Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014068.1 Kokia drynarioides strain JFW-HI SEQ_129099, 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: 12226
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.29


Found at i:2201 original size:12 final size:12

Alignment explanation


    Indices: 2184--2208  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

       2174 GAGGTTTCCT

                        
       2184 AGCCCGAACTTA
          1 AGCCCGAACTTA

                        
       2196 AGCCCGAACTTA
          1 AGCCCGAACTTA

             
       2208 A
          1 A

       2209 CTTCACAAGA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.36, C:0.32, G:0.16, T:0.16


Consensus pattern (12 bp):   
AGCCCGAACTTA

Found at i:7192 original size:18 final size:18

Alignment explanation


    Indices: 7165--7208  Score: 52
    Period size: 18  Copynumber: 2.4  Consensus size: 18

       7155 CAGATGTGAA

                              
       7165 GGAAAAGAAGAAAGAGAT
          1 GGAAAAGAAGAAAGAGAT

                 *    **      
       7183 GGAAAGGAAGCGAGAGAT
          1 GGAAAAGAAGAAAGAGAT

                    
       7201 GAGAAAAG
          1 G-GAAAAG

       7209 CACGACTGGC


Statistics
Matches: 21,  Mismatches: 4, Indels: 1
        0.81            0.15        0.04

Matches are distributed among these distances:
  18   16  0.76
  19    5  0.24

ACGTcount: A:0.55, C:0.02, G:0.39, T:0.05


Consensus pattern (18 bp):   
GGAAAAGAAGAAAGAGAT

Found at i:11777 original size:37 final size:37

Alignment explanation


    Indices: 11736--11809  Score: 148
    Period size: 37  Copynumber: 2.0  Consensus size: 37

      11726 AAAGCTGAAG

                                                 
      11736 AAACTAATCTTTGAAAATTAACATTAATCATGCACAT
          1 AAACTAATCTTTGAAAATTAACATTAATCATGCACAT

                                                 
      11773 AAACTAATCTTTGAAAATTAACATTAATCATGCACAT
          1 AAACTAATCTTTGAAAATTAACATTAATCATGCACAT

      11810 CCATCTAGTT


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  37   37  1.00

ACGTcount: A:0.46, C:0.16, G:0.05, T:0.32


Consensus pattern (37 bp):   
AAACTAATCTTTGAAAATTAACATTAATCATGCACAT

Found at i:11984 original size:49 final size:49

Alignment explanation


    Indices: 11914--12226  Score: 299
    Period size: 49  Copynumber: 6.4  Consensus size: 49

      11904 TAGTACCATT

                                                  *    *  *  
      11914 AAACATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAGTAGCATAA
          1 AAACATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCCAGTACCACAA

               *   *        *                       *     *  *
      11963 AAATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAA-CCGTGTACCTCAG
          1 AAACATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCC-AGTACCACAA

              *   *                *  *                     *
      12012 AAGCATAAAGGGAAAGATTTAAGCCGTAACGGCGAATCCAGTACCACAG
          1 AAACATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCCAGTACCACAA

             *  *                  *     *                   
      12061 AGACGTGAAGGGAAAGATTTAAGCCGCAATGGCGAATCCAGTACCACAA
          1 AAACATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCCAGTACCACAA

             * *   *                          *  *   *     *   
      12110 AGATATGGAGGGAAATG-TTTAAGTCGCAACGG-TAAACCGTGTACCTCAA
          1 AAACATGAAGGGAAA-GATTTAAGTCGCAACGGCGAATCC-AGTACCACAA

              *   *                *                        *
      12159 AAGCATAAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACAG
          1 AAACATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCCAGTACCACAA

             *  *              
      12208 AGACGTGAAGGGAAAGATT
          1 AAACATGAAGGGAAAGATT


Statistics
Matches: 209,  Mismatches: 49, Indels: 12
        0.77            0.18        0.04

Matches are distributed among these distances:
  48    6  0.03
  49  196  0.94
  50    7  0.03

ACGTcount: A:0.39, C:0.18, G:0.27, T:0.17


Consensus pattern (49 bp):   
AAACATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCCAGTACCACAA

Found at i:12190 original size:147 final size:147

Alignment explanation


    Indices: 11919--12226  Score: 517
    Period size: 147  Copynumber: 2.1  Consensus size: 147

      11909 CCATTAAACA

                              *              *    *  *                       
      11919 TGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAGTAGCATAAAAATATGGAGGGAAAGGTTTA
          1 TGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACAAAAATATGGAGGGAAAGGTTTA

                        *              *                          *          
      11984 AGTCGCAACGGCGAACCGTGTACCTCAGAAGCATAAAGGGAAAGATTTAAGCCGTAACGGCGAAT
         66 AGTCGCAACGGCAAACCGTGTACCTCAAAAGCATAAAGGGAAAGATTTAAGCCGCAACGGCGAAT

                             
      12049 CCAGTACCACAGAGACG
        131 CCAGTACCACAGAGACG

                                    *                    *             *     
      12066 TGAAGGGAAAGATTTAAGCCGCAATGGCGAATCCAGTACCACAAAGATATGGAGGGAAATGTTTA
          1 TGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACAAAAATATGGAGGGAAAGGTTTA

                       *                                                     
      12131 AGTCGCAACGGTAAACCGTGTACCTCAAAAGCATAAAGGGAAAGATTTAAGCCGCAACGGCGAAT
         66 AGTCGCAACGGCAAACCGTGTACCTCAAAAGCATAAAGGGAAAGATTTAAGCCGCAACGGCGAAT

                             
      12196 CCAGTACCACAGAGACG
        131 CCAGTACCACAGAGACG

                          
      12213 TGAAGGGAAAGATT
          1 TGAAGGGAAAGATT


Statistics
Matches: 150,  Mismatches: 11, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
 147  150  1.00

ACGTcount: A:0.38, C:0.18, G:0.27, T:0.17


Consensus pattern (147 bp):   
TGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACAAAAATATGGAGGGAAAGGTTTA
AGTCGCAACGGCAAACCGTGTACCTCAAAAGCATAAAGGGAAAGATTTAAGCCGCAACGGCGAAT
CCAGTACCACAGAGACG
Done.