Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005141.1 Kokia drynarioides strain JFW-HI SEQ_118979, 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: 4143
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31


Found at i:224 original size:35 final size:34

Alignment explanation


    Indices: 181--256  Score: 89
    Period size: 35  Copynumber: 2.1  Consensus size: 34

        171 CTTTATTTAT

                 *    *     *              *    
        181 TTTAAATTTATAATAATTTTAAATTTTGAAAGTAAA
          1 TTTAATTTTAAAATAAATTT-AATTTT-AAAATAAA

                                               
        217 TTTAATTTTTAAAATAAATTTAATTTTAAAATAAA
          1 TTTAA-TTTTAAAATAAATTTAATTTTAAAATAAA

                 
        252 TTTAA
          1 TTTAA

        257 AATGAGTTTG


Statistics
Matches: 35,  Mismatches: 4, Indels: 3
        0.83            0.10        0.07

Matches are distributed among these distances:
  35   12  0.34
  36   11  0.31
  37   12  0.34

ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49


Consensus pattern (34 bp):   
TTTAATTTTAAAATAAATTTAATTTTAAAATAAA

Found at i:245 original size:17 final size:17

Alignment explanation


    Indices: 181--256  Score: 89
    Period size: 17  Copynumber: 4.3  Consensus size: 17

        171 CTTTATTTAT

                 *    *     *
        181 TTTAAATTTATAATAAT
          1 TTTAATTTTAAAATAAA

                          *    
        198 TTTAAATTTTGAAAGTAAA
          1 TTT-AATTTT-AAAATAAA

                              
        217 TTTAATTTTTAAAATAAA
          1 TTTAA-TTTTAAAATAAA

                             
        235 TTTAATTTTAAAATAAA
          1 TTTAATTTTAAAATAAA

                 
        252 TTTAA
          1 TTTAA

        257 AATGAGTTTG


Statistics
Matches: 51,  Mismatches: 5, Indels: 6
        0.82            0.08        0.10

Matches are distributed among these distances:
  17   20  0.39
  18   19  0.37
  19   12  0.24

ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49


Consensus pattern (17 bp):   
TTTAATTTTAAAATAAA
Done.