Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003402.1 Kokia drynarioides strain JFW-HI SEQ_116146, 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: 10259
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.34


Found at i:796 original size:30 final size:28

Alignment explanation


    Indices: 753--812  Score: 66
    Period size: 28  Copynumber: 2.1  Consensus size: 28

        743 GTTTTTTTTA

                  *                       
        753 TAATTTTAACCCAAATGTTTTCATTTTATT
          1 TAATTTGAACCC-AAT-TTTTCATTTTATT

                    *          *     *  
        783 TAATTTGACCCCAATTTTTTATTTTTTT
          1 TAATTTGAACCCAATTTTTCATTTTATT

              
        811 TA
          1 TA

        813 TGTTCATATT


Statistics
Matches: 26,  Mismatches: 4, Indels: 2
        0.81            0.12        0.06

Matches are distributed among these distances:
  28   13  0.50
  29    3  0.12
  30   10  0.38

ACGTcount: A:0.27, C:0.13, G:0.03, T:0.57


Consensus pattern (28 bp):   
TAATTTGAACCCAATTTTTCATTTTATT

Found at i:2565 original size:19 final size:19

Alignment explanation


    Indices: 2537--2580  Score: 79
    Period size: 19  Copynumber: 2.3  Consensus size: 19

       2527 ACAACGTGAT

                 *             
       2537 AAGGTTGATAGCCTAGCTG
          1 AAGGTCGATAGCCTAGCTG

                               
       2556 AAGGTCGATAGCCTAGCTG
          1 AAGGTCGATAGCCTAGCTG

                  
       2575 AAGGTC
          1 AAGGTC

       2581 ATGTATCGGA


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  19   24  1.00

ACGTcount: A:0.27, C:0.18, G:0.32, T:0.23


Consensus pattern (19 bp):   
AAGGTCGATAGCCTAGCTG

Found at i:4608 original size:18 final size:18

Alignment explanation


    Indices: 4587--4643  Score: 78
    Period size: 18  Copynumber: 3.2  Consensus size: 18

       4577 GAAGCGGAAA

                            * 
       4587 TTTGAGCATACTGGCTTG
          1 TTTGAGCATACTGGCTCG

                   *  *       
       4605 TTTGAGCTTATTGGCTCG
          1 TTTGAGCATACTGGCTCG

              *               
       4623 TTAGAGCATACTGGCTCG
          1 TTTGAGCATACTGGCTCG

               
       4641 TTT
          1 TTT

       4644 ATGCGTATTA


Statistics
Matches: 32,  Mismatches: 7, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  18   32  1.00

ACGTcount: A:0.16, C:0.18, G:0.26, T:0.40


Consensus pattern (18 bp):   
TTTGAGCATACTGGCTCG

Found at i:4659 original size:36 final size:36

Alignment explanation


    Indices: 4590--4673  Score: 89
    Period size: 36  Copynumber: 2.3  Consensus size: 36

       4580 GCGGAAATTT

                         *        *    **     * 
       4590 GAGCATACTGGCTTGTTTGAGCTTATTGGCTCGTTA
          1 GAGCATACTGGCTCGTTTGAGCGTATTAACTCGTAA

                                                 
       4626 GAGCATACTGGCTCGTTT-ATGCGTATTAACTCGTAA
          1 GAGCATACTGGCTCGTTTGA-GCGTATTAACTCGTAA

              *         
       4662 GAACATTACTGG
          1 GAGCA-TACTGG

       4674 ATCGCAAGAG


Statistics
Matches: 40,  Mismatches: 6, Indels: 3
        0.82            0.12        0.06

Matches are distributed among these distances:
  35    1  0.03
  36   33  0.82
  37    6  0.15

ACGTcount: A:0.23, C:0.18, G:0.25, T:0.35


Consensus pattern (36 bp):   
GAGCATACTGGCTCGTTTGAGCGTATTAACTCGTAA
Done.