Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01015181.1 Kokia drynarioides strain JFW-HI SEQ_130225, 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: 642291
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34

Warning! 422 characters in sequence are not A, C, G, or T


File 3 of 3

Found at i:638072 original size:41 final size:41

Alignment explanation


    Indices: 638027--638406  Score: 411
    Period size: 41  Copynumber: 9.3  Consensus size: 41

     638017 GAAAAGCACT

                     *                  * * *        
     638027 GCTAAAGGTTAGAGCAATAGCGGCGCTTTTTGAAAAGCGCC
          1 GCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCGCC

                       *                     *   *   
     638068 GCTAAAGGTCAAAGCAATAGCGGCGCTTATGGGCAAGTGCC
          1 GCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCGCC

                                *            *   *   
     638109 GCTAAAGGTCAGAGCAATAGTGGCGCTTATGGGCAAGGGCC
          1 GCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCGCC

                  *        *      * *             *  *
     638150 GCTAAAAGTCA-ATGTAATAGCTGTGCTTATGGGAAAGTGCT
          1 GCTAAAGGTCAGA-GCAATAGCGGCGCTTATGGGAAAGCGCC

                                *  *         *    *  
     638191 GCTAAAGGTCAGAGCAATAGTGGTGCTTATGGGCAAGCACC
          1 GCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCGCC

                   *   * *      **       *   *       
     638232 GCTAAAGATCAAAACAATAGTAGCGCTTAAGGGCAAGCGCC
          1 GCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCGCC

            *                     *        **        
     638273 ACTAAAGGTCAGAGCAATAGCGACGCTTATGAAAAAGCGCC
          1 GCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCGCC

                  *         *              **        
     638314 GCTAAAAGTCAGAGCAGTAGCGGCGCTTATGAAAAAGCGCC
          1 GCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCGCC

            *                           *            
     638355 TCTAAAGGTCAGAGCAATAGCGGCGCTTTTGGGAAAGCGCC
          1 GCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCGCC

                       
     638396 GCTAAAGGTCA
          1 GCTAAAGGTCA

     638407 TTTAATTGAT


Statistics
Matches: 282,  Mismatches: 55, Indels: 4
        0.83            0.16        0.01

Matches are distributed among these distances:
  40    1  0.00
  41  280  0.99
  42    1  0.00

ACGTcount: A:0.32, C:0.20, G:0.29, T:0.19


Consensus pattern (41 bp):   
GCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCGCC

Found at i:638096 original size:104 final size:104

Alignment explanation


    Indices: 637923--638117  Score: 282
    Period size: 104  Copynumber: 1.9  Consensus size: 104

     637913 GAAAAGAGTC

                                            *       *           *           *
     637923 GCTAAAGGTCAAAGCAATAGCAGCGCTTATGGGAAAGCACTGCTAAAGATCAGAGCAATAGCGGT
          1 GCTAAAGGTCAAAGCAATAGCAGCGCTTATGGAAAAGCACCGCTAAAGATCAAAGCAATAGCGGC

                                                   
     637988 GCTTATGGGCAAGCGCCGCTAAAGGTTTTGAAAAGCACT
         66 GCTTATGGGCAAGCGCCGCTAAAGGTTTTGAAAAGCACT

                     * *         *      * *       *         *                
     638027 GCTAAAGGTTAGAGCAATAGCGGCGCTTTTTGAAAAGCGCCGCTAAAGGTCAAAGCAATAGCGGC
          1 GCTAAAGGTCAAAGCAATAGCAGCGCTTATGGAAAAGCACCGCTAAAGATCAAAGCAATAGCGGC

                         *            
     638092 GCTTATGGGCAAGTGCCGCTAAAGGT
         66 GCTTATGGGCAAGCGCCGCTAAAGGT

     638118 CAGAGCAATA


Statistics
Matches: 79,  Mismatches: 12, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
 104   79  1.00

ACGTcount: A:0.32, C:0.19, G:0.29, T:0.19


Consensus pattern (104 bp):   
GCTAAAGGTCAAAGCAATAGCAGCGCTTATGGAAAAGCACCGCTAAAGATCAAAGCAATAGCGGC
GCTTATGGGCAAGCGCCGCTAAAGGTTTTGAAAAGCACT


Done.