Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005852.1 Kokia drynarioides strain JFW-HI SEQ_120161, 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: 1997
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29


Found at i:120 original size:39 final size:38

Alignment explanation


    Indices: 77--197  Score: 125
    Period size: 39  Copynumber: 3.1  Consensus size: 38

         67 CCATTAATTA

                                                   
         77 ATCTCTTACACCGAGCTTGGGGCAGATTACAACCATCCG
          1 ATCTCTTAC-CCGAGCTTGGGGCAGATTACAACCATCCG

                        *   *             * *  *  *
        116 ATCTCTTACCCCAAGCCTGGGGCAGATTACCATCAACCA
          1 ATCTCTTA-CCCGAGCTTGGGGCAGATTACAACCATCCG

                       *     *             *    *  
        155 ATCTCTTACCTTGAGCTCGGGGCAGATTACAGCCATTCG
          1 ATCTCTTACC-CGAGCTTGGGGCAGATTACAACCATCCG

                
        194 ATCT
          1 ATCT

        198 TATGGTTCGG


Statistics
Matches: 64,  Mismatches: 16, Indels: 4
        0.76            0.19        0.05

Matches are distributed among these distances:
  38    2  0.03
  39   61  0.95
  40    1  0.02

ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25


Consensus pattern (38 bp):   
ATCTCTTACCCGAGCTTGGGGCAGATTACAACCATCCG

Found at i:139 original size:78 final size:78

Alignment explanation


    Indices: 37--197  Score: 216
    Period size: 78  Copynumber: 2.1  Consensus size: 78

         27 GTAACATTTT

                 *       *                    *  **                   *      
         37 GATCTTTTACCCCGAGCCTGGGGCAGATCACCATTAATTAATCTCTTACAC-CGAGCTTGGGGCA
          1 GATCTCTTACCCCAAGCCTGGGGCAGATCACCATCAACCAATCTCTTAC-CTCGAGCTCGGGGCA

                          
        101 GATTACAACCATCC
         65 GATTACAACCATCC

                                        *                      *             
        115 GATCTCTTACCCCAAGCCTGGGGCAGATTACCATCAACCAATCTCTTACCTTGAGCTCGGGGCAG
          1 GATCTCTTACCCCAAGCCTGGGGCAGATCACCATCAACCAATCTCTTACCTCGAGCTCGGGGCAG

                  *    * 
        180 ATTACAGCCATTC
         66 ATTACAACCATCC

                 
        193 GATCT
          1 GATCT

        198 TATGGTTCGG


Statistics
Matches: 72,  Mismatches: 10, Indels: 2
        0.86            0.12        0.02

Matches are distributed among these distances:
  77    1  0.01
  78   71  0.99

ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25


Consensus pattern (78 bp):   
GATCTCTTACCCCAAGCCTGGGGCAGATCACCATCAACCAATCTCTTACCTCGAGCTCGGGGCAG
ATTACAACCATCC

Found at i:1866 original size:29 final size:29

Alignment explanation


    Indices: 1834--1995  Score: 107
    Period size: 29  Copynumber: 5.5  Consensus size: 29

       1824 GCAAAATAGT

                  *                      
       1834 AATTTTCGGAGGTTCAGGGTCAAAAATGG
          1 AATTTTTGGAGGTTCAGGGTCAAAAATGG

                         *                   
       1863 AATTTTTGG-GTCATTCAAGGGT--AAAATGGG
          1 AATTTTTGGAG--GTTC-AGGGTCAAAAAT-GG

                   *  *   * *            
       1893 AATTTTTTGAAGTTTAAGGTCAAAAATGG
          1 AATTTTTGGAGGTTCAGGGTCAAAAATGG

                       *     * * *       
       1922 AATTTTTGGAGATTC-GAGACTAAAATGG
          1 AATTTTTGGAGGTTCAGGGTCAAAAATGG

                        *    *           * 
       1950 TAATTTTTGGAAAGTTCGGGGTCAAAAATAG
          1 -AATTTTTGG-AGGTTCAGGGTCAAAAATGG

               *      *    
       1981 AATCTTTGGAAGTTC
          1 AATTTTTGGAGGTTC

       1996 GA


Statistics
Matches: 101,  Mismatches: 22, Indels: 20
        0.71            0.15        0.14

Matches are distributed among these distances:
  28   14  0.14
  29   43  0.43
  30   30  0.30
  31   14  0.14

ACGTcount: A:0.33, C:0.07, G:0.26, T:0.33


Consensus pattern (29 bp):   
AATTTTTGGAGGTTCAGGGTCAAAAATGG

Found at i:1889 original size:59 final size:58

Alignment explanation


    Indices: 1807--1990  Score: 190
    Period size: 59  Copynumber: 3.1  Consensus size: 58

       1797 AAAACGATAA

                   *          *     *        *   *                     
       1807 TTTTGGACACTTCAAGGGCAAAATAGTAATTTTCGGAGGTTCAGGGTCAAAAATGGAAT
          1 TTTTGGAGA-TTCAAGGGTAAAATGGTAATTTTTGGAAGTTCAGGGTCAAAAATGGAAT

                                       *       *      * *               
       1866 TTTTGG-GTCATTCAAGGGTAAAATGGGAATTTTTTGAAGTTTAAGGTCAAAAATGGAAT
          1 TTTTGGAG--ATTCAAGGGTAAAATGGTAATTTTTGGAAGTTCAGGGTCAAAAATGGAAT

                        *  **                         *           *    
       1925 TTTTGGAGATTCGAGACTAAAATGGTAATTTTTGGAAAGTTCGGGGTCAAAAATAGAAT
          1 TTTTGGAGATTCAAGGGTAAAATGGTAATTTTTGG-AAGTTCAGGGTCAAAAATGGAAT

            *      
       1984 CTTTGGA
          1 TTTTGGA

       1991 AGTTCGA


Statistics
Matches: 102,  Mismatches: 19, Indels: 8
        0.79            0.15        0.06

Matches are distributed among these distances:
  58   22  0.22
  59   78  0.76
  60    2  0.02

ACGTcount: A:0.34, C:0.08, G:0.26, T:0.33


Consensus pattern (58 bp):   
TTTTGGAGATTCAAGGGTAAAATGGTAATTTTTGGAAGTTCAGGGTCAAAAATGGAAT

Done.