Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003126.1 Kokia drynarioides strain JFW-HI SEQ_115701, 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, 871

Length: 1452
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34


Found at i:413 original size:30 final size:30

Alignment explanation


    Indices: 391--561  Score: 238
    Period size: 30  Copynumber: 5.7  Consensus size: 30

        381 TTTCGAGAGT

                                         *
        391 AAAAATGAAATTTTTGGAAGTTTTGGGGTA
          1 AAAAATGAAATTTTTGGAAGTTTTGGGGTC

                                        * 
        421 AAAAATGAAATTTTTGGAAGTTTTGGGGCC
          1 AAAAATGAAATTTTTGGAAGTTTTGGGGTC

                                     *    
        451 AAAAATGAAATTTTTGGAAG-TTTGAGGT-
          1 AAAAATGAAATTTTTGGAAGTTTTGGGGTC

                   * *                    
        479 AAAAATGGATTTTTTGGAAGTTTTGGGGTC
          1 AAAAATGAAATTTTTGGAAGTTTTGGGGTC

                     *              *      
        509 AAAAATGAATTTTTTGGAAAGTTTCGGGGTC
          1 AAAAATGAAATTTTTGG-AAGTTTTGGGGTC

                   *       *      
        540 AAAAATGGAATTTTTAGAAGTT
          1 AAAAATGAAATTTTTGGAAGTT

        562 CGGGGGGTAA


Statistics
Matches: 126,  Mismatches: 12, Indels: 6
        0.88            0.08        0.04

Matches are distributed among these distances:
  28   18  0.14
  29   13  0.10
  30   69  0.55
  31   26  0.21

ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36


Consensus pattern (30 bp):   
AAAAATGAAATTTTTGGAAGTTTTGGGGTC

Found at i:481 original size:88 final size:91

Alignment explanation


    Indices: 372--561  Score: 278
    Period size: 88  Copynumber: 2.1  Consensus size: 91

        362 AAAAGGGTAA

                  *                                                          
        372 TTTTGGGAGTTTCGAGAGTAAAAATGAAATTTTTGGAAGTTTTGGGGTAAAAAATGAAATTTTTG
          1 TTTTGGAAGTTTCGAGAGTAAAAATGAAATTTTTGGAAGTTTTGGGGTAAAAAATGAAATTTTTG

                    *                 
        437 G-AAGTTTTGGGGCCAAAAATGAAAT
         66 GAAAGTTTCGGGGCCAAAAATGAAAT

                                      * *                   *         *      
        462 TTTTGGAAGTTT-GAG-GTAAAAATGGATTTTTTGGAAGTTTTGGGGTCAAAAATGAATTTTTTG
          1 TTTTGGAAGTTTCGAGAGTAAAAATGAAATTTTTGGAAGTTTTGGGGTAAAAAATGAAATTTTTG

                         *        *   
        525 GAAAGTTTCGGGGTCAAAAATGGAAT
         66 GAAAGTTTCGGGGCCAAAAATGAAAT

                *      
        551 TTTTAGAAGTT
          1 TTTTGGAAGTT

        562 CGGGGGGTAA


Statistics
Matches: 90,  Mismatches: 9, Indels: 3
        0.88            0.09        0.03

Matches are distributed among these distances:
  88   45  0.50
  89   34  0.38
  90   11  0.12

ACGTcount: A:0.33, C:0.03, G:0.27, T:0.37


Consensus pattern (91 bp):   
TTTTGGAAGTTTCGAGAGTAAAAATGAAATTTTTGGAAGTTTTGGGGTAAAAAATGAAATTTTTG
GAAAGTTTCGGGGCCAAAAATGAAAT

Found at i:574 original size:30 final size:29

Alignment explanation


    Indices: 389--585  Score: 209
    Period size: 30  Copynumber: 6.6  Consensus size: 29

        379 AGTTTCGAGA

                     *                   
        389 GTAAAAATGAAATTTTTGGAAGTTTTGGG
          1 GTAAAAATGGAATTTTTGGAAGTTTTGGG

                      *                   
        418 GTAAAAAATGAAATTTTTGGAAGTTTTGGG
          1 GT-AAAAATGGAATTTTTGGAAGTTTTGGG

              *       *                 * 
        448 GCCAAAAATGAAATTTTTGGAAG-TTTGAG
          1 G-TAAAAATGGAATTTTTGGAAGTTTTGGG

                       *                 
        477 GTAAAAATGGATTTTTTGGAAGTTTTGGG
          1 GTAAAAATGGAATTTTTGGAAGTTTTGGG

                                        *   
        506 GTCAAAAAT-GAATTTTTTGGAAAGTTTCGGG
          1 GT-AAAAATGGAA-TTTTTGG-AAGTTTTGGG

                              *       **   
        537 GTCAAAAATGGAATTTTTAGAAGTTCGGGGG
          1 GT-AAAAATGGAATTTTTGGAAGTT-TTGGG

                   **         
        568 GTAAAAACAGAATTTTTG
          1 GTAAAAATGGAATTTTTG

        586 AACAATTTAA


Statistics
Matches: 146,  Mismatches: 14, Indels: 15
        0.83            0.08        0.09

Matches are distributed among these distances:
  28   18  0.12
  29   17  0.12
  30   79  0.54
  31   29  0.20
  32    3  0.02

ACGTcount: A:0.35, C:0.04, G:0.27, T:0.35


Consensus pattern (29 bp):   
GTAAAAATGGAATTTTTGGAAGTTTTGGG
Done.