Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013952.1 Kokia drynarioides strain JFW-HI SEQ_128982, 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: 7886
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32

Warning! 65 characters in sequence are not A, C, G, or T


Found at i:310 original size:43 final size:43

Alignment explanation


    Indices: 263--616  Score: 175
    Period size: 43  Copynumber: 8.3  Consensus size: 43

        253 ACTAAAGATT

                         *                         *   
        263 ATGTTTTTTAGCGACGTTTGTTGAAAAAGCGTCGTTAAAAACC
          1 ATGTTTTTTAGCGGCGTTTGTTGAAAAAGCGTCGTTAAAGACC

                  *    *       * *   *     ** *       * 
        306 ATG-TTCTTAGGGGCGTTTATGGTAGAAA-CACCATTAAAGATC
          1 ATGTTTTTTAGCGGCGTTTGTTG-AAAAAGCGTCGTTAAAGACC

                 *     * *               **    *        
        348 ATGTTCTTTAGTGACGTTTG-TGATAAAATTGTCGATAAAGACC
          1 ATGTTTTTTAGCGGCGTTTGTTGA-AAAAGCGTCGTTAAAGACC

                      *   *                  * *    *   
        391 ATGTTTTTTAACGGTGTTTG-TGAGAAAAGCGTAGCTAAAAACC
          1 ATGTTTTTTAGCGGCGTTTGTTGA-AAAAGCGTCGTTAAAGACC

                 *        *      *         * *       * 
        434 ATGTTCTTTAGCGGTGTTTGTGGAAAAAGCGCCATTAAAGATC
          1 ATGTTTTTTAGCGGCGTTTGTTGAAAAAGCGTCGTTAAAGACC

                      **       * **                *   
        477 ATG-TTTTTANNGGCGTTTATACAAAAAGCGTCGTTAAATACC
          1 ATGTTTTTTAGCGGCGTTTGTTGAAAAAGCGTCGTTAAAGACC

             **        **          **      *      *   *
        519 ACATTTTTTAGTTGCGTTT-TTGGGAAAGCGCCGTTAAGGACT
          1 ATGTTTTTTAGCGGCGTTTGTTGAAAAAGCGTCGTTAAAGACC

             *                 *    **     *  *        
        561 ACGTTTTTTAGCGGCG-TTATTG-GGAAGCGCCGCTAAAGACC
          1 ATGTTTTTTAGCGGCGTTTGTTGAAAAAGCGTCGTTAAAGACC

                   *       
        602 ATGTTTTATAGCGGC
          1 ATGTTTTTTAGCGGC

        617 ATTTTTTTTC


Statistics
Matches: 227,  Mismatches: 77, Indels: 16
        0.71            0.24        0.05

Matches are distributed among these distances:
  41   31  0.14
  42   90  0.40
  43  104  0.46
  44    2  0.01

ACGTcount: A:0.28, C:0.14, G:0.23, T:0.34


Consensus pattern (43 bp):   
ATGTTTTTTAGCGGCGTTTGTTGAAAAAGCGTCGTTAAAGACC

Found at i:526 original size:128 final size:128

Alignment explanation


    Indices: 278--528  Score: 276
    Period size: 128  Copynumber: 2.0  Consensus size: 128

        268 TTTTAGCGAC

                             * *                  *             *            
        278 GTTTGTTGAAAAAGCGTCGTTAAAAACCATGTTCTTAGGGGCGTTTATGGTAGAAACACCATTAA
          1 GTTTGTTGAAAAAGCGTAGCTAAAAACCATGTTCTTAGCGGCGTTTATGGTAAAAACACCATTAA

                                    *   *    **              **            
        343 AGATCATGTTCTTTAGTGACGTTTGTGATAAAATTGTCGATAAAGACCATGTTTTTTAACGGT
         66 AGATCATGTTCTTTAGTGACGTTTATGAAAAAAGCGTCGATAAAGACCACATTTTTTAACGGT

                                                       *    *           *    
        406 GTTTG-TGAGAAAAGCGTAGCTAAAAACCATGTTCTTTAGCGGTGTTTGTGG-AAAAAGCGCCAT
          1 GTTTGTTGA-AAAAGCGTAGCTAAAAACCATGTTC-TTAGCGGCGTTTATGGTAAAAA-CACCAT

                              ** *                     *    *             
        469 TAAAGATCATGTT-TTTANNGGCGTTTAT-ACAAAAAGCGTCGTTAAATACCACATTTTTTA
         63 TAAAGATCATGTTCTTTAGTGACGTTTATGA-AAAAAGCGTCGATAAAGACCACATTTTTTA

        529 GTTGCGTTTT


Statistics
Matches: 101,  Mismatches: 18, Indels: 8
        0.80            0.14        0.06

Matches are distributed among these distances:
 127    4  0.04
 128   66  0.65
 129   31  0.31

ACGTcount: A:0.31, C:0.13, G:0.21, T:0.34


Consensus pattern (128 bp):   
GTTTGTTGAAAAAGCGTAGCTAAAAACCATGTTCTTAGCGGCGTTTATGGTAAAAACACCATTAA
AGATCATGTTCTTTAGTGACGTTTATGAAAAAAGCGTCGATAAAGACCACATTTTTTAACGGT

Found at i:589 original size:41 final size:42

Alignment explanation


    Indices: 501--616  Score: 117
    Period size: 42  Copynumber: 2.8  Consensus size: 42

        491 GTTTATACAA

                  *  *    *     *        **     *     
        501 AAAGCGTCGTTAAATACCACATTTTTTAGTTGCGTTTTTGGG
          1 AAAGCGCCGCTAAAGACCACGTTTTTTAGCGGCGTTATTGGG

                     *   *   *                        
        543 AAAGCGCCGTTAAGGACTACGTTTTTTAGCGGCGTTATTGGG
          1 AAAGCGCCGCTAAAGACCACGTTTTTTAGCGGCGTTATTGGG

                               *     *       
        585 -AAGCGCCGCTAAAGACCATGTTTTATAGCGGC
          1 AAAGCGCCGCTAAAGACCACGTTTTTTAGCGGC

        617 ATTTTTTTTC


Statistics
Matches: 61,  Mismatches: 13, Indels: 1
        0.81            0.17        0.01

Matches are distributed among these distances:
  41   27  0.44
  42   34  0.56

ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32


Consensus pattern (42 bp):   
AAAGCGCCGCTAAAGACCACGTTTTTTAGCGGCGTTATTGGG
Done.