Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000931.1 Kokia drynarioides strain JFW-HI SEQ_112082, 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: 7878
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34


Found at i:3134 original size:22 final size:22

Alignment explanation


    Indices: 3109--3152  Score: 61
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       3099 TGCAACAATT

                      *    *      
       3109 TGACATCTGTCTAAATTTTTAA
          1 TGACATCTGTATAAAATTTTAA

                    *             
       3131 TGACATCTTTATAAAATTTTAA
          1 TGACATCTGTATAAAATTTTAA

       3153 ATATATAGTA


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.36, C:0.11, G:0.07, T:0.45


Consensus pattern (22 bp):   
TGACATCTGTATAAAATTTTAA

Found at i:5946 original size:28 final size:29

Alignment explanation


    Indices: 5898--5958  Score: 72
    Period size: 29  Copynumber: 2.1  Consensus size: 29

       5888 ATCGGGGTCG

                                       * 
       5898 AAAATGAAGTTTCGAAGAG-TTTAGGGTT
          1 AAAATGAAGTTTCGAAGAGTTTTAGGGGT

                     *   *                
       5926 AAAATGAAATTTTGGAA-AGTTTTAGGGGT
          1 AAAATG-AAGTTTCGAAGAGTTTTAGGGGT

                
       5955 AAAA
          1 AAAA

       5959 ATATCATTTT


Statistics
Matches: 28,  Mismatches: 3, Indels: 3
        0.82            0.09        0.09

Matches are distributed among these distances:
  28    8  0.29
  29   20  0.71

ACGTcount: A:0.41, C:0.02, G:0.26, T:0.31


Consensus pattern (29 bp):   
AAAATGAAGTTTCGAAGAGTTTTAGGGGT

Found at i:6048 original size:30 final size:29

Alignment explanation


    Indices: 5993--6147  Score: 142
    Period size: 29  Copynumber: 5.3  Consensus size: 29

       5983 TAAAAACATG

                                         *
       5993 ATTTTTGGAAG-TACGAGGGCAAAAATGTG
          1 ATTTTTGGAAGTTA-GAGGGCAAAAATGTA

                  *            *          
       6022 ATTTTTAGAAGATTAGAGGACAAAAATGTA
          1 ATTTTTGGAAG-TTAGAGGGCAAAAATGTA

                                *         
       6052 ATTTTTGGAAGTTTA-AGGGTAAAAATGTA
          1 ATTTTTGGAAG-TTAGAGGGCAAAAATGTA

                      *                   
       6081 ATTTTTGGAACTTCA-AGGGC-AAAATGTA
          1 ATTTTTGGAAGTT-AGAGGGCAAAAATGTA

                   *             *      *  
       6109 ATTTTTAAGAAGTTTA-AGGGAAAAAATATA
          1 ATTTTT-GGAAG-TTAGAGGGCAAAAATGTA

                      
       6139 A-TTTTGGAA
          1 ATTTTTGGAA

       6148 AAGTTTAGGT


Statistics
Matches: 106,  Mismatches: 14, Indels: 13
        0.80            0.11        0.10

Matches are distributed among these distances:
  28   19  0.18
  29   49  0.46
  30   36  0.34
  31    2  0.02

ACGTcount: A:0.41, C:0.04, G:0.23, T:0.33


Consensus pattern (29 bp):   
ATTTTTGGAAGTTAGAGGGCAAAAATGTA

Found at i:6056 original size:88 final size:86

Alignment explanation


    Indices: 5955--6147  Score: 210
    Period size: 88  Copynumber: 2.2  Consensus size: 86

       5945 TTTTAGGGGT

                    *              **            *          *   *            
       5955 AAAAATATCATTTTAGGAAGATTCGGGGTAAAAACATGATTTTTGGAAGTACGAGGGCAAAAATG
          1 AAAAATATAATTTT-GGAAGATTAAGGGTAAAAACATAATTTTTGGAACTACAAGGGC-AAAATG

             *                      
       6020 TGATTTTT-AGAAGATT-AGAGGA
         64 TAATTTTTAAGAAGATTAAG-GGA

                   *             *             **              *             
       6042 CAAAAATGTAATTTTTGGAAGTTTAAGGGTAAAAATGTAATTTTTGGAACTTCAAGGGCAAAATG
          1 -AAAAATATAA-TTTTGGAAGATTAAGGGTAAAAACATAATTTTTGGAACTACAAGGGCAAAATG

                          *        
       6107 TAATTTTTAAGAAGTTTAAGGGA
         64 TAATTTTTAAGAAGATTAAGGGA

                              
       6130 AAAAATATAATTTTGGAA
          1 AAAAATATAATTTTGGAA

       6148 AAGTTTAGGT


Statistics
Matches: 88,  Mismatches: 14, Indels: 8
        0.80            0.13        0.07

Matches are distributed among these distances:
  86    8  0.09
  87   22  0.25
  88   52  0.59
  89    6  0.07

ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32


Consensus pattern (86 bp):   
AAAAATATAATTTTGGAAGATTAAGGGTAAAAACATAATTTTTGGAACTACAAGGGCAAAATGTA
ATTTTTAAGAAGATTAAGGGA

Done.