Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014573.1 Kokia drynarioides strain JFW-HI SEQ_129612, 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: 18244
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.37


Found at i:9913 original size:24 final size:24

Alignment explanation


    Indices: 9885--10182  Score: 346
    Period size: 24  Copynumber: 12.4  Consensus size: 24

       9875 GAATTTCTGG

                                   *
       9885 CGAGCGTAAACGCATATTAGCTGG
          1 CGAGCGTAAACGCATATTAGCTGA

                        *         * 
       9909 CGAGCGTAAACGTATATTAGCTAA
          1 CGAGCGTAAACGCATATTAGCTGA

                                    
       9933 CGAGCGTAAACGCATATTAGCTGA
          1 CGAGCGTAAACGCATATTAGCTGA

                 *    *         *   
       9957 CGAGCATAAATGCATATTAGTTGA
          1 CGAGCGTAAACGCATATTAGCTGA

                      * *          *
       9981 CGAGCGTAAATGTATATTAGCTGG
          1 CGAGCGTAAACGCATATTAGCTGA

             * * *    **            
      10005 CAAACATAAATACATATTAGCTGA
          1 CGAGCGTAAACGCATATTAGCTGA

                                    
      10029 CGAGCGTAAACGCATATTAGCTGA
          1 CGAGCGTAAACGCATATTAGCTGA

            *           *       *   
      10053 TGAGCGTAAACGTATATTAGTTG-
          1 CGAGCGTAAACGCATATTAGCTGA

                        *        *   
      10076 CTGAGCGTAAACACATATTAGATGA
          1 C-GAGCGTAAACGCATATTAGCTGA

                        *       *   
      10101 CGAGCGTAAACGTATATTAGATGA
          1 CGAGCGTAAACGCATATTAGCTGA

                        *          *
      10125 CGAGCGTAAACGTATATTAGCTGG
          1 CGAGCGTAAACGCATATTAGCTGA

             *          *           
      10149 CAAGCGTAAACGTATATTAGCTGA
          1 CGAGCGTAAACGCATATTAGCTGA

                *     
      10173 CGAGAGTAAA
          1 CGAGCGTAAA

      10183 TGTACTGAAC


Statistics
Matches: 234,  Mismatches: 38, Indels: 4
        0.85            0.14        0.01

Matches are distributed among these distances:
  24  233  1.00
  25    1  0.00

ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25


Consensus pattern (24 bp):   
CGAGCGTAAACGCATATTAGCTGA

Found at i:10002 original size:72 final size:72

Alignment explanation


    Indices: 9885--10182  Score: 391
    Period size: 72  Copynumber: 4.1  Consensus size: 72

       9875 GAATTTCTGG

                                   *                      ** *         *     
       9885 CGAGCGTAAACGCATATTAGCTGGCGAGCGTAAACGTATATTAGCTAACGAGCGTAAACGCATAT
          1 CGAGCGTAAACGCATATTAGCTGACGAGCGTAAACGTATATTAGCTGGCAAGCGTAAACACATAT

                   
       9950 TAGCTGA
         66 TAGCTGA

                 *    *         *             *                * *    *      
       9957 CGAGCATAAATGCATATTAGTTGACGAGCGTAAATGTATATTAGCTGGCAAACATAAATACATAT
          1 CGAGCGTAAACGCATATTAGCTGACGAGCGTAAACGTATATTAGCTGGCAAGCGTAAACACATAT

                   
      10022 TAGCTGA
         66 TAGCTGA

                                    *                     *   *              
      10029 CGAGCGTAAACGCATATTAGCTGATGAGCGTAAACGTATATTAG-TTGCTGAGCGTAAACACATA
          1 CGAGCGTAAACGCATATTAGCTGACGAGCGTAAACGTATATTAGCTGGC-AAGCGTAAACACATA

                *   
      10093 TTAGATGA
         65 TTAGCTGA

                        *       *                                      **    
      10101 CGAGCGTAAACGTATATTAGATGACGAGCGTAAACGTATATTAGCTGGCAAGCGTAAACGTATAT
          1 CGAGCGTAAACGCATATTAGCTGACGAGCGTAAACGTATATTAGCTGGCAAGCGTAAACACATAT

                   
      10166 TAGCTGA
         66 TAGCTGA

                *     
      10173 CGAGAGTAAA
          1 CGAGCGTAAA

      10183 TGTACTGAAC


Statistics
Matches: 192,  Mismatches: 32, Indels: 4
        0.84            0.14        0.02

Matches are distributed among these distances:
  71    3  0.02
  72  186  0.97
  73    3  0.02

ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25


Consensus pattern (72 bp):   
CGAGCGTAAACGCATATTAGCTGACGAGCGTAAACGTATATTAGCTGGCAAGCGTAAACACATAT
TAGCTGA

Found at i:17201 original size:35 final size:35

Alignment explanation


    Indices: 17162--17242  Score: 90
    Period size: 35  Copynumber: 2.3  Consensus size: 35

      17152 TTAGAAATCT

                          * **   *      *      
      17162 ATTAAACTAGGGTTTTTTTAATAGTATATATGTTA
          1 ATTAAACTAGGGTTCTACTAACAGTATAGATGTTA

                  *                           *
      17197 ATTAAAATAGGGTTCTACTAACAGTATAGATGTTG
          1 ATTAAACTAGGGTTCTACTAACAGTATAGATGTTA

             *         
      17232 ACTAAACTAGG
          1 ATTAAACTAGG

      17243 ATGTTATTAC


Statistics
Matches: 37,  Mismatches: 9, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
  35   37  1.00

ACGTcount: A:0.37, C:0.07, G:0.17, T:0.38


Consensus pattern (35 bp):   
ATTAAACTAGGGTTCTACTAACAGTATAGATGTTA
Done.