Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003325.1 Kokia drynarioides strain JFW-HI SEQ_116023, 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: 12508
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.35

Warning! 62 characters in sequence are not A, C, G, or T


Found at i:2494 original size:49 final size:49

Alignment explanation


    Indices: 2439--2780  Score: 299
    Period size: 49  Copynumber: 7.0  Consensus size: 49

       2429 TGAATTTTTT

                                       *                  *  
       2439 CCTTCATGTCTCTGTGGTACAAGGTTCTCCATTGCGACTTAAATCTATC
          1 CCTTCATGTCTCTGTGGTACAAGGTTCGCCATTGCGACTTAAATCTTTC

                                                       *    *
       2488 CCTTCATGTCTCTGTGGTACAAGGTTCGCCATTGCGACTTAAACCTTTT
          1 CCTTCATGTCTCTGTGGTACAAGGTTCGCCATTGCGACTTAAATCTTTC

                     *             *       ***     *            
       2537 CCTT--TGTATCTTCGTGGTAC-TGGATTCGTTGTTGCGGCTTAAATCTTTC
          1 CCTTCATGTCTC-T-GTGGTACAAGG-TTCGCCATTGCGACTTAAATCTTTC

                   *      *               *            *     
       2586 CCTTCATATCTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTC
          1 CCTTCATGTCTCTGTGGTACAAGGTTCGCCATTGCGACTTAAATCTTTC

                     *             *        *   * *            
       2635 CCTTTGCATCT-TC-GTGGTAC-TGGTTCGCCGTTGTGGCTTAAATCTTTC
          1 CC-TT-CATGTCTCTGTGGTACAAGGTTCGCCATTGCGACTTAAATCTTTC

             *         *  *                                   
       2683 CTTTCATGTCTTTGAGGTACAAGGTTCGCCATTGCGACTTAAA-CTTTTC
          1 CCTTCATGTCTCTGTGGTACAAGGTTCGCCATTGCGACTTAAATC-TTTC

                     *             *      *  *                  
       2732 CCTTTGCATCT-TC-GTGGTAC-TGGATTCACCGTTGCGACTTAAATCTTTC
          1 CC-TT-CATGTCTCTGTGGTACAAGG-TTCGCCATTGCGACTTAAATCTTTC

       2781 ATTTCGTGTC


Statistics
Matches: 236,  Mismatches: 41, Indels: 32
        0.76            0.13        0.10

Matches are distributed among these distances:
  46    4  0.02
  47    8  0.03
  48   37  0.16
  49  164  0.69
  50   11  0.05
  51   12  0.05

ACGTcount: A:0.17, C:0.25, G:0.19, T:0.39


Consensus pattern (49 bp):   
CCTTCATGTCTCTGTGGTACAAGGTTCGCCATTGCGACTTAAATCTTTC

Found at i:2588 original size:98 final size:98

Alignment explanation


    Indices: 2470--2780  Score: 473
    Period size: 98  Copynumber: 3.2  Consensus size: 98

       2460 AGGTTCTCCA

                           *                *                                
       2470 TTGCGACTTAAATCTATCCCTTCATGTCTCTGTGGTACAAGGTTCGCCATTGCGACTTAAACCTT
          1 TTGCGACTTAAATCTTTCCCTTCATGTCTCTGAGGTACAAGGTTCGCCATTGCGACTTAAACCTT

                    *                     ** 
       2535 TTCCTTTGTATCTTCGTGGTACTGGATTCGTTG
         66 TTCCTTTGCATCTTCGTGGTACTGGATTCGCCG

                 *                   *                      *                
       2568 TTGCGGCTTAAATCTTTCCCTTCATATCTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTT
          1 TTGCGACTTAAATCTTTCCCTTCATGTCTCTGAGGTACAAGGTTCGCCATTGCGACTTAAACCTT

             *                               
       2633 TCCCTTTGCATCTTCGTGGTACTGG-TTCGCCG
         66 TTCCTTTGCATCTTCGTGGTACTGGATTCGCCG

               * *             *         *                                   
       2665 TTGTGGCTTAAATCTTTCCTTTCATGTCTTTGAGGTACAAGGTTCGCCATTGCGACTTAAA-CTT
          1 TTGCGACTTAAATCTTTCCCTTCATGTCTCTGAGGTACAAGGTTCGCCATTGCGACTTAAACCTT

                                          *   
       2729 TTCCCTTTGCATCTTCGTGGTACTGGATTCACCG
         66 TT-CCTTTGCATCTTCGTGGTACTGGATTCGCCG

                              
       2763 TTGCGACTTAAATCTTTC
          1 TTGCGACTTAAATCTTTC

       2781 ATTTCGTGTC


Statistics
Matches: 193,  Mismatches: 18, Indels: 4
        0.90            0.08        0.02

Matches are distributed among these distances:
  96    4  0.02
  97   84  0.44
  98  105  0.54

ACGTcount: A:0.17, C:0.25, G:0.19, T:0.39


Consensus pattern (98 bp):   
TTGCGACTTAAATCTTTCCCTTCATGTCTCTGAGGTACAAGGTTCGCCATTGCGACTTAAACCTT
TTCCTTTGCATCTTCGTGGTACTGGATTCGCCG

Found at i:8154 original size:4 final size:4

Alignment explanation


    Indices: 8147--8183  Score: 65
    Period size: 4  Copynumber: 9.2  Consensus size: 4

       8137 AGATTATATA

                              *                           
       8147 TATG TATG TATG TATT TATG TATG TATG TATG TATG T
          1 TATG TATG TATG TATG TATG TATG TATG TATG TATG T

       8184 GAATGATTGG


Statistics
Matches: 31,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   4   31  1.00

ACGTcount: A:0.24, C:0.00, G:0.22, T:0.54


Consensus pattern (4 bp):   
TATG

Done.