Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007621.1 Kokia drynarioides strain JFW-HI SEQ_122252, 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: 6789
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.32


Found at i:396 original size:21 final size:21

Alignment explanation


    Indices: 372--423  Score: 104
    Period size: 21  Copynumber: 2.5  Consensus size: 21

        362 AGTAAGGGTA

                                 
        372 GTATCGGTAGTACCTATACTT
          1 GTATCGGTAGTACCTATACTT

                                 
        393 GTATCGGTAGTACCTATACTT
          1 GTATCGGTAGTACCTATACTT

                      
        414 GTATCGGTAG
          1 GTATCGGTAG

        424 AACTCCCACT


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   31  1.00

ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37


Consensus pattern (21 bp):   
GTATCGGTAGTACCTATACTT

Found at i:5824 original size:24 final size:24

Alignment explanation


    Indices: 5797--5991  Score: 153
    Period size: 24  Copynumber: 8.2  Consensus size: 24

       5787 CGTAGAACTA

                   *             *  
       5797 CGTAAACATGTACAAGCTGACAAG
          1 CGTAAACGTGTACAAGCTGACGAG

                       *      *  * *
       5821 CGTAAACGTGTTCAAGCTAACTAA
          1 CGTAAACGTGTACAAGCTGACGAG

                  *  *          *   
       5845 CGTAAATGTATACAAGCTGATGAG
          1 CGTAAACGTGTACAAGCTGACGAG

             *         *            
       5869 CATAAACGTGTGCAA---GACGAG
          1 CGTAAACGTGTACAAGCTGACGAG

                     *  *   *       
       5890 CGTAAACGTATATAAGTTGACGAG
          1 CGTAAACGTGTACAAGCTGACGAG

             *         *      *     
       5914 CATAAACGTGTGCAAGCTAACGAG
          1 CGTAAACGTGTACAAGCTGACGAG

             *     * *  *     *     
       5938 CATAAACATATATAAGCTAACGAG
          1 CGTAAACGTGTACAAGCTGACGAG

                   *   *            
       5962 CGTAAACATGTGCAAGCTGACGAG
          1 CGTAAACGTGTACAAGCTGACGAG

                  
       5986 CGTAAA
          1 CGTAAA

       5992 AGTACATGAG


Statistics
Matches: 132,  Mismatches: 36, Indels: 6
        0.76            0.21        0.03

Matches are distributed among these distances:
  21   16  0.12
  24  116  0.88

ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20


Consensus pattern (24 bp):   
CGTAAACGTGTACAAGCTGACGAG

Found at i:5862 original size:48 final size:48

Alignment explanation


    Indices: 5797--5991  Score: 207
    Period size: 48  Copynumber: 4.1  Consensus size: 48

       5787 CGTAGAACTA

                   * *           *   *         *         * *
       5797 CGTAAACATGTACAAGCTGACAAGCGTAAACGTGTTCAAGCTAACTAA
          1 CGTAAACGTATACAAGCTGACGAGCATAAACGTGTGCAAGCTAACGAG

                  *             *                           
       5845 CGTAAATGTATACAAGCTGATGAGCATAAACGTGTGCAAG---ACGAG
          1 CGTAAACGTATACAAGCTGACGAGCATAAACGTGTGCAAGCTAACGAG

                        *   *                               
       5890 CGTAAACGTATATAAGTTGACGAGCATAAACGTGTGCAAGCTAACGAG
          1 CGTAAACGTATACAAGCTGACGAGCATAAACGTGTGCAAGCTAACGAG

             *     *    *     *      *     *          *     
       5938 CATAAACATATATAAGCTAACGAGCGTAAACATGTGCAAGCTGACGAG
          1 CGTAAACGTATACAAGCTGACGAGCATAAACGTGTGCAAGCTAACGAG

                  
       5986 CGTAAA
          1 CGTAAA

       5992 AGTACATGAG


Statistics
Matches: 123,  Mismatches: 21, Indels: 6
        0.82            0.14        0.04

Matches are distributed among these distances:
  45   39  0.32
  48   84  0.68

ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20


Consensus pattern (48 bp):   
CGTAAACGTATACAAGCTGACGAGCATAAACGTGTGCAAGCTAACGAG

Found at i:5968 original size:93 final size:94

Alignment explanation


    Indices: 5814--5991  Score: 214
    Period size: 93  Copynumber: 1.9  Consensus size: 94

       5804 ATGTACAAGC

                    *         *         *   *    **          * *          *  
       5814 TGACAAGCGTAAACGTGTTCAAGCTAACTAACGTAAATGTATACAAGCTGATGAGCATAAACGTG
          1 TGACAAGCATAAACGTGTGCAAGCTAACGAACATAAACATATACAAGCTAACGAGCATAAACATG

                                         
       5879 TGCAA-GACGAGCGTAAACGTATATAAGT
         66 TGCAACGACGAGCGTAAACGTATATAAGT

                *                         *            *            *        
       5907 TGACGAGCATAAACGTGTGCAAGCTAACGAGCATAAACATATATAAGCTAACGAGCGTAAACATG
          1 TGACAAGCATAAACGTGTGCAAGCTAACGAACATAAACATATACAAGCTAACGAGCATAAACATG

                                
       5972 TGCAAGCTGACGAGCGTAAA
         66 TGCAA-C-GACGAGCGTAAA

       5992 AGTACATGAG


Statistics
Matches: 69,  Mismatches: 13, Indels: 3
        0.81            0.15        0.04

Matches are distributed among these distances:
  93   57  0.83
  96   12  0.17

ACGTcount: A:0.39, C:0.17, G:0.23, T:0.20


Consensus pattern (94 bp):   
TGACAAGCATAAACGTGTGCAAGCTAACGAACATAAACATATACAAGCTAACGAGCATAAACATG
TGCAACGACGAGCGTAAACGTATATAAGT

Found at i:6676 original size:21 final size:21

Alignment explanation


    Indices: 6652--6703  Score: 104
    Period size: 21  Copynumber: 2.5  Consensus size: 21

       6642 AGTAAGGGTA

                                 
       6652 GTATCGGTAGTACCTATACTT
          1 GTATCGGTAGTACCTATACTT

                                 
       6673 GTATCGGTAGTACCTATACTT
          1 GTATCGGTAGTACCTATACTT

                      
       6694 GTATCGGTAG
          1 GTATCGGTAG

       6704 AACTCCCACT


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   31  1.00

ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37


Consensus pattern (21 bp):   
GTATCGGTAGTACCTATACTT
Done.