Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000098.1 Kokia drynarioides strain JFW-HI SEQ_110729, 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: 1765
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37


Found at i:976 original size:41 final size:41

Alignment explanation


    Indices: 919--1112  Score: 210
    Period size: 41  Copynumber: 4.7  Consensus size: 41

        909 TTGTATAAAT

                                             *   *   
        919 GGAAGACTCATGTCTCGAAATGAGAATAAGATTTTGACTAA
          1 GGAAGACTCATGTCTCGAAATGAGAATAAGATTATGATTAA

                                      **         *   
        960 GGAAGACTCATGTCTCGAAATGAGAACGAGATTATGAATAA
          1 GGAAGACTCATGTCTCGAAATGAGAATAAGATTATGATTAA

            *        *     *           *     *       
       1001 AGAAGACTCGTGTCTTGAAATGAGAATGAGATTTTGATTAA
          1 GGAAGACTCATGTCTCGAAATGAGAATAAGATTATGATTAA

                              **      *    *    *     
       1042 GGAAGACTCATGTCTCGAGTTGAGAACAAGAATATGGTTAAA
          1 GGAAGACTCATGTCTCGAAATGAGAATAAGATTATGATT-AA

                    *   *           *     
       1084 GGAAGACTTATGACTCGAAA-GAGCATAAG
          1 GGAAGACTCATGTCTCGAAATGAGAATAAG

       1113 GTTGTTTTCA


Statistics
Matches: 126,  Mismatches: 26, Indels: 2
        0.82            0.17        0.01

Matches are distributed among these distances:
  41  108  0.86
  42   18  0.14

ACGTcount: A:0.39, C:0.11, G:0.25, T:0.25


Consensus pattern (41 bp):   
GGAAGACTCATGTCTCGAAATGAGAATAAGATTATGATTAA

Found at i:1033 original size:82 final size:83

Alignment explanation


    Indices: 873--1112  Score: 261
    Period size: 82  Copynumber: 2.9  Consensus size: 83

        863 GGTGTATGAA

                                ***    * **         *                        
        873 TAAGGAAGACTCATGTCTCGGGTTGAGCATGAGAA-ATTGTATAAATGGAAGACTCATGTCTCGA
          1 TAAGGAAGACTCATGTCTCGAAATGAGAACAAGAATA-TGAATAAA-GGAAGACTCATGTCTCGA

                                
        937 AATGAGAATAAGATTTTGAC
         64 AATGAGAATAAGATTTTGAC

                                          *   *                   *     *    
        957 TAAGGAAGACTCATGTCTCGAAATGAGAACGAGATTATGAATAAA-GAAGACTCGTGTCTTGAAA
          1 TAAGGAAGACTCATGTCTCGAAATGAGAACAAGAATATGAATAAAGGAAGACTCATGTCTCGAAA

                   *         *
       1021 TGAGAATGAGATTTTGAT
         66 TGAGAATAAGATTTTGAC

                                 **                **            *   *       
       1039 TAAGGAAGACTCATGTCTCGAGTTGAGAACAAGAATATGGTTAAAGGAAGACTTATGACTCGAAA
          1 TAAGGAAGACTCATGTCTCGAAATGAGAACAAGAATATGAATAAAGGAAGACTCATGTCTCGAAA

                *     
       1104 -GAGCATAAG
         66 TGAGAATAAG

       1113 GTTGTTTTCA


Statistics
Matches: 131,  Mismatches: 23, Indels: 6
        0.82            0.14        0.04

Matches are distributed among these distances:
  82   79  0.60
  83   15  0.11
  84   36  0.27
  85    1  0.01

ACGTcount: A:0.38, C:0.11, G:0.25, T:0.25


Consensus pattern (83 bp):   
TAAGGAAGACTCATGTCTCGAAATGAGAACAAGAATATGAATAAAGGAAGACTCATGTCTCGAAA
TGAGAATAAGATTTTGAC
Done.