Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001108.1 Kokia drynarioides strain JFW-HI SEQ_112388, 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, 862

Length: 1438
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32


Found at i:94 original size:59 final size:59

Alignment explanation


    Indices: 20--337  Score: 397
    Period size: 59  Copynumber: 5.4  Consensus size: 59

         10 ATTCGGGGAC

                            *      *                *       *       *   
         20 AAAATGGTAATTTTTGAAAGTTTTAAGGTCAAAAATGGAAATTTTGGAGGTTCGAGTGTA
          1 AAAATGG-AATTTTTGGAAGTTTCAAGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTA

                                   *     *                 *           
         80 AAAATGGAATTTTTGGAAGTTTCGAGGTCGAAAATGGAATTTTTGGAGGTTCGAGGGTA
          1 AAAATGGAATTTTTGGAAGTTTCAAGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTA

                                   *                                   
        139 AAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTA
          1 AAAATGGAATTTTTGGAAGTTTCAAGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTA

                     *               *  *        *             * *     
        198 AAAATGGAAATTTTGGAAGTTTCAATGTTAAAAATGGGATTTTTGGAAGTTTGGGGGT-
          1 AAAATGGAATTTTTGGAAGTTTCAAGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTA

                          *       * *            *       *   *         
        256 AAAATGGAATTTTTTGAAGTTTTAGGGTCAAAAATGGGATTTTTGAAAGCTCGAGGGTA
          1 AAAATGGAATTTTTGGAAGTTTCAAGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTA

                   *                
        315 AAAAT-GTATTTTTAGGACAGTTT
          1 AAAATGGAATTTTT-GGA-AGTTT

        338 AGGGACCTTT


Statistics
Matches: 228,  Mismatches: 27, Indels: 6
        0.87            0.10        0.02

Matches are distributed among these distances:
  58   55  0.24
  59  161  0.71
  60   12  0.05

ACGTcount: A:0.34, C:0.04, G:0.28, T:0.35


Consensus pattern (59 bp):   
AAAATGGAATTTTTGGAAGTTTCAAGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTA

Found at i:313 original size:30 final size:29

Alignment explanation


    Indices: 20--320  Score: 311
    Period size: 30  Copynumber: 10.2  Consensus size: 29

         10 ATTCGGGGAC

                            *     ** *     
         20 AAAATGGTAATTTTTGAAAGTTTTAAGGTCA
          1 AAAATGG-AATTTTTGGAAGTTCGAGGGT-A

                     *       *       *   
         51 AAAATGGAAATTTTGGAGGTTCGAGTGTA
          1 AAAATGGAATTTTTGGAAGTTCGAGGGTA

                                          *
         80 AAAATGGAATTTTTGGAAGTTTCGA-GGTCG
          1 AAAATGGAATTTTTGGAAG-TTCGAGGGT-A

                             *           
        110 AAAATGGAATTTTTGGAGGTTCGAGGGTA
          1 AAAATGGAATTTTTGGAAGTTCGAGGGTA

                                           
        139 AAAATGGAATTTTTGGAAGTTTCGA-GGTCA
          1 AAAATGGAATTTTTGGAAG-TTCGAGGGT-A

                                         
        169 AAAATGGAATTTTTGGAAGTTCGAGGGTA
          1 AAAATGGAATTTTTGGAAGTTCGAGGGTA

                     *             * * *  
        198 AAAATGGAAATTTTGGAAGTTTCAATGTTA
          1 AAAATGGAATTTTTGGAAG-TTCGAGGGTA

                   *             * *     
        228 AAAATGGGATTTTTGGAAGTTTGGGGGT-
          1 AAAATGGAATTTTTGGAAGTTCGAGGGTA

                          *      **       
        256 AAAATGGAATTTTTTGAAGTTTTAGGGTCA
          1 AAAATGGAATTTTTGGAAGTTCGAGGGT-A

                   *       *   *         
        286 AAAATGGGATTTTTGAAAGCTCGAGGGTA
          1 AAAATGGAATTTTTGGAAGTTCGAGGGTA

                  
        315 AAAATG
          1 AAAATG

        321 TATTTTTAGG


Statistics
Matches: 226,  Mismatches: 35, Indels: 20
        0.80            0.12        0.07

Matches are distributed among these distances:
  28   24  0.11
  29   81  0.36
  30  114  0.50
  31    7  0.03

ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34


Consensus pattern (29 bp):   
AAAATGGAATTTTTGGAAGTTCGAGGGTA
Done.