Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012157.1 Kokia drynarioides strain JFW-HI SEQ_127158, 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: 11277
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.32


Found at i:139 original size:41 final size:41

Alignment explanation


    Indices: 1--182  Score: 181
    Period size: 41  Copynumber: 4.4  Consensus size: 41

                             * *         *       *   
          1 AAAGGTCAG-GCATTAGTGGCGTTTATGAGAAAGCACTGCT
          1 AAAGGTCAGAGCATTAGCGACGTTTATGAAAAAGCACCGCT

                    *  * *        *              *  *  
         41 AAAGGTCAAAGTAATAGCGACGCTTATGGGAAAAA-CGCCACT
          1 AAAGGTCAGAGCATTAGCGACGTTTAT--GAAAAAGCACCGCT

                      *                              
         83 AAAGGTCAGAACATTAGCGACGTTTATGAAAAAGCACCGCT
          1 AAAGGTCAGAGCATTAGCGACGTTTATGAAAAAGCACCGCT

                                 *                *   
        124 AAAGGTCAGAGCATTAGC-AGTGTTTATGAAAAAGCACTGCT
          1 AAAGGTCAGAGCATTAGCGA-CGTTTATGAAAAAGCACCGCT

               * *            
        165 AAAAGCCAGAGCATTAGC
          1 AAAGGTCAGAGCATTAGC

        183 AGCGCTTTCT


Statistics
Matches: 115,  Mismatches: 22, Indels: 9
        0.79            0.15        0.06

Matches are distributed among these distances:
  40   15  0.13
  41   69  0.60
  42   26  0.23
  43    5  0.04

ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20


Consensus pattern (41 bp):   
AAAGGTCAGAGCATTAGCGACGTTTATGAAAAAGCACCGCT

Found at i:207 original size:41 final size:39

Alignment explanation


    Indices: 71--208  Score: 98
    Period size: 41  Copynumber: 3.4  Consensus size: 39

         61 CGCTTATGGG

                     *     * *    *                 *
         71 AAAAACGCCACTAAAGGTCAGAACATTAGC-GACGTTTATG
          1 AAAAA-GCCGCTAAAAGCCAGAGCATTAGCAG-CGTTTATC

                            * *              *      *
        111 AAAAAGCACCGCTAAAGGTCAGAGCATTAGCAGTGTTTATG
          1 AAAAAG--CCGCTAAAAGCCAGAGCATTAGCAGCGTTTATC

                                                   *  
        152 AAAAAGCACTGCTAAAAGCCAGAGCATTAGCAGCGCTTTCTC
          1 AAAAAGC-C-GCTAAAAGCCAGAGCATTAGCAGCG-TTTATC

                 *         
        194 ATAAATGCCGCTAAA
          1 A-AAAAGCCGCTAAA

        209 GGTTAAGACG


Statistics
Matches: 82,  Mismatches: 9, Indels: 13
        0.79            0.09        0.12

Matches are distributed among these distances:
  39    2  0.02
  40    6  0.07
  41   62  0.76
  42    7  0.09
  43    5  0.06

ACGTcount: A:0.38, C:0.21, G:0.20, T:0.20


Consensus pattern (39 bp):   
AAAAAGCCGCTAAAAGCCAGAGCATTAGCAGCGTTTATC

Found at i:4364 original size:30 final size:30

Alignment explanation


    Indices: 4330--4575  Score: 182
    Period size: 30  Copynumber: 8.2  Consensus size: 30

       4320 AATTATTTTA

                  *         *             
       4330 TGACCCCCAAACTTTTTAAAAATTTAAATT
          1 TGACCCTCAAACTTTTCAAAAATTTAAATT

                 *    *              *    
       4360 TGACCTTCAACCTTTTCAAAAATTTGAATT
          1 TGACCCTCAAACTTTTCAAAAATTTAAATT

             *                  *      *    
       4390 TAACCC-CTAAAC-TTTCTAGAAATTTGAATT
          1 TGACCCTC-AAACTTTTC-AAAAATTTAAATT

             *     *                *     
       4420 TAACCCTTAAACTTTTCAAAAATTCAAATT
          1 TGACCCTCAAACTTTTCAAAAATTTAAATT

             *                     *       *
       4450 TAACCC-CTAAAC-TTTCAAAAAATTAATATA
          1 TGACCCTC-AAACTTTTCAAAAATTTAA-ATT

                                      **   
       4480 TGACCCTCAAA-TTTTCCAAAAATTTTGATT
          1 TGACCCTCAAACTTTT-CAAAAATTTAAATT

                    *                  *    
       4510 TGACCCTCGAA-TTTTCTAAAAATTCTGAA-T
          1 TGACCCTCAAACTTTTC-AAAAATT-TAAATT

                   **  *   *              
       4540 TGACCCTTGAAGTTTCCAAAAATTTAAATT
          1 TGACCCTCAAACTTTTCAAAAATTTAAATT

                  
       4570 TGACCC
          1 TGACCC

       4576 GGTTTTAATG


Statistics
Matches: 175,  Mismatches: 28, Indels: 26
        0.76            0.12        0.11

Matches are distributed among these distances:
  29   21  0.12
  30  135  0.77
  31   19  0.11

ACGTcount: A:0.38, C:0.20, G:0.06, T:0.36


Consensus pattern (30 bp):   
TGACCCTCAAACTTTTCAAAAATTTAAATT

Done.