCCCGAACTTCC

                                  *  *    
        741 AAAAATTCCATTTTTAACCCCAAAATTTCC
          1 AAAAATTCCATTTTT-ACCCC-GAACTTCC

                *                *       
        771 AAAATTTCCATTTTTACCCTCAAACTTCC
          1 AAAAATTCCATTTTTACCC-CGAACTTCC

                   *      *   **         *
        800 AAAAATTTCATTTTGACCTTGAAACTTCAA
          1 AAAAATTCCATTTTTACCCCG-AACTTC-C

                                 *         
        830 AAAAATT-CATTTTTACCCTCAAAGC-TCTC
          1 AAAAATTCCATTTTTACCC-CGAA-CTTC-C

                            *    *  *     
        859 AAAAATTACCA-TTTTGCCCCCAAATATCC
          1 AAAAATT-CCATTTTTACCCCGAACT-TCC

                 *        
        888 AAAAACTCCATTTT
          1 AAAAATTCCATTTT

        902 CGACCTCGAA


Statistics
Matches: 202,  Mismatches: 29, Indels: 32
        0.77            0.11        0.12

Matches are distributed among these distances:
  27    7  0.03
  28   35  0.17
  29   95  0.47
  30   63  0.31
  31    2  0.01

ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34


Consensus pattern (28 bp):   
AAAAATTCCATTTTTACCCCGAACTTCC

Found at i:780 original size:87 final size:87

Alignment explanation


    Indices: 647--901  Score: 259
    Period size: 87  Copynumber: 2.9  Consensus size: 87

        637 ATTTACCCCG

                                  *    **       *                     *      
        647 AACTTCCAAAAATTCCATTTTTGACCCTGAAACTTCTAAAAATTCCATTTTTACCCTCGAACCTC
          1 AACTTCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCTCAAACCTC

                                  
        712 CAAAAATTCCATTTTTAACCTC
         66 CAAAAATTCCATTTTTAACCTC

                                            *        *                    *  
        734 AACTTCCAAAAATTCCATTTTTAACCCCAAAATTTCCAAAATTTCCATTTTTACCCTCAAACTTC
          1 AACTTCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCTCAAACCTC

                    *       *      *
        799 CAAAAATTTCA-TTTTGACCTTGA
         66 CAAAAATTCCATTTTTAACC-T-C

                   *                         *                      *   *    
        822 AACTTCAAAAAAATT-CATTTTT-ACCCTCAAAGC-TCTCAAAAATTACCA-TTTTGCCCCCAAA
          1 AACTTC-CAAAAATTCCATTTTTAACCC-CAAAACTTC-CAAAAATT-CCATTTTTACCCTCAAA

            **        *        
        883 TATCCAAAAACTCCATTTT
         62 CCTCCAAAAATTCCATTTT

        902 CGACCTCGAA


Statistics
Matches: 140,  Mismatches: 21, Indels: 12
        0.81            0.12        0.07

Matches are distributed among these distances:
  86    7  0.05
  87   74  0.53
  88   46  0.33
  89   13  0.09

ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34


Consensus pattern (87 bp):   
AACTTCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCTCAAACCTC
CAAAAATTCCATTTTTAACCTC
Done.