Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009229.1 Kokia drynarioides strain JFW-HI SEQ_123934, 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, 680

Length: 1134
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.35


Found at i:42 original size:29 final size:30

Alignment explanation


    Indices: 4--129  Score: 96
    Period size: 29  Copynumber: 4.3  Consensus size: 30

          1 TTT

                            *       *     
          4 TGGAAGTTTTGAGG-TCAAAATGGGATTTG
          1 TGGAAGTTTTGAGGTTAAAAATGGAATTTG

                       *                 *
         33 TGGAAGTTTTGGGGTTAAAAATGGAATTTT
          1 TGGAAGTTTTGAGGTTAAAAATGGAATTTG

                     * *  **      *      *
         63 TGGAAG-TTCGGGGAAAAAAATAGAATTTT
          1 TGGAAGTTTTGAGGTTAAAAATGGAATTTG

                      *     *        *    *
         92 TGGAAG-TTTCAGGGTCAAAAATGGGATTTT
          1 TGGAAGTTTTGA-GGTTAAAAATGGAATTTG

                    
        122 TGGAAGTT
          1 TGGAAGTT

        130 CATAGATAAA


Statistics
Matches: 79,  Mismatches: 15, Indels: 4
        0.81            0.15        0.04

Matches are distributed among these distances:
  29   40  0.51
  30   38  0.48
  31    1  0.01

ACGTcount: A:0.32, C:0.03, G:0.31, T:0.34


Consensus pattern (30 bp):   
TGGAAGTTTTGAGGTTAAAAATGGAATTTG

Found at i:56 original size:30 final size:30

Alignment explanation


    Indices: 1--129  Score: 136
    Period size: 30  Copynumber: 4.4  Consensus size: 30

                        * *    *       *  
          1 TTTTGGAAGTTTTGAGG-TCAAAATGGGAT
          1 TTTTGGAAGTTTCGGGGTTAAAAATGGAAT

              *         *                 
         30 TTGTGGAAGTTTTGGGGTTAAAAATGGAAT
          1 TTTTGGAAGTTTCGGGGTTAAAAATGGAAT

                             **      *    
         60 TTTTGGAAG-TTCGGGGAAAAAAATAGAAT
          1 TTTTGGAAGTTTCGGGGTTAAAAATGGAAT

                         *    *        *  
         89 TTTTGGAAGTTTCAGGGTCAAAAATGGGAT
          1 TTTTGGAAGTTTCGGGGTTAAAAATGGAAT

                       
        119 TTTTGGAAGTT
          1 TTTTGGAAGTT

        130 CATAGATAAA


Statistics
Matches: 84,  Mismatches: 14, Indels: 3
        0.83            0.14        0.03

Matches are distributed among these distances:
  29   40  0.48
  30   44  0.52

ACGTcount: A:0.31, C:0.03, G:0.30, T:0.36


Consensus pattern (30 bp):   
TTTTGGAAGTTTCGGGGTTAAAAATGGAAT

Found at i:140 original size:29 final size:28

Alignment explanation


    Indices: 48--156  Score: 110
    Period size: 29  Copynumber: 3.8  Consensus size: 28

         38 GTTTTGGGGT

                                     *   
         48 TAAAAATGGAATTTTTGGAAGTTCGGGGA
          1 TAAAAATGGAATTTTTGGAAGTTC-AGGA

            *      *                    *
         77 AAAAAATAGAATTTTTGGAAGTTTCAGGG
          1 TAAAAATGGAATTTTTGGAAG-TTCAGGA

                      *                *  
        106 TCAAAAATGGGATTTTTGGAAGTTCATAGA
          1 T-AAAAATGGAATTTTTGGAAGTTCA-GGA

                    *       *    
        136 TAAAAATGAAATTTTTCGAAG
          1 TAAAAATGGAATTTTTGGAAG

        157 GTTTAAGGAC


Statistics
Matches: 65,  Mismatches: 12, Indels: 6
        0.78            0.14        0.07

Matches are distributed among these distances:
  29   42  0.65
  30   23  0.35

ACGTcount: A:0.39, C:0.05, G:0.24, T:0.32


Consensus pattern (28 bp):   
TAAAAATGGAATTTTTGGAAGTTCAGGA

Found at i:141 original size:59 final size:59

Alignment explanation


    Indices: 28--156  Score: 152
    Period size: 59  Copynumber: 2.2  Consensus size: 59

         18 TCAAAATGGG

                *         **    *                       * *             
         28 ATTTGTGGAAGTTTTGGGGTTAAAAATGGAATTTTTGGAAGTTCGGGGAAAAAAAT-AGA
          1 ATTTTTGGAAGTTTCAGGGTCAAAAATGGAATTTTTGGAAGTTCAGAGAAAAAAATGA-A

                                         *               *   *         
         87 ATTTTTGGAAGTTTCAGGGTCAAAAATGGGATTTTTGGAAGTTCATAGATAAAAATGAA
          1 ATTTTTGGAAGTTTCAGGGTCAAAAATGGAATTTTTGGAAGTTCAGAGAAAAAAATGAA

                  *    
        146 ATTTTTCGAAG
          1 ATTTTTGGAAG

        157 GTTTAAGGAC


Statistics
Matches: 59,  Mismatches: 10, Indels: 2
        0.83            0.14        0.03

Matches are distributed among these distances:
  59   58  0.98
  60    1  0.02

ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34


Consensus pattern (59 bp):   
ATTTTTGGAAGTTTCAGGGTCAAAAATGGAATTTTTGGAAGTTCAGAGAAAAAAATGAA
Done.