Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000474.1 Kokia drynarioides strain JFW-HI SEQ_111348, 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: 2753
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32


Found at i:189 original size:36 final size:36

Alignment explanation


    Indices: 109--342  Score: 145
    Period size: 36  Copynumber: 6.5  Consensus size: 36

         99 AGAGTTTATA

                         *     * *      *   *   *
        109 TCTCGGTTAGAGCATAATGTTGTGTG-ATTGCATACA
          1 TCTCGGTTAGAGCGTAATGCTATG-GAAATGCTTACG

               *         *  *                   
        145 TCTTGGTTAGAGCATATTGCTATGGAAATGCTTACG
          1 TCTCGGTTAGAGCGTAATGCTATGGAAATGCTTACG

                        *          *       *    *
        181 TCTCGGTTAGAGTGTAATG-TAAAGGAAATGGTTACT
          1 TCTCGGTTAGAGCGTAATGCT-ATGGAAATGCTTACG

                        *        *      * * *   *
        217 TCTCGGTTAGAGTGTAATGCTGTGTG-ATTACATACA
          1 TCTCGGTTAGAGCGTAATGCTATG-GAAATGCTTACG

                *           * *     *            
        253 TCTCAGTTAGAGCGTATTTCTAT-AAAAGTGCTTACG
          1 TCTCGGTTAGAGCGTAATGCTATGGAAA-TGCTTACG

               **                  *             
        289 TCTTAGTTAGAGCGTAATGCTA-AGAAAGTGCTTACG
          1 TCTCGGTTAGAGCGTAATGCTATGGAAA-TGCTTACG

               *              
        325 TCTTGGTTAGAGCGTAAT
          1 TCTCGGTTAGAGCGTAAT

        343 TCTAAAGAAG


Statistics
Matches: 155,  Mismatches: 36, Indels: 14
        0.76            0.18        0.07

Matches are distributed among these distances:
  35    3  0.02
  36  150  0.97
  37    2  0.01

ACGTcount: A:0.27, C:0.13, G:0.25, T:0.35


Consensus pattern (36 bp):   
TCTCGGTTAGAGCGTAATGCTATGGAAATGCTTACG

Found at i:298 original size:108 final size:108

Alignment explanation


    Indices: 109--342  Score: 285
    Period size: 108  Copynumber: 2.2  Consensus size: 108

         99 AGAGTTTATA

                         *     *         *         **                   *    
        109 TCTCGGTTAGAGCATAATGTTGTGTGATTGCATACATCTTGGTTAGAGCATATTGCTATGGAAAT
          1 TCTCGGTTAGAGCGTAATGCTGTGTGATTACATACATCTCAGTTAGAGCATATTGCTATGAAAAT

                       *       *                   *    *
        174 GCTTACGTCTCGGTTAGAGTGTAATG-TAAAGGAAA-TGGTTACT
         66 GCTTACGTCTCAGTTAGAGCGTAATGCT-AA-GAAAGTGCTTACG

                        *                                    *    *          
        217 TCTCGGTTAGAGTGTAATGCTGTGTGATTACATACATCTCAGTTAGAGCGTATTTCTAT-AAAAG
          1 TCTCGGTTAGAGCGTAATGCTGTGTGATTACATACATCTCAGTTAGAGCATATTGCTATGAAAA-

                       *                                
        281 TGCTTACGTCTTAGTTAGAGCGTAATGCTAAGAAAGTGCTTACG
         65 TGCTTACGTCTCAGTTAGAGCGTAATGCTAAGAAAGTGCTTACG

               *              
        325 TCTTGGTTAGAGCGTAAT
          1 TCTCGGTTAGAGCGTAAT

        343 TCTAAAGAAG


Statistics
Matches: 107,  Mismatches: 16, Indels: 6
        0.83            0.12        0.05

Matches are distributed among these distances:
 107    7  0.07
 108   99  0.93
 109    1  0.01

ACGTcount: A:0.27, C:0.13, G:0.25, T:0.35


Consensus pattern (108 bp):   
TCTCGGTTAGAGCGTAATGCTGTGTGATTACATACATCTCAGTTAGAGCATATTGCTATGAAAAT
GCTTACGTCTCAGTTAGAGCGTAATGCTAAGAAAGTGCTTACG

Found at i:354 original size:36 final size:36

Alignment explanation


    Indices: 257--358  Score: 145
    Period size: 36  Copynumber: 2.8  Consensus size: 36

        247 CATACATCTC

                        *                        
        257 AGTTAGAGCGTATTTCTATAA-AAGTGCTTACGTCTT
          1 AGTTAGAGCGTAATTCTA-AAGAAGTGCTTACGTCTT

                          *                      
        293 AGTTAGAGCGTAATGCT-AAGAAAGTGCTTACGTCTT
          1 AGTTAGAGCGTAATTCTAAAG-AAGTGCTTACGTCTT

            *                             
        329 GGTTAGAGCGTAATTCTAAAGAAGTGCTTA
          1 AGTTAGAGCGTAATTCTAAAGAAGTGCTTA

        359 TCTCACGAAT


Statistics
Matches: 59,  Mismatches: 4, Indels: 6
        0.86            0.06        0.09

Matches are distributed among these distances:
  34    2  0.03
  36   54  0.92
  37    3  0.05

ACGTcount: A:0.30, C:0.13, G:0.24, T:0.33


Consensus pattern (36 bp):   
AGTTAGAGCGTAATTCTAAAGAAGTGCTTACGTCTT
Done.