Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013362.1 Kokia drynarioides strain JFW-HI SEQ_128385, 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: 17660
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:814 original size:129 final size:131

Alignment explanation


    Indices: 561--843  Score: 408
    Period size: 129  Copynumber: 2.2  Consensus size: 131

        551 AAAAATTCAG

                 *    *      *              *                       *        
        561 GTTCTATAGCAGCGTTTTTGCGAGAAAAGCGCTGCTAAAGAAAATGCTCTTTAGCGGCGTTTGTA
          1 GTTCTTTAGCGGCGTTTGTGCGAGAAAAGCGCCGCTAAAGAAAATGCTCTTTAGCGACGTTTGTA

                                             *                   *      *    
        626 TGAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTTTGGGAAAAGCGCTGCTAAAGACCA
         66 TGAAAAACGCCGCTAAAGATCATGTTCTTTAGCAGCGTTTTTGGGAAAAGCGCCGCTAAAAACCA

             
        691 T
        131 T

                                                     **   *                 *
        692 GTTCTTTAGCGGCGTTTGTG-G-GAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGACGTTTGTG
          1 GTTCTTTAGCGGCGTTTGTGCGAGAAAAGCGCCGCTAAAGAAAATGCTCTTTAGCGACGTTTGTA

             *    *     *                                                    
        755 TTAAAAGCGCCGTTAAAGATCATGTTCTTTAGCAGCGTTTTTGGGAAAAGCGCCGCTAAAAACCA
         66 TGAAAAACGCCGCTAAAGATCATGTTCTTTAGCAGCGTTTTTGGGAAAAGCGCCGCTAAAAACCA

             
        820 T
        131 T

                             *     
        821 GTTCTTTAGCGGCGTTTTTGCGA
          1 GTTCTTTAGCGGCGTTTGTGCGA

        844 CTTTTAACGG


Statistics
Matches: 134,  Mismatches: 16, Indels: 4
        0.87            0.10        0.03

Matches are distributed among these distances:
 129  115  0.86
 130    2  0.01
 131   17  0.13

ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30


Consensus pattern (131 bp):   
GTTCTTTAGCGGCGTTTGTGCGAGAAAAGCGCCGCTAAAGAAAATGCTCTTTAGCGACGTTTGTA
TGAAAAACGCCGCTAAAGATCATGTTCTTTAGCAGCGTTTTTGGGAAAAGCGCCGCTAAAAACCA
T

Found at i:838 original size:43 final size:43

Alignment explanation


    Indices: 561--840  Score: 353
    Period size: 43  Copynumber: 6.5  Consensus size: 43

        551 AAAAATTCAG

                 *    *                     *        **  
        561 GTTCTATAGCAGCGTTTTTGCGAGAAAAGCGCTGCTAAAGAAAAT
          1 GTTCTTTAGCGGCGTTTTTG-G-GAAAAGCGCCGCTAAAGACCAT

             *               * **     *            *   
        606 GCTCTTTAGCGGCGTTTGTATGAAAAACGCCGCTAAAGATCAT
          1 GTTCTTTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGACCAT

                                          *            
        649 GTTCTTTAGCGGCGTTTTTGGGAAAAGCGCTGCTAAAGACCAT
          1 GTTCTTTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGACCAT

                             *                         
        692 GTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCAT
          1 GTTCTTTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGACCAT

                       *     *  **          *      *   
        735 GTTCTTTAGCGACGTTTGTGTTAAAAGCGCCGTTAAAGATCAT
          1 GTTCTTTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGACCAT

                      *                          *     
        778 GTTCTTTAGCAGCGTTTTTGGGAAAAGCGCCGCTAAAAACCAT
          1 GTTCTTTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGACCAT

                                
        821 GTTCTTTAGCGGCGTTTTTG
          1 GTTCTTTAGCGGCGTTTTTG

        841 CGACTTTTAA


Statistics
Matches: 202,  Mismatches: 33, Indels: 2
        0.85            0.14        0.01

Matches are distributed among these distances:
  43  187  0.93
  45   15  0.07

ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30


Consensus pattern (43 bp):   
GTTCTTTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGACCAT

Found at i:1907 original size:11 final size:11

Alignment explanation


    Indices: 1893--1922  Score: 51
    Period size: 11  Copynumber: 2.7  Consensus size: 11

       1883 TTCTTCTTTC

                       
       1893 TTTTTCTTTGT
          1 TTTTTCTTTGT

                     * 
       1904 TTTTTCTTTTT
          1 TTTTTCTTTGT

                    
       1915 TTTTTCTT
          1 TTTTTCTT

       1923 AACTTTAGTC


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  11   18  1.00

ACGTcount: A:0.00, C:0.10, G:0.03, T:0.87


Consensus pattern (11 bp):   
TTTTTCTTTGT

Found at i:4535 original size:14 final size:14

Alignment explanation


    Indices: 4516--4545  Score: 60
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       4506 TTTCCTGAAA

                          
       4516 ATAATAAAATTTTG
          1 ATAATAAAATTTTG

                          
       4530 ATAATAAAATTTTG
          1 ATAATAAAATTTTG

              
       4544 AT
          1 AT

       4546 TTATTTCTAA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   16  1.00

ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43


Consensus pattern (14 bp):   
ATAATAAAATTTTG

Found at i:17413 original size:26 final size:26

Alignment explanation


    Indices: 17377--17431  Score: 110
    Period size: 26  Copynumber: 2.1  Consensus size: 26

      17367 TGCTGATTTT

                                      
      17377 TTTATGTTCAATCAAAAATCAAAGAA
          1 TTTATGTTCAATCAAAAATCAAAGAA

                                      
      17403 TTTATGTTCAATCAAAAATCAAAGAA
          1 TTTATGTTCAATCAAAAATCAAAGAA

               
      17429 TTT
          1 TTT

      17432 GCCATTTTTT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   29  1.00

ACGTcount: A:0.47, C:0.11, G:0.07, T:0.35


Consensus pattern (26 bp):   
TTTATGTTCAATCAAAAATCAAAGAA
Done.