Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007214.1 Kokia drynarioides strain JFW-HI SEQ_121828, 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: 5816
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34


Found at i:2522 original size:14 final size:14

Alignment explanation


    Indices: 2505--2543  Score: 51
    Period size: 14  Copynumber: 2.8  Consensus size: 14

       2495 TTCAATATTA

                *         
       2505 TTAAACATATATAT
          1 TTAATCATATATAT

                 *  *     
       2519 TTAATTATTTATAT
          1 TTAATCATATATAT

                       
       2533 TTAATCATATA
          1 TTAATCATATA

       2544 ATAAATTATT


Statistics
Matches: 20,  Mismatches: 5, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
  14   20  1.00

ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51


Consensus pattern (14 bp):   
TTAATCATATATAT

Found at i:2590 original size:16 final size:19

Alignment explanation


    Indices: 2542--2591  Score: 52
    Period size: 18  Copynumber: 2.6  Consensus size: 19

       2532 TTTAATCATA

                                
       2542 TAATAAATTATTAGTATAAT
          1 TAATAAATTATTAGTAT-AT

                                 
       2562 TAATATAATTTATTA-T-T-T
          1 TAATA-AA-TTATTAGTATAT

                        
       2580 TAATAAATTATT
          1 TAATAAATTATT

       2592 TAATATTTCA


Statistics
Matches: 28,  Mismatches: 0, Indels: 8
        0.78            0.00        0.22

Matches are distributed among these distances:
  16    5  0.18
  17    2  0.07
  18    6  0.21
  20    6  0.21
  21    3  0.11
  22    6  0.21

ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52


Consensus pattern (19 bp):   
TAATAAATTATTAGTATAT

Found at i:2700 original size:15 final size:15

Alignment explanation


    Indices: 2680--2737  Score: 53
    Period size: 15  Copynumber: 3.6  Consensus size: 15

       2670 ATTCAATATT

                           
       2680 AATATTTTAATAATA
          1 AATATTTTAATAATA

                           *   
       2695 AATATTTATTACAATTATA
          1 AATA-TT-TT--AATAATA

                 *  *      
       2714 AATATATTCATAATA
          1 AATATTTTAATAATA

                     
       2729 AATATTTTA
          1 AATATTTTA

       2738 TAGTATAAAA


Statistics
Matches: 33,  Mismatches: 6, Indels: 8
        0.70            0.13        0.17

Matches are distributed among these distances:
  15   16  0.48
  16    2  0.06
  17    4  0.12
  18    1  0.03
  19   10  0.30

ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47


Consensus pattern (15 bp):   
AATATTTTAATAATA

Found at i:3511 original size:7 final size:7

Alignment explanation


    Indices: 3501--3546  Score: 56
    Period size: 7  Copynumber: 6.6  Consensus size: 7

       3491 TAGATTTTGG

                 * 
       3501 ATTTCGA
          1 ATTTCAA

                   
       3508 ATTTCAA
          1 ATTTCAA

                   
       3515 ATTTCAA
          1 ATTTCAA

                ** 
       3522 ATTTTGA
          1 ATTTCAA

                *  
       3529 ATTTTAA
          1 ATTTCAA

                   
       3536 ATTTCAA
          1 ATTTCAA

                
       3543 ATTT
          1 ATTT

       3547 TTGATGTTTT


Statistics
Matches: 34,  Mismatches: 5, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
   7   34  1.00

ACGTcount: A:0.37, C:0.09, G:0.04, T:0.50


Consensus pattern (7 bp):   
ATTTCAA

Found at i:3547 original size:21 final size:21

Alignment explanation


    Indices: 3501--3547  Score: 76
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       3491 TAGATTTTGG

                *                
       3501 ATTTCGAATTTCAAATTTCAA
          1 ATTTTGAATTTCAAATTTCAA

                       *         
       3522 ATTTTGAATTTTAAATTTCAA
          1 ATTTTGAATTTCAAATTTCAA

                 
       3543 ATTTT
          1 ATTTT

       3548 TGATGTTTTA


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  21   24  1.00

ACGTcount: A:0.36, C:0.09, G:0.04, T:0.51


Consensus pattern (21 bp):   
ATTTTGAATTTCAAATTTCAA
Done.