Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002666.1 Kokia drynarioides strain JFW-HI SEQ_114919, 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: 16207
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34


Found at i:13698 original size:14 final size:14

Alignment explanation


    Indices: 13679--13705  Score: 54
    Period size: 14  Copynumber: 1.9  Consensus size: 14

      13669 TCGAGTTGAA

                          
      13679 TCGAGTGAAATTAT
          1 TCGAGTGAAATTAT

                         
      13693 TCGAGTGAAATTA
          1 TCGAGTGAAATTA

      13706 AAAAAATTAA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   13  1.00

ACGTcount: A:0.37, C:0.07, G:0.22, T:0.33


Consensus pattern (14 bp):   
TCGAGTGAAATTAT

Found at i:13889 original size:9 final size:9

Alignment explanation


    Indices: 13870--13936  Score: 55
    Period size: 9  Copynumber: 7.1  Consensus size: 9

      13860 CAAAATTATT

                      
      13870 ATTTTTGAAA
          1 ATTTTT-AAA

                     
      13880 ATTTTTAAA
          1 ATTTTTAAA

                      
      13889 A-TTTTAACA
          1 ATTTTTAA-A

            *          
      13898 TTTTTTATATA
          1 ATTTTTA-A-A

            *      * 
      13909 TTTTTTAGA
          1 ATTTTTAAA

                   * 
      13918 ATTTTTATA
          1 ATTTTTAAA

                     
      13927 ATTTTTAAA
          1 ATTTTTAAA

             
      13936 A
          1 A

      13937 ATATATATAA


Statistics
Matches: 48,  Mismatches: 6, Indels: 7
        0.79            0.10        0.11

Matches are distributed among these distances:
   8    6  0.12
   9   22  0.46
  10   11  0.23
  11    9  0.19

ACGTcount: A:0.37, C:0.01, G:0.03, T:0.58


Consensus pattern (9 bp):   
ATTTTTAAA

Found at i:13998 original size:19 final size:18

Alignment explanation


    Indices: 13958--14000  Score: 50
    Period size: 19  Copynumber: 2.3  Consensus size: 18

      13948 TTTTGATTTT

                 *         *  
      13958 TTTTATAAATATTTTTAA
          1 TTTTAAAAATATTTTGAA

                              *
      13976 TTTTAAAAATTATTTTGAG
          1 TTTTAAAAA-TATTTTGAA

                  
      13995 TTTTAA
          1 TTTTAA

      14001 GTAATTTTTG


Statistics
Matches: 21,  Mismatches: 3, Indels: 1
        0.84            0.12        0.04

Matches are distributed among these distances:
  18    8  0.38
  19   13  0.62

ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58


Consensus pattern (18 bp):   
TTTTAAAAATATTTTGAA
Done.