Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001896.1 Kokia drynarioides strain JFW-HI SEQ_113680, 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: 2821
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.35


Found at i:1357 original size:24 final size:24

Alignment explanation


    Indices: 1315--1563  Score: 158
    Period size: 24  Copynumber: 10.2  Consensus size: 24

       1305 GTTTAGTGCG

                 *    *   *         
       1315 TTTACGCTCGCCAGGTAATGTACA
          1 TTTACACTCGTCAGCTAATGTACA

                                  * *
       1339 TTTACAC-CTGTCAGCTAATGTGCG
          1 TTTACACTC-GTCAGCTAATGTACA

                     **             
       1363 TTTACACTCACCAGCTAATGTACA
          1 TTTACACTCGTCAGCTAATGTACA

                 *                 *
       1387 TTTACGCTCGTCAGCTAATGTACG
          1 TTTACACTCGTCAGCTAATGTACA

                 *  * *  *     *  **
       1411 TTTACGCTAGACAACTAATATATG
          1 TTTACACTCGTCAGCTAATGTACA

                     **            *
       1435 TTTACACTCACCAGCTAATGTACG
          1 TTTACACTCGTCAGCTAATGTACA

                **                **
       1459 TTTATGCTCGTCAGCTAATGTATG
          1 TTTACACTCGTCAGCTAATGTACA

                *      *       *   *
       1483 TTTATACTCGTTAGCTAATTTACG
          1 TTTACACTCGTCAGCTAATGTACA

                 *    *              *
       1507 TTTACGCTCGCCAGCTAATGTATACG
          1 TTTACACTCGTCAGCTAATG--TACA

                 *    *               
       1533 TTTACGCTCGCCAGCTAATGTATACA
          1 TTTACACTCGTCAGCTAATG--TACA

                 
       1559 TTTAC
          1 TTTAC

       1564 GCTCTCCAGT


Statistics
Matches: 181,  Mismatches: 40, Indels: 6
        0.80            0.18        0.03

Matches are distributed among these distances:
  23    1  0.01
  24  145  0.80
  25    1  0.01
  26   34  0.19

ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34


Consensus pattern (24 bp):   
TTTACACTCGTCAGCTAATGTACA

Found at i:1438 original size:72 final size:72

Alignment explanation


    Indices: 1313--1554  Score: 261
    Period size: 72  Copynumber: 3.3  Consensus size: 72

       1303 AAGTTTAGTG

                        *   *        *           *  *     * *                
       1313 CGTTTACGCTCGCCAGGTAATGTACATTTACACCT-GTCAGCTAATGTGCGTTTACACTCACCAG
          1 CGTTTACGCTCGTCAGCTAATGTACGTTTACA-CTAGACAACTAATATACGTTTACACTCACCAG

                    
       1377 CTAATGTA
         65 CTAATGTA

             *                             *                *                
       1385 CATTTACGCTCGTCAGCTAATGTACGTTTACGCTAGACAACTAATATATGTTTACACTCACCAGC
          1 CGTTTACGCTCGTCAGCTAATGTACGTTTACACTAGACAACTAATATACGTTTACACTCACCAGC

                   
       1450 TAATGTA
         66 TAATGTA

                  *                 *     *   * ** *     *         *   *     
       1457 CGTTTATGCTCGTCAGCTAATGTATGTTTATACTCGTTAGCTAATTTACGTTTACGCTCGCCAGC
          1 CGTTTACGCTCGTCAGCTAATGTACGTTTACACTAGACAACTAATATACGTTTACACTCACCAGC

                     
       1522 TAATGTATA
         66 TAATG--TA

                        *           
       1531 CGTTTACGCTCGCCAGCTAATGTA
          1 CGTTTACGCTCGTCAGCTAATGTA

       1555 TACATTTACG


Statistics
Matches: 142,  Mismatches: 25, Indels: 4
        0.83            0.15        0.02

Matches are distributed among these distances:
  71    2  0.01
  72  116  0.82
  74   24  0.17

ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33


Consensus pattern (72 bp):   
CGTTTACGCTCGTCAGCTAATGTACGTTTACACTAGACAACTAATATACGTTTACACTCACCAGC
TAATGTA

Found at i:1986 original size:37 final size:37

Alignment explanation


    Indices: 1894--1987  Score: 125
    Period size: 37  Copynumber: 2.5  Consensus size: 37

       1884 ATTTTCGGAG

                       *   *                     
       1894 TGCACCCAAGATTGTTACTGCATAAATATTCTTCAAT
          1 TGCACCCAAGAATGTCACTGCATAAATATTCTTCAAT

                *   *  * *           *           
       1931 TGCATCCAGGACTATCACTGCATAAGTATTCTTCAAT
          1 TGCACCCAAGAATGTCACTGCATAAATATTCTTCAAT

                                
       1968 TGCACCCAAGAATGTCACTG
          1 TGCACCCAAGAATGTCACTG

       1988 TATGAACATG


Statistics
Matches: 47,  Mismatches: 10, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  37   47  1.00

ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31


Consensus pattern (37 bp):   
TGCACCCAAGAATGTCACTGCATAAATATTCTTCAAT
Done.