Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002596.1 Kokia drynarioides strain JFW-HI SEQ_114805, 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: 4239
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38


Found at i:304 original size:13 final size:14

Alignment explanation


    Indices: 283--315  Score: 50
    Period size: 13  Copynumber: 2.4  Consensus size: 14

        273 ATAGCTTTAC

                *         
        283 TAATTTTTAGAAA-
          1 TAATATTTAGAAAG

                          
        296 TAATATTTAGAAAG
          1 TAATATTTAGAAAG

                  
        310 TAATAT
          1 TAATAT

        316 GTGCATAAAC


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  13   12  0.67
  14    6  0.33

ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42


Consensus pattern (14 bp):   
TAATATTTAGAAAG

Found at i:2531 original size:9 final size:9

Alignment explanation


    Indices: 2517--2574  Score: 57
    Period size: 9  Copynumber: 6.4  Consensus size: 9

       2507 ATTAAAATTA

                     
       2517 TTTAATAAT
          1 TTTAATAAT

                     
       2526 TTTAATAAT
          1 TTTAATAAT

                     
       2535 TTT-AT-AT
          1 TTTAATAAT

              *  *   
       2542 TTAAAAAAT
          1 TTTAATAAT

               *       
       2551 AATATAATAAT
          1 --TTTAATAAT

                     
       2562 TTTAATAAT
          1 TTTAATAAT

                
       2571 TTTA
          1 TTTA

       2575 TATTTCAAAA


Statistics
Matches: 39,  Mismatches: 6, Indels: 8
        0.74            0.11        0.15

Matches are distributed among these distances:
   7    4  0.10
   8    3  0.08
   9   26  0.67
  11    6  0.15

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (9 bp):   
TTTAATAAT

Found at i:2559 original size:36 final size:37

Alignment explanation


    Indices: 2510--2605  Score: 140
    Period size: 36  Copynumber: 2.6  Consensus size: 37

       2500 ATTAAAAATT

                 *                               
       2510 AAAATTATTTAATAATTTTAATAATTTTATATTT-AA
          1 AAAATAATTTAATAATTTTAATAATTTTATATTTAAA

                    *                             
       2546 AAAATAATATAATAATTTTAATAATTTTATATTTCAAA
          1 AAAATAATTTAATAATTTTAATAATTTTATATTT-AAA

                           *      
       2584 AAAATAATTTTAATAGTTTTAA
          1 AAAATAA-TTTAATAATTTTAA

       2606 AATCATTTGC


Statistics
Matches: 53,  Mismatches: 4, Indels: 3
        0.88            0.07        0.05

Matches are distributed among these distances:
  36   32  0.60
  38    9  0.17
  39   12  0.23

ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48


Consensus pattern (37 bp):   
AAAATAATTTAATAATTTTAATAATTTTATATTTAAA

Found at i:3604 original size:16 final size:16

Alignment explanation


    Indices: 3583--3618  Score: 54
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       3573 ATTAAAAAAA

                          * 
       3583 AAATTAAACTCTAAGT
          1 AAATTAAACTCTAAAT

                      *     
       3599 AAATTAAACTTTAAAT
          1 AAATTAAACTCTAAAT

                
       3615 AAAT
          1 AAAT

       3619 AAATGCATCG


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  16   18  1.00

ACGTcount: A:0.56, C:0.08, G:0.03, T:0.33


Consensus pattern (16 bp):   
AAATTAAACTCTAAAT
Done.