Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011714.1 Kokia drynarioides strain JFW-HI SEQ_126708, 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: 10794
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:8755 original size:36 final size:36

Alignment explanation


    Indices: 8701--8935  Score: 208
    Period size: 36  Copynumber: 6.6  Consensus size: 36

       8691 TCGATGGAAA

                                                
       8701 GCTTACGTCTCGATTAGAGCGTAATGCTATGTGAAT
          1 GCTTACGTCTCGATTAGAGCGTAATGCTATGTGAAT

              *   *     *          *             
       8737 GCATACTTCTCGGTTAGAGCGTATTGCTATGT-AATT
          1 GCTTACGTCTCGATTAGAGCGTAATGCTATGTGAA-T

            *                   *        * *  * 
       8773 TCTTACGTCTCGATTAGAGCATAATGCTAAGAGATT
          1 GCTTACGTCTCGATTAGAGCGTAATGCTATGTGAAT

                                      *  *    * 
       8809 GCTTAC-TCTCGATTAGAGCGTAATGATACGTGATT
          1 GCTTACGTCTCGATTAGAGCGTAATGCTATGTGAAT

              *   *             *  *             
       8844 GCATACATCTCGATTAGAGCTTATTGCTATGT-AATT
          1 GCTTACGTCTCGATTAGAGCGTAATGCTATGTGAA-T

            *           *      *               * 
       8880 ACTTACGTCTCGGTTAGAGGGTAATGCTAAT-TGACT
          1 GCTTACGTCTCGATTAGAGCGTAATGCT-ATGTGAAT

            *    *      *       
       8916 ACTTATGTCTCGGTTAGAGC
          1 GCTTACGTCTCGATTAGAGC

       8936 ATAAGCCCAT


Statistics
Matches: 159,  Mismatches: 34, Indels: 12
        0.78            0.17        0.06

Matches are distributed among these distances:
  35   33  0.21
  36  122  0.77
  37    4  0.03

ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35


Consensus pattern (36 bp):   
GCTTACGTCTCGATTAGAGCGTAATGCTATGTGAAT

Found at i:8860 original size:71 final size:72

Alignment explanation


    Indices: 8708--8905  Score: 211
    Period size: 71  Copynumber: 2.8  Consensus size: 72

       8698 AAAGCTTACG

                         *          *  *   *   *                *  *  *      
       8708 TCTCGATTAGAGCGTAATGCTATGTGAATGCATACTTCTCGGTTAGAGCGTATTGCTATGTAATT
          1 TCTCGATTAGAGCATAATGCTATGAGATTGCTTACGTCTCGGTTAGAGCGTAATGATACGTAATT

            * *   *
       8773 TCTTACG
         66 GCATACA

                                  *                  *                   *   
       8780 TCTCGATTAGAGCATAATGCTAAGAGATTGCTTAC-TCTCGATTAGAGCGTAATGATACGTGATT
          1 TCTCGATTAGAGCATAATGCTATGAGATTGCTTACGTCTCGGTTAGAGCGTAATGATACGTAATT

                   
       8844 GCATACA
         66 GCATACA

                         *  *             *                  *      
       8851 TCTCGATTAGAGCTTATTGCTATGTA-ATTACTTACGTCTCGGTTAGAGGGTAATG
          1 TCTCGATTAGAGCATAATGCTATG-AGATTGCTTACGTCTCGGTTAGAGCGTAATG

       8906 CTAATTGACT


Statistics
Matches: 105,  Mismatches: 19, Indels: 4
        0.82            0.15        0.03

Matches are distributed among these distances:
  71   57  0.54
  72   48  0.46

ACGTcount: A:0.26, C:0.16, G:0.22, T:0.35


Consensus pattern (72 bp):   
TCTCGATTAGAGCATAATGCTATGAGATTGCTTACGTCTCGGTTAGAGCGTAATGATACGTAATT
GCATACA

Found at i:8897 original size:107 final size:108

Alignment explanation


    Indices: 8701--8909  Score: 321
    Period size: 107  Copynumber: 1.9  Consensus size: 108

       8691 TCGATGGAAA

                                      *  *            *     *                
       8701 GCTTACGTCTCGATTAGAGCGTAATGCTATGTGAATGCATACTTCTCGGTTAGAGCGTATTGCTA
          1 GCTTACGTCTCGATTAGAGCGTAATGATACGTGAATGCATACATCTCGATTAGAGCGTATTGCTA

                   *                                   
       8766 TGTAATTTCTTACGTCTCGATTAGAGCATAATGCTAAGAGATT
         66 TGTAATTACTTACGTCTCGATTAGAGCATAATGCTAAGAGATT

                                              *                     *        
       8809 GCTTAC-TCTCGATTAGAGCGTAATGATACGTGATTGCATACATCTCGATTAGAGCTTATTGCTA
          1 GCTTACGTCTCGATTAGAGCGTAATGATACGTGAATGCATACATCTCGATTAGAGCGTATTGCTA

                               *      **         
       8873 TGTAATTACTTACGTCTCGGTTAGAGGGTAATGCTAA
         66 TGTAATTACTTACGTCTCGATTAGAGCATAATGCTAA

       8910 TTGACTACTT


Statistics
Matches: 91,  Mismatches: 10, Indels: 1
        0.89            0.10        0.01

Matches are distributed among these distances:
 107   85  0.93
 108    6  0.07

ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35


Consensus pattern (108 bp):   
GCTTACGTCTCGATTAGAGCGTAATGATACGTGAATGCATACATCTCGATTAGAGCGTATTGCTA
TGTAATTACTTACGTCTCGATTAGAGCATAATGCTAAGAGATT
Done.