Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005818.1 Kokia drynarioides strain JFW-HI SEQ_120102, 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, 837

Length: 1395
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28


Found at i:544 original size:27 final size:27

Alignment explanation


    Indices: 506--561  Score: 112
    Period size: 27  Copynumber: 2.1  Consensus size: 27

        496 ATCACTAACT

                                       
        506 AATACTAATCTAATACTAATAGAATAG
          1 AATACTAATCTAATACTAATAGAATAG

                                       
        533 AATACTAATCTAATACTAATAGAATAG
          1 AATACTAATCTAATACTAATAGAATAG

              
        560 AA
          1 AA

        562 AAAATAGAAT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   29  1.00

ACGTcount: A:0.54, C:0.11, G:0.07, T:0.29


Consensus pattern (27 bp):   
AATACTAATCTAATACTAATAGAATAG

Found at i:546 original size:5 final size:6

Alignment explanation


    Indices: 503--553  Score: 56
    Period size: 6  Copynumber: 9.2  Consensus size: 6

        493 GGGATCACTA

                                          *      *                 
        503 ACTAAT ACTAAT -CTAAT ACTAAT A-GAAT A-GAAT ACTAAT -CTAAT
          1 ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT

                    
        547 ACTAAT A
          1 ACTAAT A

        554 GAATAGAAAA


Statistics
Matches: 40,  Mismatches: 2, Indels: 6
        0.83            0.04        0.12

Matches are distributed among these distances:
   5   19  0.47
   6   21  0.52

ACGTcount: A:0.51, C:0.14, G:0.04, T:0.31


Consensus pattern (6 bp):   
ACTAAT

Found at i:569 original size:14 final size:14

Alignment explanation


    Indices: 550--577  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

        540 ATCTAATACT

                          
        550 AATAGAATAGAAAA
          1 AATAGAATAGAAAA

                          
        564 AATAGAATAGAAAA
          1 AATAGAATAGAAAA

        578 TACTAATATA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14


Consensus pattern (14 bp):   
AATAGAATAGAAAA
Done.