Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008460.1 Kokia drynarioides strain JFW-HI SEQ_123135, 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: 5566
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28


Found at i:655 original size:174 final size:176

Alignment explanation


    Indices: 365--712  Score: 628
    Period size: 174  Copynumber: 2.0  Consensus size: 176

        355 ATCTATTTTC

                                                                             
        365 CTTTTGCCAATTATCTATGGAGCTTCCAAATTGTGCTCCAATGCATAAACCATAACCAATAAGAA
          1 CTTTTGCCAATTATCTATGGAGCTTCCAAATTGTGCTCCAATGCATAAACCATAACCAATAAGAA

                                       *          *                 *        
        430 TCTCAAATTTCCCCCACTCTCATTTTTTTATAAAGCCAGAAGCCCACAGATTCCAACTGATACAG
         66 TCTCAAATTTCCCCCACTCTCATTTTTCTATAAAGCCAAAAGCCCACAGATTCCAAATGATACAG

                                                          
        495 TT-CAAGCACAATGAAGTGAAGTAATTGGGGC-ACAGGCTTTGCAG
        131 TTACAAGCACAATGAAGTGAAGTAATTGGGGCAACAGGCTTTGCAG

                                                                             
        539 CTTTTGCCAATTATCTATGGAGCTTCCAAATTGTGCTCCAATGCATAAACCATAACCAATAAGAA
          1 CTTTTGCCAATTATCTATGGAGCTTCCAAATTGTGCTCCAATGCATAAACCATAACCAATAAGAA

                *                           *                               *
        604 TCTCGAATTTCCCCCACTCTCATTTTTCTATAGAGCCAAAAGCCCACAGATTCCAAATGATACAT
         66 TCTCAAATTTCCCCCACTCTCATTTTTCTATAAAGCCAAAAGCCCACAGATTCCAAATGATACAG

                                                        
        669 TTACAAGCACAATGAAGTGAAGTAATTGGGGCAACAGGCTTTGC
        131 TTACAAGCACAATGAAGTGAAGTAATTGGGGCAACAGGCTTTGC

        713 GCCTTTTCAG


Statistics
Matches: 166,  Mismatches: 6, Indels: 2
        0.95            0.03        0.01

Matches are distributed among these distances:
 174  126  0.76
 175   29  0.17
 176   11  0.07

ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28


Consensus pattern (176 bp):   
CTTTTGCCAATTATCTATGGAGCTTCCAAATTGTGCTCCAATGCATAAACCATAACCAATAAGAA
TCTCAAATTTCCCCCACTCTCATTTTTCTATAAAGCCAAAAGCCCACAGATTCCAAATGATACAG
TTACAAGCACAATGAAGTGAAGTAATTGGGGCAACAGGCTTTGCAG

Found at i:3492 original size:30 final size:31

Alignment explanation


    Indices: 3428--3499  Score: 96
    Period size: 30  Copynumber: 2.4  Consensus size: 31

       3418 AAGCCAAGAG

                                       *   
       3428 GACTGTTTTGTCACTTTTCGATAACTTTAGT
          1 GACTGTTTTGTCACTTTTCGATAACTTGAGT

                                             
       3459 GACTGTTTTGTCACATTTTC-A-AAGC-TGAGT
          1 GACTGTTTTGTCAC-TTTTCGATAA-CTTGAGT

                       
       3489 GACTGTTTTGT
          1 GACTGTTTTGT

       3500 TAAATATAAC


Statistics
Matches: 38,  Mismatches: 1, Indels: 5
        0.86            0.02        0.11

Matches are distributed among these distances:
  30   17  0.45
  31   16  0.42
  32    5  0.13

ACGTcount: A:0.19, C:0.15, G:0.19, T:0.46


Consensus pattern (31 bp):   
GACTGTTTTGTCACTTTTCGATAACTTGAGT
Done.