Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001281.1 Kokia drynarioides strain JFW-HI SEQ_112670, 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: 4032
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34


Found at i:1209 original size:24 final size:24

Alignment explanation


    Indices: 1167--1415  Score: 158
    Period size: 24  Copynumber: 10.2  Consensus size: 24

       1157 GTTTAGTGCG

                 *    *   *         
       1167 TTTACGCTCGCCAGGTAATGTACA
          1 TTTACACTCGTCAGCTAATGTACA

                                  * *
       1191 TTTACAC-CTGTCAGCTAATGTGCG
          1 TTTACACTC-GTCAGCTAATGTACA

                     **             
       1215 TTTACACTCACCAGCTAATGTACA
          1 TTTACACTCGTCAGCTAATGTACA

                 *                 *
       1239 TTTACGCTCGTCAGCTAATGTACG
          1 TTTACACTCGTCAGCTAATGTACA

                 *  * *  *     *  **
       1263 TTTACGCTAGACAACTAATATATG
          1 TTTACACTCGTCAGCTAATGTACA

                     **            *
       1287 TTTACACTCACCAGCTAATGTACG
          1 TTTACACTCGTCAGCTAATGTACA

                **                **
       1311 TTTATGCTCGTCAGCTAATGTATG
          1 TTTACACTCGTCAGCTAATGTACA

                *      *       *   *
       1335 TTTATACTCGTTAGCTAATTTACG
          1 TTTACACTCGTCAGCTAATGTACA

                 *    *              *
       1359 TTTACGCTCGCCAGCTAATGTATACG
          1 TTTACACTCGTCAGCTAATG--TACA

                 *    *               
       1385 TTTACGCTCGCCAGCTAATGTATACA
          1 TTTACACTCGTCAGCTAATG--TACA

                 
       1411 TTTAC
          1 TTTAC

       1416 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:1290 original size:72 final size:72

Alignment explanation


    Indices: 1165--1406  Score: 261
    Period size: 72  Copynumber: 3.3  Consensus size: 72

       1155 AAGTTTAGTG

                        *   *        *           *  *     * *                
       1165 CGTTTACGCTCGCCAGGTAATGTACATTTACACCT-GTCAGCTAATGTGCGTTTACACTCACCAG
          1 CGTTTACGCTCGTCAGCTAATGTACGTTTACA-CTAGACAACTAATATACGTTTACACTCACCAG

                    
       1229 CTAATGTA
         65 CTAATGTA

             *                             *                *                
       1237 CATTTACGCTCGTCAGCTAATGTACGTTTACGCTAGACAACTAATATATGTTTACACTCACCAGC
          1 CGTTTACGCTCGTCAGCTAATGTACGTTTACACTAGACAACTAATATACGTTTACACTCACCAGC

                   
       1302 TAATGTA
         66 TAATGTA

                  *                 *     *   * ** *     *         *   *     
       1309 CGTTTATGCTCGTCAGCTAATGTATGTTTATACTCGTTAGCTAATTTACGTTTACGCTCGCCAGC
          1 CGTTTACGCTCGTCAGCTAATGTACGTTTACACTAGACAACTAATATACGTTTACACTCACCAGC

                     
       1374 TAATGTATA
         66 TAATG--TA

                        *           
       1383 CGTTTACGCTCGCCAGCTAATGTA
          1 CGTTTACGCTCGTCAGCTAATGTA

       1407 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:1838 original size:37 final size:37

Alignment explanation


    Indices: 1746--1839  Score: 125
    Period size: 37  Copynumber: 2.5  Consensus size: 37

       1736 ATTTTCGGAG

                       *   *                     
       1746 TGCACCCAAGATTGTTACTGCATAAATATTCTTCAAT
          1 TGCACCCAAGAATGTCACTGCATAAATATTCTTCAAT

                *   *  * *           *           
       1783 TGCATCCAGGACTATCACTGCATAAGTATTCTTCAAT
          1 TGCACCCAAGAATGTCACTGCATAAATATTCTTCAAT

                                
       1820 TGCACCCAAGAATGTCACTG
          1 TGCACCCAAGAATGTCACTG

       1840 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

Found at i:2702 original size:16 final size:16

Alignment explanation


    Indices: 2681--2711  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       2671 TTGCGGATCC

                            
       2681 CATTTTACCTTTATTA
          1 CATTTTACCTTTATTA

                   *       
       2697 CATTTTATCTTTATT
          1 CATTTTACCTTTATT

       2712 TTCACATTAT


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61


Consensus pattern (16 bp):   
CATTTTACCTTTATTA
Done.