Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011841.1 Kokia drynarioides strain JFW-HI SEQ_126837, 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: 1901
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.30

Warning! 50 characters in sequence are not A, C, G, or T


Found at i:74 original size:29 final size:30

Alignment explanation


    Indices: 27--88  Score: 81
    Period size: 29  Copynumber: 2.1  Consensus size: 30

         17 ATCGGAGTTC

                     *                    
         27 AAAATGAGACTTTTCGGATTCCCGGGGGCA
          1 AAAATGAGAATTTTCGGATTCCCGGGGGCA

                   *             *      * 
         57 AAAATGATAATTTT-GGATTCTCGGGGGTA
          1 AAAATGAGAATTTTCGGATTCCCGGGGGCA

               
         86 AAA
          1 AAA

         89 CGGTAATTTT


Statistics
Matches: 28,  Mismatches: 4, Indels: 1
        0.85            0.12        0.03

Matches are distributed among these distances:
  29   16  0.57
  30   12  0.43

ACGTcount: A:0.32, C:0.13, G:0.27, T:0.27


Consensus pattern (30 bp):   
AAAATGAGAATTTTCGGATTCCCGGGGGCA

Found at i:95 original size:28 final size:29

Alignment explanation


    Indices: 37--100  Score: 76
    Period size: 28  Copynumber: 2.2  Consensus size: 29

         27 AAAATGAGAC

                                    *     
         37 TTTTCGGATTCCCGGGGGCAAAAATGATAA
          1 TTTT-GGATTCCCGGGGGCAAAAACGATAA

                      *       *      *   
         67 TTTTGGATTCTCGGGGG-TAAAACGGTAA
          1 TTTTGGATTCCCGGGGGCAAAAACGATAA

                  
         95 TTTTGG
          1 TTTTGG

        101 GAAAATTCGG


Statistics
Matches: 30,  Mismatches: 4, Indels: 2
        0.83            0.11        0.06

Matches are distributed among these distances:
  28   14  0.47
  29   12  0.40
  30    4  0.13

ACGTcount: A:0.25, C:0.12, G:0.30, T:0.33


Consensus pattern (29 bp):   
TTTTGGATTCCCGGGGGCAAAAACGATAA

Found at i:133 original size:29 final size:28

Alignment explanation


    Indices: 101--220  Score: 89
    Period size: 29  Copynumber: 4.1  Consensus size: 28

         91 GTAATTTTGG

                                * *      
        101 GAAAATTCGGGGTCAAAAATGGGATTTTT
          1 GAAAATTCGGGGT-AAAAATAGAATTTTT

                 *  *           * *      
        130 GAAAGTTTGGGGGT-AAAATGGGATTTTT
          1 GAAA-ATTCGGGGTAAAAATAGAATTTTT

                **   **                   
        158 GGAAGTTTCAAGGTCAAAAATAGAATTTTT
          1 -GAAAATTCGGGGT-AAAAATAGAATTTTT

             *                           
        188 GGAAATTCGGGGGTAAAAATAGAATTTTT
          1 GAAAATTC-GGGGTAAAAATAGAATTTTT

                
        217 GAAA
          1 GAAA

        221 GTTTTAGGTT


Statistics
Matches: 72,  Mismatches: 14, Indels: 10
        0.75            0.15        0.10

Matches are distributed among these distances:
  28   20  0.28
  29   30  0.42
  30   22  0.31

ACGTcount: A:0.37, C:0.04, G:0.28, T:0.32


Consensus pattern (28 bp):   
GAAAATTCGGGGTAAAAATAGAATTTTT

Found at i:155 original size:28 final size:29

Alignment explanation


    Indices: 109--275  Score: 117
    Period size: 30  Copynumber: 5.7  Consensus size: 29

         99 GGGAAAATTC

                        * *               
        109 GGGGTCAAAAATGGGATTTTTGAAAGTTTG
          1 GGGGT-AAAAATAGAATTTTTGAAAGTTTG

                       * *       *      *
        139 GGGGT-AAAATGGGATTTTTGGAAGTTTC
          1 GGGGTAAAAATAGAATTTTTGAAAGTTTG

            **                           * 
        167 AAGGTCAAAAATAGAATTTTTGGAAA-TTCG
          1 GGGGT-AAAAATAGAATTTTT-GAAAGTTTG

                                         *
        197 GGGGTAAAAATAGAATTTTTGAAAGTTTTA
          1 GGGGTAAAAATAGAATTTTTGAAAG-TTTG

              **                         * 
        227 GGTTTAAAAAT-GAGATTTTT-AGAAGTTCG
          1 GGGGTAAAAATAGA-ATTTTTGA-AAGTTTG

            *          *        
        256 AGGGTAAAAATGGAATTTTT
          1 GGGGTAAAAATAGAATTTTT

        276 AACAATTTAG


Statistics
Matches: 109,  Mismatches: 20, Indels: 17
        0.75            0.14        0.12

Matches are distributed among these distances:
  28   28  0.26
  29   34  0.31
  30   44  0.40
  31    3  0.03

ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35


Consensus pattern (29 bp):   
GGGGTAAAAATAGAATTTTTGAAAGTTTG

Found at i:236 original size:59 final size:57

Alignment explanation


    Indices: 111--275  Score: 172
    Period size: 59  Copynumber: 2.8  Consensus size: 57

        101 GAAAATTCGG

                        *             *              *       *         
        111 GGTCAAAAATGGGATTTTTGAAAGTTTGGGGGT-AAAATGGGATTTTTGGAAGTTTCAA
          1 GGTCAAAAAT-GAATTTTTGAAA-TTCGGGGGTAAAAATGGAATTTTTGAAAGTTTCAA

                                                   *                 * 
        169 GGTCAAAAATAGAATTTTTGGAAATTCGGGGGTAAAAATAGAATTTTTGAAAGTTT-TA
          1 GGTCAAAAAT-GAATTTTT-GAAATTCGGGGGTAAAAATGGAATTTTTGAAAGTTTCAA

                *                   *    *                   
        227 GGTTTAAAAATGAGATTTTTAGAAGTTCGAGGGTAAAAATGGAATTTTT
          1 GG-TCAAAAATGA-ATTTTT-GAAATTCGGGGGTAAAAATGGAATTTTT

        276 AACAATTTAG


Statistics
Matches: 91,  Mismatches: 12, Indels: 7
        0.83            0.11        0.06

Matches are distributed among these distances:
  58   30  0.33
  59   61  0.67

ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35


Consensus pattern (57 bp):   
GGTCAAAAATGAATTTTTGAAATTCGGGGGTAAAAATGGAATTTTTGAAAGTTTCAA

Done.