Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011730.1 Kokia drynarioides strain JFW-HI SEQ_126724, 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: 11219
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32

Warning! 6 characters in sequence are not A, C, G, or T


Found at i:411 original size:29 final size:29

Alignment explanation


    Indices: 378--444  Score: 125
    Period size: 29  Copynumber: 2.3  Consensus size: 29

        368 ATAAAAACCC

                                         
        378 AACTGTATATGTATAATAATTGAATTAGA
          1 AACTGTATATGTATAATAATTGAATTAGA

                                         
        407 AACTGTATATGTATAATAATTGAATTAGA
          1 AACTGTATATGTATAATAATTGAATTAGA

              *      
        436 AATTGTATA
          1 AACTGTATA

        445 ATTTAACTCT


Statistics
Matches: 37,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  29   37  1.00

ACGTcount: A:0.45, C:0.03, G:0.13, T:0.39


Consensus pattern (29 bp):   
AACTGTATATGTATAATAATTGAATTAGA

Found at i:2035 original size:18 final size:18

Alignment explanation


    Indices: 2001--2043  Score: 52
    Period size: 18  Copynumber: 2.3  Consensus size: 18

       1991 GATATTTTCA

                             * 
       2001 TGCATTTTTTTACTGTCCC
          1 TGCATTTTTTTA-TGTCAC

                               
       2020 TGCATTTTATTT-TGTCAC
          1 TGCATTTT-TTTATGTCAC

                  
       2038 TGCATT
          1 TGCATT

       2044 CCTTTTGTTA


Statistics
Matches: 22,  Mismatches: 1, Indels: 3
        0.85            0.04        0.12

Matches are distributed among these distances:
  18   11  0.50
  19    8  0.36
  20    3  0.14

ACGTcount: A:0.14, C:0.21, G:0.12, T:0.53


Consensus pattern (18 bp):   
TGCATTTTTTTATGTCAC

Found at i:3647 original size:20 final size:20

Alignment explanation


    Indices: 3622--3661  Score: 80
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       3612 GCAAAGCAAG

                                
       3622 AGGAACGATTAAGGAATAGT
          1 AGGAACGATTAAGGAATAGT

                                
       3642 AGGAACGATTAAGGAATAGT
          1 AGGAACGATTAAGGAATAGT

       3662 CCTAGTAGTC


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.45, C:0.05, G:0.30, T:0.20


Consensus pattern (20 bp):   
AGGAACGATTAAGGAATAGT

Found at i:4236 original size:13 final size:14

Alignment explanation


    Indices: 4204--4237  Score: 54
    Period size: 14  Copynumber: 2.6  Consensus size: 14

       4194 TACTTTCAGT

                          
       4204 ACAT-TGACATTTA
          1 ACATCTGACATTTA

                          
       4217 ACATCTGACATTTA
          1 ACATCTGACATTTA

                    
       4231 AC-TCTGA
          1 ACATCTGA

       4238 TTGCTTGGCA


Statistics
Matches: 20,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  13    9  0.45
  14   11  0.55

ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35


Consensus pattern (14 bp):   
ACATCTGACATTTA
Done.