Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002556.1 Kokia drynarioides strain JFW-HI SEQ_114752, 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: 8329
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.37

Warning! 10 characters in sequence are not A, C, G, or T


Found at i:2087 original size:29 final size:31

Alignment explanation


    Indices: 2054--2113  Score: 79
    Period size: 29  Copynumber: 2.0  Consensus size: 31

       2044 AATTTTGATT

                        *                  
       2054 ATTTTGAATTTTTAAGG-TTTT-GATATTTA
          1 ATTTTGAATTTTCAAGGATTTTGGATATTTA

                 *        *                
       2083 ATTTTTAATTTTCATGGATTTTGGATATTTA
          1 ATTTTGAATTTTCAAGGATTTTGGATATTTA

       2114 TGTTTTAATT


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  29   14  0.54
  30    4  0.15
  31    8  0.31

ACGTcount: A:0.27, C:0.02, G:0.13, T:0.58


Consensus pattern (31 bp):   
ATTTTGAATTTTCAAGGATTTTGGATATTTA

Found at i:7093 original size:30 final size:30

Alignment explanation


    Indices: 7032--7348  Score: 325
    Period size: 30  Copynumber: 10.7  Consensus size: 30

       7022 TTCAAAGACG

                                            
       7032 AAAATGGAGA-TTTTGGAAG-TTCGAGGG-CA
          1 AAAATGGA-ATTTTTGGAAGTTTCG-GGGTCA

                 *        *           *   
       7061 AAAATTGAATTTTTTGAAGTTTCGGGATCA
          1 AAAATGGAATTTTTGGAAGTTTCGGGGTCA

                   *                        
       7091 AAAATGGCATTTTTGGAAG-TTCGAGGGGT-A
          1 AAAATGGAATTTTTGGAAGTTTC--GGGGTCA

                           *              
       7121 AAAATGGAA-TTTTGAAAGTTTCGGGGTC-
          1 AAAATGGAATTTTTGGAAGTTTCGGGGTCA

                                          
       7149 AAAATGGAATTTTTGGAAGTTTCGGGGTCA
          1 AAAATGGAATTTTTGGAAGTTTCGGGGTCA

                               *   *  *    
       7179 AAAAT-GAGATTTTTGGAAATTTTGGTGT-A
          1 AAAATGGA-ATTTTTGGAAGTTTCGGGGTCA

                 *        *             * 
       7208 AAAATAGAATTTTTTGAAGTTTCGGGGTTA
          1 AAAATGGAATTTTTGGAAGTTTCGGGGTCA

                   *              *       
       7238 AAAATGGGATTTTTGGAAGTTTGGGGGT-A
          1 AAAATGGAATTTTTGGAAGTTTCGGGGTCA

                    *             *     * 
       7267 AAAATGGATTTTTTGGAAGTTTTGGGGTTA
          1 AAAATGGAATTTTTGGAAGTTTCGGGGTCA

                                *         * 
       7297 AAAAT-GAGATTTTTGGAA-ATTCGAGGGTAA
          1 AAAATGGA-ATTTTTGGAAGTTTCG-GGGTCA

                                  
       7327 AAAATGGAATTTTTGGAAGTTT
          1 AAAATGGAATTTTTGGAAGTTT

       7349 TAGGGACCTC


Statistics
Matches: 242,  Mismatches: 29, Indels: 32
        0.80            0.10        0.11

Matches are distributed among these distances:
  28   15  0.06
  29  101  0.42
  30  118  0.49
  31    8  0.03

ACGTcount: A:0.32, C:0.04, G:0.28, T:0.35


Consensus pattern (30 bp):   
AAAATGGAATTTTTGGAAGTTTCGGGGTCA

Found at i:7105 original size:59 final size:59

Alignment explanation


    Indices: 7032--7348  Score: 326
    Period size: 59  Copynumber: 5.4  Consensus size: 59

       7022 TTCAAAGACG

                                          *               *           *   
       7032 AAAATGGAGA-TTTTGGAAG-TTCGAGGG-CAAAAATTGAATTTTTTGAAGTTTCGGGATCA
          1 AAAATGGA-ATTTTTGGAAGTTTCG-GGGTTAAAAATTGAATTTTTGGAAGTTTCGGGGT-A

                   *                    *       *         *            *
       7091 AAAATGGCATTTTTGGAAG-TTCGAGGGGTAAAAATGGAA-TTTTGAAAGTTTCGGGGTC
          1 AAAATGGAATTTTTGGAAGTTTCG-GGGTTAAAAATTGAATTTTTGGAAGTTTCGGGGTA

                                        *                    *   *  *   
       7149 AAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAA-TGAGATTTTTGGAAATTTTGGTGTA
          1 AAAATGGAATTTTTGGAAGTTTCGGGGTTAAAAATTGA-ATTTTTGGAAGTTTCGGGGTA

                 *        *                    * *              *      
       7208 AAAATAGAATTTTTTGAAGTTTCGGGGTTAAAAATGGGATTTTTGGAAGTTTGGGGGTA
          1 AAAATGGAATTTTTGGAAGTTTCGGGGTTAAAAATTGAATTTTTGGAAGTTTCGGGGTA

                    *             *                           *           
       7267 AAAATGGATTTTTTGGAAGTTTTGGGGTTAAAAA-TGAGATTTTTGGAA-ATTCGAGGGTAA
          1 AAAATGGAATTTTTGGAAGTTTCGGGGTTAAAAATTGA-ATTTTTGGAAGTTTCG-GGGT-A

                                  
       7327 AAAATGGAATTTTTGGAAGTTT
          1 AAAATGGAATTTTTGGAAGTTT

       7349 TAGGGACCTC


Statistics
Matches: 216,  Mismatches: 33, Indels: 17
        0.81            0.12        0.06

Matches are distributed among these distances:
  57    2  0.01
  58   32  0.15
  59  150  0.69
  60   32  0.15

ACGTcount: A:0.32, C:0.04, G:0.28, T:0.35


Consensus pattern (59 bp):   
AAAATGGAATTTTTGGAAGTTTCGGGGTTAAAAATTGAATTTTTGGAAGTTTCGGGGTA
Done.