Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012516.1 Kokia drynarioides strain JFW-HI SEQ_127521, 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: 2239
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28


Found at i:1560 original size:29 final size:29

Alignment explanation


    Indices: 1527--1690  Score: 166
    Period size: 29  Copynumber: 5.6  Consensus size: 29

       1517 ATTCGAGGTC

                    *                    
       1527 AAAAATGGGATTTTTGGAAGTTCGGGGGT
          1 AAAAATGGAATTTTTGGAAGTTCGGGGGT

                           **            * 
       1556 AAAAATGGAATTTTTAAAAGGTTTCGGGGTT
          1 AAAAATGGAATTTTTGGAA-G-TTCGGGGGT

                    *  *                 
       1587 AAAAATGGGATGTTTGGAAGTTCGGGGGT
          1 AAAAATGGAATTTTTGGAAGTTCGGGGGT

                  **       **      *    * 
       1616 AAAAATAAAATTTTTAAAAGTTTAGGGGTT
          1 AAAAATGGAATTTTTGGAAG-TTCGGGGGT

                    *              *     
       1646 AAAAATGGGATTTTTGGAAGTTCAGGGGT
          1 AAAAATGGAATTTTTGGAAGTTCGGGGGT

                  *         
       1675 AAAAATAGAATTTTTG
          1 AAAAATGGAATTTTTG

       1691 AACAATTTAG


Statistics
Matches: 105,  Mismatches: 27, Indels: 6
        0.76            0.20        0.04

Matches are distributed among these distances:
  29   58  0.55
  30   24  0.23
  31   23  0.22

ACGTcount: A:0.35, C:0.02, G:0.29, T:0.33


Consensus pattern (29 bp):   
AAAAATGGAATTTTTGGAAGTTCGGGGGT

Found at i:1568 original size:59 final size:59

Alignment explanation


    Indices: 1505--1688  Score: 244
    Period size: 59  Copynumber: 3.1  Consensus size: 59

       1495 GTGAAATGGT

                              *   *                                   * 
       1505 AATTTTGGAAAA-ATTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGG
          1 AATTTT-GAAAAGATTCGGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATAG

                  *      *                    *                        *
       1564 AATTTTTAAAAGGTTTCGGGGTTAAAAATGGGATGTTTGGAAGTTCGGGGGTAAAAATAA
          1 AATTTTGAAAA-GATTCGGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATAG

                  *     *  *                             *             
       1624 AATTTTTAAAAGTTTAGGGGTTAAAAATGGGATTTTTGGAAGTTCAGGGGTAAAAATAG
          1 AATTTTGAAAAGATTCGGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATAG

                  
       1683 AATTTT
          1 AATTTT

       1689 TGAACAATTT


Statistics
Matches: 112,  Mismatches: 11, Indels: 4
        0.88            0.09        0.03

Matches are distributed among these distances:
  58    4  0.04
  59   56  0.50
  60   52  0.46

ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33


Consensus pattern (59 bp):   
AATTTTGAAAAGATTCGGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATAG

Found at i:1689 original size:59 final size:59

Alignment explanation


    Indices: 1527--1702  Score: 273
    Period size: 60  Copynumber: 2.9  Consensus size: 59

       1517 ATTCGAGGTC

                                               *                 *      
       1527 AAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTAAAAGGTTTCGGGGTT
          1 AAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATAGAATTTTTAAAA-GTTTAGGGGTT

                       *                        *                      
       1587 AAAAATGGGATGTTTGGAAGTTCGGGGGTAAAAATAAAATTTTTAAAAGTTTAGGGGTT
          1 AAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATAGAATTTTTAAAAGTTTAGGGGTT

                                   *                                  
       1646 AAAAATGGGATTTTTGGAAGTTCAGGGGTAAAAATAGAATTTTTGAACAA-TTTAGGG
          1 AAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATAGAATTTTT-AA-AAGTTTAGGG

       1703 ACCTACGGGA


Statistics
Matches: 107,  Mismatches: 7, Indels: 4
        0.91            0.06        0.03

Matches are distributed among these distances:
  59   51  0.48
  60   54  0.50
  61    2  0.02

ACGTcount: A:0.36, C:0.03, G:0.29, T:0.32


Consensus pattern (59 bp):   
AAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATAGAATTTTTAAAAGTTTAGGGGTT
Done.