Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006732.1 Kokia drynarioides strain JFW-HI SEQ_121330, 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: 6044
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:3479 original size:41 final size:41

Alignment explanation


    Indices: 3417--3693  Score: 315
    Period size: 41  Copynumber: 6.7  Consensus size: 41

       3407 TGTAAATAAA

                  *       * *                        
       3417 TTAGCGGCGCTTTCACGAAAACGCCGCTAATGCTCCGACCT
          1 TTAGCGACGCTTTCTCAAAAACGCCGCTAATGCTCCGACCT

                    *                *     *         
       3458 TTAGCGACACTTTCTCAAAAACGCCACTAATACTCCGACCT
          1 TTAGCGACGCTTTCTCAAAAACGCCGCTAATGCTCCGACCT

                  *   *            *          *      
       3499 TTAGCGGCGCCTTCTCAAAAACGTCGCTAATGCTTCGACCT
          1 TTAGCGACGCTTTCTCAAAAACGCCGCTAATGCTCCGACCT

                                        *        *     
       3540 TTAGCGACGCTTTAC-CAAAAAACGCCGTTAATGCTCTGACCT
          1 TTAGCGACGCTTT-CTC-AAAAACGCCGCTAATGCTCCGACCT

                  **      *                   **     
       3582 TTAGCGGTGCTTTCCCAAAAACGCCGCTAATGCTTTGACCT
          1 TTAGCGACGCTTTCTCAAAAACGCCGCTAATGCTCCGACCT

                  *                * *  *              
       3623 TTAGCGGCGCTTT-TCCAAAAAATGTCGATAATGCTCCGACCT
          1 TTAGCGACGCTTTCT-C-AAAAACGCCGCTAATGCTCCGACCT

                                         
       3665 TTAGCGACGCTTTCTCAAAAACGCCGCTA
          1 TTAGCGACGCTTTCTCAAAAACGCCGCTA

       3694 TTTATTTACC


Statistics
Matches: 196,  Mismatches: 34, Indels: 12
        0.81            0.14        0.05

Matches are distributed among these distances:
  41  128  0.65
  42   67  0.34
  43    1  0.01

ACGTcount: A:0.26, C:0.31, G:0.18, T:0.26


Consensus pattern (41 bp):   
TTAGCGACGCTTTCTCAAAAACGCCGCTAATGCTCCGACCT

Found at i:3610 original size:83 final size:82

Alignment explanation


    Indices: 3417--3693  Score: 360
    Period size: 83  Copynumber: 3.4  Consensus size: 82

       3407 TGTAAATAAA

                          * *                 *              *               
       3417 TTAGCGGCGCTTTCACGAAAACGCCGCTAATGCTCCGACCTTTAGCGACACTTTCTC-AAAAACG
          1 TTAGCGGCGCTTTCTCAAAAACGCCGCTAATGCTTCGACCTTTAGCGACGCTTTC-CAAAAAACG

                     *         
       3481 CC-ACTAATACTCCGACCT
         65 CCGA-TAATGCTCCGACCT

                      *            *                                         
       3499 TTAGCGGCGCCTTCTCAAAAACGTCGCTAATGCTTCGACCTTTAGCGACGCTTTACCAAAAAACG
          1 TTAGCGGCGCTTTCTCAAAAACGCCGCTAATGCTTCGACCTTTAGCGACGCTTT-CCAAAAAACG

               *        *     
       3564 CCGTTAATGCTCTGACCT
         65 CCGATAATGCTCCGACCT

                   *      *                    *           *               * 
       3582 TTAGCGGTGCTTTCCCAAAAACGCCGCTAATGCTTTGACCTTTAGCGGCGCTTTTCCAAAAAATG
          1 TTAGCGGCGCTTTCTCAAAAACGCCGCTAATGCTTCGACCTTTAGCGACGC-TTTCCAAAAAACG

