Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006860.1 Kokia drynarioides strain JFW-HI SEQ_121459, 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: 7831
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33


Found at i:3352 original size:29 final size:29

Alignment explanation


    Indices: 3320--3385  Score: 89
    Period size: 29  Copynumber: 2.3  Consensus size: 29

       3310 AAAAATCATG

                 *                        
       3320 TTTTTGTAATTAATCTATTTTTTA-TATTA
          1 TTTTTATAATTAATC-ATTTTTTAGTATTA

                    *                    
       3349 TTTTTATATTTAATCATTTTTTAGTATTA
          1 TTTTTATAATTAATCATTTTTTAGTATTA

            *       
       3378 CTTTTATA
          1 TTTTTATA

       3386 TATATATAAA


Statistics
Matches: 33,  Mismatches: 3, Indels: 2
        0.87            0.08        0.05

Matches are distributed among these distances:
  28    8  0.24
  29   25  0.76

ACGTcount: A:0.27, C:0.05, G:0.03, T:0.65


Consensus pattern (29 bp):   
TTTTTATAATTAATCATTTTTTAGTATTA

Found at i:3386 original size:29 final size:29

Alignment explanation


    Indices: 3329--3386  Score: 91
    Period size: 29  Copynumber: 2.0  Consensus size: 29

       3319 GTTTTTGTAA

                                *        
       3329 TTAATCTATTTTTTATATTATTTTTATAT
          1 TTAATCTATTTTTTATATTACTTTTATAT

                                          
       3358 TTAATC-ATTTTTTAGTATTACTTTTATAT
          1 TTAATCTATTTTTTA-TATTACTTTTATAT

       3387 ATATATAAAA


Statistics
Matches: 27,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  28    8  0.30
  29   19  0.70

ACGTcount: A:0.28, C:0.05, G:0.02, T:0.66


Consensus pattern (29 bp):   
TTAATCTATTTTTTATATTACTTTTATAT

Found at i:6246 original size:12 final size:12

Alignment explanation


    Indices: 6229--6261  Score: 57
    Period size: 12  Copynumber: 2.8  Consensus size: 12

       6219 AATTTTTATA

                        
       6229 AATTATTAATAC
          1 AATTATTAATAC

                       *
       6241 AATTATTAATAT
          1 AATTATTAATAC

                     
       6253 AATTATTAA
          1 AATTATTAA

       6262 ATTATTCATC


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  12   20  1.00

ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45


Consensus pattern (12 bp):   
AATTATTAATAC
Done.