Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012889.1 Kokia drynarioides strain JFW-HI SEQ_127903, 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: 4692
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.38

Warning! 50 characters in sequence are not A, C, G, or T


Found at i:1536 original size:29 final size:29

Alignment explanation


    Indices: 1499--1554  Score: 85
    Period size: 29  Copynumber: 1.9  Consensus size: 29

       1489 TAACTATTTG

                *      *                 
       1499 AACTGATTAATTACATTACAAAAATATTA
          1 AACTAATTAATAACATTACAAAAATATTA

                              *        
       1528 AACTAATTAATAACATTATAAAAATAT
          1 AACTAATTAATAACATTACAAAAATAT

       1555 AGAAAATAAA


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  29   24  1.00

ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34


Consensus pattern (29 bp):   
AACTAATTAATAACATTACAAAAATATTA

Found at i:2172 original size:18 final size:19

Alignment explanation


    Indices: 2149--2207  Score: 61
    Period size: 18  Copynumber: 3.3  Consensus size: 19

       2139 GGCGTTCAAT

                               
       2149 ATTTATATTTT-TTTGTTA
          1 ATTTATATTTTATTTGTTA

                  *        *   
       2167 ATTTATTTTTTATTTTTTA
          1 ATTTATATTTTATTTGTTA

                 *       *     
       2186 A-TTAAATTTTATCT-TTA
          1 ATTTATATTTTATTTGTTA

                 
       2203 ATTTA
          1 ATTTA

       2208 AAAAAATTAA


Statistics
Matches: 34,  Mismatches: 5, Indels: 4
        0.79            0.12        0.09

Matches are distributed among these distances:
  17    4  0.12
  18   23  0.68
  19    7  0.21

ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69


Consensus pattern (19 bp):   
ATTTATATTTTATTTGTTA

Found at i:3691 original size:18 final size:20

Alignment explanation


    Indices: 3654--3692  Score: 55
    Period size: 18  Copynumber: 2.0  Consensus size: 20

       3644 AAAATGGAAT

                                 
       3654 TTTTTTATTTAAGTATTTTAA
          1 TTTTTTATTTAAG-ATTTTAA

                                
       3675 TTTTTT-TTTAA-ATTTTAA
          1 TTTTTTATTTAAGATTTTAA

       3693 ATTAGTAAAG


Statistics
Matches: 18,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  18    7  0.39
  20    5  0.28
  21    6  0.33

ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69


Consensus pattern (20 bp):   
TTTTTTATTTAAGATTTTAA

Found at i:4059 original size:18 final size:20

Alignment explanation


    Indices: 4022--4060  Score: 55
    Period size: 18  Copynumber: 2.0  Consensus size: 20

       4012 AAAATGGAAT

                                 
       4022 TTTTTTATTTAAGTATTTTAA
          1 TTTTTTATTTAAG-ATTTTAA

                                
       4043 TTTTTT-TTTAA-ATTTTAA
          1 TTTTTTATTTAAGATTTTAA

       4061 ATTAGTAAAG


Statistics
Matches: 18,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  18    7  0.39
  20    5  0.28
  21    6  0.33

ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69


Consensus pattern (20 bp):   
TTTTTTATTTAAGATTTTAA
Done.