Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012094.1 Kokia drynarioides strain JFW-HI SEQ_127093, 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: 10174
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33


Found at i:8750 original size:30 final size:28

Alignment explanation


    Indices: 8715--9171  Score: 289
    Period size: 30  Copynumber: 15.5  Consensus size: 28

       8705 CGAAACGATA

                 *          *            
       8715 ATTTTGGGAAATTTGGAGTCAAAAATGGG
          1 ATTTTTGGAAATTTGGGGT-AAAAATGGG

                                       * *
       8744 ATTTTT-GAAAGTTTGGGGGTAAAAATAGA
          1 ATTTTTGGAAA-TTT-GGGGTAAAAATGGG

                        *                  
       8773 ATTTTT-GAATGTTTTGGGGTTAAAAATGGG
          1 ATTTTTGGAA--ATTTGGGG-TAAAAATGGG

                      *               * *
       8803 ATTTTTGGAAGTTTGGGGGTAAAAATAGA
          1 ATTTTTGGAAATTT-GGGGTAAAAATGGG

             *         *                  
       8832 AGTTTTGGAAGTTTTGGGGTTAAAAATGGG
          1 ATTTTTGGAA-ATTTGGGG-TAAAAATGGG

                      *  *            * *
       8862 ATTTTTGGAAGTTCGAGGGTAAAAATAGA
          1 ATTTTTGGAAATTTG-GGGTAAAAATGGG

                                           
       8891 ATTTTT-GAAAGTTTCGGGGTTAAAAATGGG
          1 ATTTTTGGAAA-TTT-GGGG-TAAAAATGGG

                      *               * *
       8921 ATTTTTGGAAGTTTAGGGGTAAAAATAGA
          1 ATTTTTGGAAATTT-GGGGTAAAAATGGG

                   *            *          
       8950 ATTTTT-AAAAGTTTTAGGGTTAAAAATGGG
          1 ATTTTTGGAAA--TTT-GGGGTAAAAATGGG

                      *  *            * *
       8980 ATTTTTGGAAGTTCGAGGGTAAAAATAGA
          1 ATTTTTGGAAATTTG-GGGTAAAAATGGG

              *                            
       9009 ATGTTT-GAAAGTTTCGGGGTTAAAAATGGG
          1 ATTTTTGGAAA-TTT-GGGG-TAAAAATGGG

                      *  *            * *
       9039 ATTTTTGGAAGTTCGAGGGTAAAAATAGA
          1 ATTTTTGGAAATTTG-GGGTAAAAATGGG

                                *          
       9068 ATTTTT-GAAAGTTTTAGGGTTAAAAATGGG
          1 ATTTTTGGAAA--TTT-GGGGTAAAAATGGG

                  *   *               * *
       9098 ATTTTTAGAAGTTTGGTGGTAAAAATAGA
          1 ATTTTTGGAAATTTGG-GGTAAAAATGGG

                                *          
       9127 ATTTTT-GAAAGTTTTGAGGTTAAAAATGGG
          1 ATTTTTGGAAA--TTTG-GGGTAAAAATGGG

                           
       9157 ATTTTTGGACAATTT
          1 ATTTTTGGA-AATTT

       9172 AGGGACTTAC


Statistics
Matches: 334,  Mismatches: 61, Indels: 65
        0.73            0.13        0.14

Matches are distributed among these distances:
  28   21  0.06
  29  143  0.43
  30  150  0.45
  31   18  0.05
  32    2  0.01

ACGTcount: A:0.34, C:0.02, G:0.28, T:0.36


Consensus pattern (28 bp):   
ATTTTTGGAAATTTGGGGTAAAAATGGG

Found at i:8799 original size:59 final size:59

Alignment explanation


    Indices: 8726--9165  Score: 682
    Period size: 59  Copynumber: 7.5  Consensus size: 59

       8716 TTTTGGGAAA

                 *  *                *                              *  
       8726 TTTGGAGTCAAAAATGGGATTTTTGAAAGTTTGGGGGTAAAAATAGAATTTTTGAATGT
          1 TTTGGGGTTAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATAGAATTTTTGAAAGT

                                                            *     *    
       8785 TTTGGGGTTAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATAGAAGTTTTGGAAGT
          1 TTTGGGGTTAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATAGAATTTTTGAAAGT

                                           * *                         
       8844 TTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATAGAATTTTTGAAAGT
          1 TTTGGGGTTAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATAGAATTTTTGAAAGT

              *                             *                    *     
       8903 TTCGGGGTTAAAAATGGGATTTTTGGAAGTTTAGGGGTAAAAATAGAATTTTTAAAAGT
          1 TTTGGGGTTAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATAGAATTTTTGAAAGT

               *                           * *               *         
       8962 TTTAGGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATAGAATGTTTGAAAGT
          1 TTTGGGGTTAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATAGAATTTTTGAAAGT

              *                            * *                         
       9021 TTCGGGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATAGAATTTTTGAAAGT
          1 TTTGGGGTTAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATAGAATTTTTGAAAGT

               *                    *         *                        
       9080 TTTAGGGTTAAAAATGGGATTTTTAGAAGTTTGGTGGTAAAAATAGAATTTTTGAAAGT
          1 TTTGGGGTTAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATAGAATTTTTGAAAGT

                *                      
       9139 TTTGAGGTTAAAAATGGGATTTTTGGA
          1 TTTGGGGTTAAAAATGGGATTTTTGGA

       9166 CAATTTAGGG


Statistics
Matches: 347,  Mismatches: 34, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  59  347  1.00

ACGTcount: A:0.34, C:0.01, G:0.29, T:0.36


Consensus pattern (59 bp):   
TTTGGGGTTAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATAGAATTTTTGAAAGT

Done.