            *                 
       3647 TCGATAATGCTCCGACCT
         65 CCGATAATGCTCCGACCT

                  *                      
       3665 TTAGCGACGCTTTCTCAAAAACGCCGCTA
          1 TTAGCGGCGCTTTCTCAAAAACGCCGCTA

       3694 TTTATTTACC


Statistics
Matches: 169,  Mismatches: 22, Indels: 7
        0.85            0.11        0.04

Matches are distributed among these distances:
  82   49  0.29
  83  117  0.69
  84    3  0.02

ACGTcount: A:0.26, C:0.31, G:0.18, T:0.26


Consensus pattern (82 bp):   
TTAGCGGCGCTTTCTCAAAAACGCCGCTAATGCTTCGACCTTTAGCGACGCTTTCCAAAAAACGC
CGATAATGCTCCGACCT

Found at i:3685 original size:124 final size:122

Alignment explanation


    Indices: 3417--3693  Score: 349
    Period size: 124  Copynumber: 2.2  Consensus size: 122

       3407 TGTAAATAAA

                  *         *                                      *         
       3417 TTAGCGGCGCTTTCACGAAAACGCCGCTAATGCTCCGACCTTTAGCGACACTTTCTCAAAAACGC
          1 TTAGCGACGCTTTC-CAAAAACGCCGCTAATGCTCCGACCTTTAGCGACACTTTCCCAAAAACGC

                                                       *       *      
       3482 CACTAATACTCCGACCTTTAGCGGCGCCTTCTCAAAAACGTCGCTAATGCTTCGACCT
         65 CACTAATACTCCGACCTTTAGCGGCGCCTTCTCAAAAACGTCGATAATGCTCCGACCT

                                       *        *           ***              
       3540 TTAGCGACGCTTTACCAAAAAACGCCGTTAATGCTCTGACCTTTAGCGGTGCTTTCCCAAAAACG
          1 TTAGCGACGCTTT-CC-AAAAACGCCGCTAATGCTCCGACCTTTAGCGACACTTTCCCAAAAACG

              *     *  **                  *         *                   
       3605 CCGCTAATGCTTTGACCTTTAGCGGCG-CTTTTCCAAAAAATGTCGATAATGCTCCGACCT
         64 CCACTAATACTCCGACCTTTAGCGGCGCCTTCT-C-AAAAACGTCGATAATGCTCCGACCT

                                         
       3665 TTAGCGACGCTTTCTCAAAAACGCCGCTA
          1 TTAGCGACGCTTTC-CAAAAACGCCGCTA

       3694 TTTATTTACC


Statistics
Matches: 132,  Mismatches: 17, Indels: 9
        0.84            0.11        0.06

Matches are distributed among these distances:
 123   17  0.13
 124   79  0.60
 125   36  0.27

ACGTcount: A:0.26, C:0.31, G:0.18, T:0.26


Consensus pattern (122 bp):   
TTAGCGACGCTTTCCAAAAACGCCGCTAATGCTCCGACCTTTAGCGACACTTTCCCAAAAACGCC
ACTAATACTCCGACCTTTAGCGGCGCCTTCTCAAAAACGTCGATAATGCTCCGACCT

Found at i:3725 original size:40 final size:40

Alignment explanation


    Indices: 3681--3756  Score: 107
    Period size: 40  Copynumber: 1.9  Consensus size: 40

       3671 ACGCTTTCTC

                         * *                        
       3681 AAAAACGCCGCTATTTATTTACCTTTTGCGGCGTTTGTGT
          1 AAAAACGCCGCTAGTGATTTACCTTTTGCGGCGTTTGTGT

                            *     *    *        
       3721 AAAAACGCCGCTAGTGCTTTACTTTTTTCGGCGTTT
          1 AAAAACGCCGCTAGTGATTTACCTTTTGCGGCGTTT

       3757 TCTTTCCAAA


Statistics
Matches: 31,  Mismatches: 5, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  40   31  1.00

ACGTcount: A:0.20, C:0.21, G:0.20, T:0.39


Consensus pattern (40 bp):   
AAAAACGCCGCTAGTGATTTACCTTTTGCGGCGTTTGTGT
Done.