Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009349.1 Kokia drynarioides strain JFW-HI SEQ_124056, 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: 8079
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35


Found at i:3802 original size:16 final size:16

Alignment explanation


    Indices: 3781--3845  Score: 64
    Period size: 16  Copynumber: 4.1  Consensus size: 16

       3771 TTATATTTAG

                    *       
       3781 TATAATATGTTAGATT
          1 TATAATATTTTAGATT

                     *       
       3797 TATAATA-TATAGTATT
          1 TATAATATTTTAG-ATT

                             
       3813 TAT--TATTTCTAGATT
          1 TATAATATTT-TAGATT

                        *   
       3828 TATAATATTTTATATT
          1 TATAATATTTTAGATT

              
       3844 TA
          1 TA

       3846 ATAGTCTAAT


Statistics
Matches: 40,  Mismatches: 4, Indels: 10
        0.74            0.07        0.19

Matches are distributed among these distances:
  14    2  0.05
  15   10  0.25
  16   23  0.57
  17    5  0.12

ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55


Consensus pattern (16 bp):   
TATAATATTTTAGATT

Found at i:5217 original size:25 final size:24

Alignment explanation


    Indices: 5182--5234  Score: 70
    Period size: 24  Copynumber: 2.2  Consensus size: 24

       5172 ATCACGATTT

                  *                  
       5182 ATTTTTGAAAATAAAAATTATCTAA
          1 ATTTTTAAAAAT-AAAATTATCTAA

                           *      * 
       5207 ATTTTTAAAAATAAAGTTATCTCA
          1 ATTTTTAAAAATAAAATTATCTAA

                
       5231 ATTT
          1 ATTT

       5235 ATTTTTTAAA


Statistics
Matches: 25,  Mismatches: 3, Indels: 1
        0.86            0.10        0.03

Matches are distributed among these distances:
  24   14  0.56
  25   11  0.44

ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43


Consensus pattern (24 bp):   
ATTTTTAAAAATAAAATTATCTAA

Found at i:6313 original size:38 final size:37

Alignment explanation


    Indices: 6261--6365  Score: 115
    Period size: 36  Copynumber: 2.8  Consensus size: 37

       6251 AGTATCAAAC

                    *                             
       6261 AAATTATCTCAATTTATTTTTAAATTATTTTAAAAGAA
          1 AAATTATCACAATTTATTTTTAAATTATTTTAAAA-AA

                        *       *          **   * 
       6299 AAATTATCA-AAATT-TTTTAAAATTACTTTGGAAACA
          1 AAATTATCACAATTTATTTTTAAATTA-TTTTAAAAAA

                    *                      
       6335 AAATTATCCCAATTTATTTTTAAATTATTTT
          1 AAATTATCACAATTTATTTTTAAATTATTTT

       6366 TATTTTTTAC


Statistics
Matches: 54,  Mismatches: 10, Indels: 7
        0.76            0.14        0.10

Matches are distributed among these distances:
  36   19  0.35
  37   17  0.31
  38   18  0.33

ACGTcount: A:0.43, C:0.08, G:0.03, T:0.47


Consensus pattern (37 bp):   
AAATTATCACAATTTATTTTTAAATTATTTTAAAAAA
Done.