Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001120.1 Kokia drynarioides strain JFW-HI SEQ_112403, 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: 5796
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.32


Found at i:697 original size:18 final size:17

Alignment explanation


    Indices: 676--768  Score: 105
    Period size: 17  Copynumber: 5.4  Consensus size: 17

        666 TTTTATTTAT

                             *
        676 TTTAAATTTGAAAATAAT
          1 TTTAAATTT-AAAATAAA

                  *  *  *    
        694 TTTAAACTTCAATTAAA
          1 TTTAAATTTAAAATAAA

                             
        711 TTTAAATTTAAAATAAA
          1 TTTAAATTTAAAATAAA

                      *   *   
        728 TTTAAATTTTTAAAGAAA
          1 TTTAAA-TTTAAAATAAA

                 *           
        746 TTTAATTTTAAAATAAA
          1 TTTAAATTTAAAATAAA

                  
        763 TTTAAA
          1 TTTAAA

        769 GGGAGTTTGA


Statistics
Matches: 61,  Mismatches: 13, Indels: 3
        0.79            0.17        0.04

Matches are distributed among these distances:
  17   39  0.64
  18   22  0.36

ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44


Consensus pattern (17 bp):   
TTTAAATTTAAAATAAA

Found at i:730 original size:35 final size:36

Alignment explanation


    Indices: 676--765  Score: 105
    Period size: 35  Copynumber: 2.6  Consensus size: 36

        666 TTTTATTTAT

                                            **   
        676 TTTAAATTTGAAAAT-AATTTTAAA-CTTCAATTAAA
          1 TTTAAATTT-AAAATAAATTTTAAATCTTCAAAGAAA

                                     *  *       
        711 TTTAAATTTAAAATAAA-TTTAAATTTTTAAAGAAA
          1 TTTAAATTTAAAATAAATTTTAAATCTTCAAAGAAA

                 *              
        746 TTTAATTTTAAAATAAATTT
          1 TTTAAATTTAAAATAAATTT

        766 AAAGGGAGTT


Statistics
Matches: 47,  Mismatches: 5, Indels: 5
        0.82            0.09        0.09

Matches are distributed among these distances:
  34   11  0.23
  35   34  0.72
  36    2  0.04

ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46


Consensus pattern (36 bp):   
TTTAAATTTAAAATAAATTTTAAATCTTCAAAGAAA

Found at i:1486 original size:29 final size:29

Alignment explanation


    Indices: 1444--1503  Score: 120
    Period size: 29  Copynumber: 2.1  Consensus size: 29

       1434 GAGATGAAAG

                                         
       1444 AAATGAAAATTAAGCAAATTTTTTAGCTT
          1 AAATGAAAATTAAGCAAATTTTTTAGCTT

                                         
       1473 AAATGAAAATTAAGCAAATTTTTTAGCTT
          1 AAATGAAAATTAAGCAAATTTTTTAGCTT

              
       1502 AA
          1 AA

       1504 GTACCTAATG


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  29   31  1.00

ACGTcount: A:0.47, C:0.07, G:0.10, T:0.37


Consensus pattern (29 bp):   
AAATGAAAATTAAGCAAATTTTTTAGCTT
Done.