Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000695.1 Kokia drynarioides strain JFW-HI SEQ_111695, 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, 799

Length: 1333
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24


Found at i:62 original size:43 final size:43

Alignment explanation


    Indices: 1--1309  Score: 1284
    Period size: 43  Copynumber: 30.7  Consensus size: 43

                     *                              *  
          1 ATCTATACTAGCACACACAGTGCATCATCGGGTAAATCGAAGC
          1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC

                 *     *          *       **        *  
         44 ATCTACACTGGTACACACAGTGTATCATCGAATAAATCGAAGC
          1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC

              *      *   *        *     **           * 
         87 ATTTATACTAGCATACACAGTGTATCATTAGGTAAATCGAGAC
          1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC

                   *         * *     *   * *            
        130 ATCTATATTGGCACACATAATGCATTATCAGATAAATCG-GGAC
          1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGG-C

              *              *            *         ** 
        173 ATTTATACT-G-ACACATAGTGCATCATCGAGTAAATCGATTC
          1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC

              *                      *            *    
        214 ATTTATACTGGCACACACAGTGCATTATCGGGTAAATCAAGGC
          1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC

              *        *     *                      *  
        257 ATTTATACTGGTACACAGAGTGCATCATCGGGTAAATCGATGC
          1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC

                     *       *           *      * * * *
        300 ATCTATACTAGCACACAAAGTGCATCATCTGGTAAACCAATGT
          1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC

              *       *              *    *     *   * *
        343 ATTTATACTGACACACACAGTGCATAATCGAGTAAACCGAAGA
          1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC

                                 * *      *     *       
        386 ATCTATACTGGCACACACAGTACGTCATCGAGTAAACCG-GTGC
          1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAG-GC

                   * *         *                *       
        429 ATCTATATTAGCACACACAATGCATCATCGGG-AAAACTGAGGC
          1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATC-GAGGC

                      *      *                      *  
        472 ATCTATACTGACACACAGAGTGCATCATCGGGTAAATCGATGC
          1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC

              *    *       * *           *              
        515 ATTTATATTGGCACATAGAGTGCATCATCAGGTAAA-CTGAGGC
          1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATC-GAGGC

                      *                                
        558 ATCTATACTGACACACACAGTGCATCATCGGGTAAATCGAGGC
          1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC

                              *                   *      
        601 ATCTATACTGGCGCACACTCAGTGCATCATCGGGTAAACCGAGGC
          1 ATCTATACT-G-GCACACACAGTGCATCATCGGGTAAATCGAGGC

                                                      * 
        646 ATCTATACTGG--CACACAGTGCATCATCGGGTAAA-CTGAGAC
          1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATC-GAGGC

                                     *          *      
        687 ATCTATACTGGCACACACAGTGCATTATCGGGTAAACCGAGGC
          1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC

              *                             *          
        730 ATTTATACTGGCACACACAGTGCATCATCGGGCAAATCGAGGC
          1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC

              *                           *      *     
        773 ATTTATACTGGCACACACAGTGCATCATCGAGTAAATTGAGGC
          1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC

              *      *                          *    * 
        816 ATTTATACTAGCACACACAGTGCATCATCGGGTAAACCGAGAC
          1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC

                     *       * *      * *       * *    
        859 ATCTATACTAGCACACATAATGCATCCTTGGGTAAACCAAGGC
          1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC

                   *       *              *     *     *
        902 ATCTATATTGGCACAAACAGTGCATCATCGAGTAAACCGAGGT
          1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC

              *    * *                   **            
        945 ATTTATATTAGCACACACAGTGCATCATCAAGTAAATCGAGGC
          1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC

              *                           *            
        988 ATTTATACTGGCACACACAGTGCATCATCGAGTAAATCGAGGC
          1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC

              *      *                  *       *    * 
       1031 ATTTATACTAGCACACACAGTGCATCATTGGGTAAACCGAGAC
          1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC

                     *       *        * *       *      
       1074 ATCTATACTAGCACACATAGTGCATCCTTGGGTAAACCGAGGC
          1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC

                   *                      *     *     *
       1117 ATCTATATTGGCACACACAGTGCATCATCGAGTAAACCGAGGT
          1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC

              *    * *                   **            
       1160 ATTTATATTAGCACACACAGTGCATCATCAAGTAAATCGAGGC
          1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC

              *    * **                 **             
       1203 ATTTATAGTTACACACACAGTGCATCATTAGGT--A---A---
          1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC

                       *       *          *   *        
       1238 ATCTATACTGGTACACACAATGCATCATCGAGTATATCGAGGC
          1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC

                     *           *       
       1281 ATCTATACTAGCACACACAGTACATCATC
          1 ATCTATACTGGCACACACAGTGCATCATC

       1310 CTGTACTAGC


Statistics
Matches: 1059,  Mismatches: 183, Indels: 48
        0.82            0.14        0.04

Matches are distributed among these distances:
  35   24  0.02
  37    1  0.00
  38    1  0.00
  40    2  0.00
  41   70  0.07
  42    8  0.01
  43  905  0.85
  44    9  0.01
  45   39  0.04

ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24


Consensus pattern (43 bp):   
ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC

Found at i:281 original size:23 final size:22

Alignment explanation


    Indices: 213--281  Score: 63
    Period size: 22  Copynumber: 3.1  Consensus size: 22

        203 TAAATCGATT

                        *          
        213 CATTTATACTGGCACACACAGTG
          1 CATTTATACTGGTACACA-AGTG

                     *    *        
        236 CA-TTAT-CGGGTAAATCAAG-G
          1 CATTTATACTGGTACA-CAAGTG

                                   
        256 CATTTATACTGGTACACAGAGTG
          1 CATTTATACTGGTACACA-AGTG

               
        279 CAT
          1 CAT

        282 CATCGGGTAA


Statistics
Matches: 36,  Mismatches: 5, Indels: 10
        0.71            0.10        0.20

Matches are distributed among these distances:
  20    3  0.08
  21   13  0.36
  22   14  0.39
  23    6  0.17

ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28


Consensus pattern (22 bp):   
CATTTATACTGGTACACAAGTG
Done.