Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012543.1 Kokia drynarioides strain JFW-HI SEQ_127552, 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: 15554
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33


Found at i:2752 original size:10 final size:10

Alignment explanation


    Indices: 2737--2771  Score: 52
    Period size: 10  Copynumber: 3.5  Consensus size: 10

       2727 ATTGTGGGTG

                   *  
       2737 AATTACCCAA
          1 AATTACCAAA

                      
       2747 AATTACCAAA
          1 AATTACCAAA

                  *   
       2757 AATTACGAAA
          1 AATTACCAAA

                 
       2767 AATTA
          1 AATTA

       2772 TTAGATTGGG


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  10   23  1.00

ACGTcount: A:0.57, C:0.17, G:0.03, T:0.23


Consensus pattern (10 bp):   
AATTACCAAA

Found at i:5389 original size:43 final size:42

Alignment explanation


    Indices: 5337--5426  Score: 146
    Period size: 43  Copynumber: 2.1  Consensus size: 42

       5327 ACTTAAAATA

                                  *                    
       5337 AATAAATTTAGTCAAAATAAAATTAAGAAAATAACAAAC-TTG
          1 AATAAATTTAGTCAAAATAAAAATAAGAAAATAAC-AACTTTG

                                                       
       5379 AATATAATTTAGTCAAAATAAAAATAAGAAAATAACAACTTTG
          1 AATA-AATTTAGTCAAAATAAAAATAAGAAAATAACAACTTTG

                 
       5422 AATAA
          1 AATAA

       5427 GCTTATTTGA


Statistics
Matches: 45,  Mismatches: 1, Indels: 4
        0.90            0.02        0.08

Matches are distributed among these distances:
  42    8  0.18
  43   37  0.82

ACGTcount: A:0.60, C:0.07, G:0.07, T:0.27


Consensus pattern (42 bp):   
AATAAATTTAGTCAAAATAAAAATAAGAAAATAACAACTTTG

Found at i:5574 original size:19 final size:19

Alignment explanation


    Indices: 5550--5587  Score: 76
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       5540 TGCTTTTAGG

                               
       5550 TAAAGAAGCAGCAATTTGT
          1 TAAAGAAGCAGCAATTTGT

                               
       5569 TAAAGAAGCAGCAATTTGT
          1 TAAAGAAGCAGCAATTTGT

       5588 GTACCTGATA


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   19  1.00

ACGTcount: A:0.42, C:0.11, G:0.21, T:0.26


Consensus pattern (19 bp):   
TAAAGAAGCAGCAATTTGT

Found at i:7503 original size:18 final size:18

Alignment explanation


    Indices: 7477--7514  Score: 67
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       7467 AGAGTAAGAG

                              
       7477 TTAGAGAATTTCATGATT
          1 TTAGAGAATTTCATGATT

                *             
       7495 TTAGGGAATTTCATGATT
          1 TTAGAGAATTTCATGATT

              
       7513 TT
          1 TT

       7515 GCTAATCAAA


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  18   19  1.00

ACGTcount: A:0.29, C:0.05, G:0.18, T:0.47


Consensus pattern (18 bp):   
TTAGAGAATTTCATGATT

Found at i:12409 original size:27 final size:27

Alignment explanation


    Indices: 12379--12454  Score: 89
    Period size: 27  Copynumber: 2.8  Consensus size: 27

      12369 GACATCAATA

                  *                    
      12379 AATAGCTTTTGTGGCAAATTCTGAATG
          1 AATAGCCTTTGTGGCAAATTCTGAATG

                *   *      *  *        
      12406 AATAACCTCTGTGGCGAACTCTGAATG
          1 AATAGCCTTTGTGGCAAATTCTGAATG

                      *   *       
      12433 AATAGCCTTTATGGTAAATTCT
          1 AATAGCCTTTGTGGCAAATTCT

      12455 AAATAAACAA


Statistics
Matches: 38,  Mismatches: 11, Indels: 0
        0.78            0.22        0.00

Matches are distributed among these distances:
  27   38  1.00

ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34


Consensus pattern (27 bp):   
AATAGCCTTTGTGGCAAATTCTGAATG

Found at i:15171 original size:144 final size:145

Alignment explanation


    Indices: 14989--15320  Score: 569
    Period size: 144  Copynumber: 2.3  Consensus size: 145

      14979 AAAGCTTGCC

                        *                    *                               
      14989 AATTTCTTGGGGGATAGGACCTTTTAATAGATTTGAACCAAGGTC-TAAGGACCGCATCTTTGAT
          1 AATTTCTTGGGGAATAGGACCTTTTAATAGATTAGAACCAAGGTCTTAAGGACCGCATCTTTGAT

                    * *     *         *                                      
      15053 AAACTACCTATACAAGCAGGGATTGAGCCACTCAATTTGTTTTGGGAGAGGTACAATGAAGTTAA
         66 AAACTACCAACACAAGAAGGGATTGAACCACTCAATTTGTTTTGGGAGAGGTACAATGAAGTTAA

                           
      15118 ATTTTCTAGGTTACA
        131 ATTTTCTAGGTTACA

                                                              *  *           
      15133 AATTTCTTGGGGAATAGGACCTTTTAATAGATTAGAACCAAGG-CTTAAGTACTGCATCTTTGAT
          1 AATTTCTTGGGGAATAGGACCTTTTAATAGATTAGAACCAAGGTCTTAAGGACCGCATCTTTGAT

              *                                                              
      15197 AAGCTACCAACACAAGAAGGGATTGAACCACTCAATTTGTTTTGGGAGAGGTACAATGAAGTTAA
         66 AAACTACCAACACAAGAAGGGATTGAACCACTCAATTTGTTTTGGGAGAGGTACAATGAAGTTAA

                           
      15262 ATTTTCTAGGTTACA
        131 ATTTTCTAGGTTACA

                                                        
      15277 AATTTCTTGGGGAATAGGACCTTTTAATAGATTAGAACCAAGGT
          1 AATTTCTTGGGGAATAGGACCTTTTAATAGATTAGAACCAAGGT

      15321 ATAAAATATT


Statistics
Matches: 177,  Mismatches: 9, Indels: 3
        0.94            0.05        0.02

Matches are distributed among these distances:
 143    1  0.01
 144  176  0.99

ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31


Consensus pattern (145 bp):   
AATTTCTTGGGGAATAGGACCTTTTAATAGATTAGAACCAAGGTCTTAAGGACCGCATCTTTGAT
AAACTACCAACACAAGAAGGGATTGAACCACTCAATTTGTTTTGGGAGAGGTACAATGAAGTTAA
ATTTTCTAGGTTACA

Done.