Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008929.1 Kokia drynarioides strain JFW-HI SEQ_123620, 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: 14556
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.33


Found at i:3980 original size:51 final size:51

Alignment explanation


    Indices: 3920--4018  Score: 189
    Period size: 51  Copynumber: 1.9  Consensus size: 51

       3910 ACAAGGTCTG

                                                               
       3920 GCACACAGTTTGGGGCACAACCGTGTGACCCATTTTTTAATGAATTCTCTA
          1 GCACACAGTTTGGGGCACAACCGTGTGACCCATTTTTTAATGAATTCTCTA

                                          *                 
       3971 GCACACAGTTTGGGGCACAACCGTGTGACCTATTTTTTAATGAATTCT
          1 GCACACAGTTTGGGGCACAACCGTGTGACCCATTTTTTAATGAATTCT

       4019 ATGTATAATC


Statistics
Matches: 47,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  51   47  1.00

ACGTcount: A:0.25, C:0.22, G:0.20, T:0.32


Consensus pattern (51 bp):   
GCACACAGTTTGGGGCACAACCGTGTGACCCATTTTTTAATGAATTCTCTA

Found at i:10109 original size:36 final size:36

Alignment explanation


    Indices: 10073--10261  Score: 200
    Period size: 36  Copynumber: 5.2  Consensus size: 36

      10063 TATAAAGTTA

                     *           *             *
      10073 CATACGTCTTGGTTAGAGCGTGTTACTATGATGTTA
          1 CATACGTCTCGGTTAGAGCGTATTACTATGATGTTG

                *          *        *           
      10109 CATATGTCTCGGTTATAGCGTATTGCTATGATGTTG
          1 CATACGTCTCGGTTAGAGCGTATTACTATGATGTTG

                       *       *     *          
      10145 CATACGTCTCGATTAGAGCATATTATTATGATGTTG
          1 CATACGTCTCGGTTAGAGCGTATTACTATGATGTTG

                 *       * * *         * *       
      10181 CATACATCTCGGTAAAAACGTA-TAGCAAAGATGTTG
          1 CATACGTCTCGGTTAGAGCGTATTA-CTATGATGTTG

                 *                   *     *    
      10217 CATACATCTCGGTTAGAGCGTATTATTATGAAGTTG
          1 CATACGTCTCGGTTAGAGCGTATTACTATGATGTTG

                     
      10253 CATACGTCT
          1 CATACGTCT

      10262 ACGTCCCAGT


Statistics
Matches: 122,  Mismatches: 29, Indels: 4
        0.79            0.19        0.03

Matches are distributed among these distances:
  35    2  0.02
  36  118  0.97
  37    2  0.02

ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36


Consensus pattern (36 bp):   
CATACGTCTCGGTTAGAGCGTATTACTATGATGTTG

Found at i:10175 original size:72 final size:72

Alignment explanation


    Indices: 10073--10261  Score: 234
    Period size: 72  Copynumber: 2.6  Consensus size: 72

      10063 TATAAAGTTA

                     *           *   *         *    *        * * *     *  * *
      10073 CATACGTCTTGGTTAGAGCGTGTTACTATGATGTTACATATGTCTCGGTTATAGCGTATTGCTAT
          1 CATACGTCTCGGTTAGAGCGTATTATTATGATGTTGCATACGTCTCGGTAAAAACGTATAGCAAA

                   
      10138 GATGTTG
         66 GATGTTG

                       *       *                     *                       
      10145 CATACGTCTCGATTAGAGCATATTATTATGATGTTGCATACATCTCGGTAAAAACGTATAGCAAA
          1 CATACGTCTCGGTTAGAGCGTATTATTATGATGTTGCATACGTCTCGGTAAAAACGTATAGCAAA

                   
      10210 GATGTTG
         66 GATGTTG

                 *                         *             
      10217 CATACATCTCGGTTAGAGCGTATTATTATGAAGTTGCATACGTCT
          1 CATACGTCTCGGTTAGAGCGTATTATTATGATGTTGCATACGTCT

      10262 ACGTCCCAGT


Statistics
Matches: 98,  Mismatches: 19, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  72   98  1.00

ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36


Consensus pattern (72 bp):   
CATACGTCTCGGTTAGAGCGTATTATTATGATGTTGCATACGTCTCGGTAAAAACGTATAGCAAA
GATGTTG

Found at i:10322 original size:36 final size:36

Alignment explanation


    Indices: 10270--10355  Score: 104
    Period size: 36  Copynumber: 2.4  Consensus size: 36

      10260 CTACGTCCCA

                       *                        * 
      10270 GTTAGAGCATATTGCT-A-TGAATTTGCTTATGTCTTG
          1 GTTAGAGCATAATGCTAAGTG-A-TTGCTTATGTCTCG

                    *                *          
      10306 GTTAGAGCTTAATGCTAAGTGATTGTTTATGTCTCG
          1 GTTAGAGCATAATGCTAAGTGATTGCTTATGTCTCG

                          
      10342 GTTAGAGCATAATG
          1 GTTAGAGCATAATG

      10356 TCATTTTAGC


Statistics
Matches: 43,  Mismatches: 5, Indels: 4
        0.83            0.10        0.08

Matches are distributed among these distances:
  36   39  0.91
  37    2  0.05
  38    2  0.05

ACGTcount: A:0.24, C:0.10, G:0.24, T:0.41


Consensus pattern (36 bp):   
GTTAGAGCATAATGCTAAGTGATTGCTTATGTCTCG

Found at i:14530 original size:21 final size:21

Alignment explanation


    Indices: 14506--14546  Score: 55
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      14496 AGCTTTAAAG

                  *              
      14506 ATTACATAATTGAAAAGAATA
          1 ATTACAAAATTGAAAAGAATA

                *      *        
      14527 ATTATAAAATTTAAAAGAAT
          1 ATTACAAAATTGAAAAGAAT

      14547 TAATATTTAT


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32


Consensus pattern (21 bp):   
ATTACAAAATTGAAAAGAATA
Done.