Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009310.1 Kokia drynarioides strain JFW-HI SEQ_124017, 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: 16163
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29


Found at i:1195 original size:21 final size:20

Alignment explanation


    Indices: 1165--1216  Score: 59
    Period size: 21  Copynumber: 2.5  Consensus size: 20

       1155 GTTCCTTTTT

                                
       1165 TTAAAACTTTGAATTTCACC
          1 TTAAAACTTTGAATTTCACC

                  *    * *       
       1185 TCTAAATCTTTTATTTTCACC
          1 T-TAAAACTTTGAATTTCACC

                  *    
       1206 TTAAAATTTTG
          1 TTAAAACTTTG

       1217 TTAAATATTT


Statistics
Matches: 25,  Mismatches: 6, Indels: 2
        0.76            0.18        0.06

Matches are distributed among these distances:
  20    8  0.32
  21   17  0.68

ACGTcount: A:0.31, C:0.17, G:0.04, T:0.48


Consensus pattern (20 bp):   
TTAAAACTTTGAATTTCACC

Found at i:13023 original size:49 final size:49

Alignment explanation


    Indices: 12937--13202  Score: 199
    Period size: 49  Copynumber: 5.4  Consensus size: 49

      12927 TGAAGACATG

                     *                                       
      12937 AAGGGAAAGATTTAAGTCGCAACGACGAATCCAGTACCGTAAAGATATA
          1 AAGGGAAAGGTTTAAGTCGCAACGACGAATCCAGTACCGTAAAGATATA

                               *     *      **              *  *
      12986 AAGGGAAAAGGTTTAAGTCACAACGGCGAA-CTTGTACC-TGAGAAG-CATG
          1 AAGGG-AAAGGTTTAAGTCGCAACGACGAATCCAGTACCGT-A-AAGATATA

                    **      *                                
      13035 AAGGGAAAATTTTAAGCCGCAACGACGAATCCAGTACCGTAAAGATATA
          1 AAGGGAAAGGTTTAAGTCGCAACGACGAATCCAGTACCGTAAAGATATA

                    *                    *   *                 * 
      13084 AAGGGAAATGTTTAAGTCGCAACGAC-AAACCTTGTACC-TCAGAAGCAT-GA
          1 AAGGGAAAGGTTTAAGTCGCAACGACGAATCC-AGTACCGT-A-AAG-ATATA

                     *               * *     *     **      ** 
      13134 AA-GGAAA-ATTTAA-TCCGCAACGGCAAATCCGGTACCACAAAGATGCA
          1 AAGGGAAAGGTTTAAGT-CGCAACGACGAATCCAGTACCGTAAAGATATA

                                  
      13181 AAGGGAAAGGTTTAAGTCGCAA
          1 AAGGGAAAGGTTTAAGTCGCAA

      13203 TGGCGAACCT


Statistics
Matches: 171,  Mismatches: 29, Indels: 34
        0.73            0.12        0.15

Matches are distributed among these distances:
  46    2  0.01
  47    7  0.04
  48   52  0.30
  49   76  0.44
  50   32  0.19
  51    2  0.01

ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18


Consensus pattern (49 bp):   
AAGGGAAAGGTTTAAGTCGCAACGACGAATCCAGTACCGTAAAGATATA

Found at i:13118 original size:98 final size:98

Alignment explanation


    Indices: 12928--13251  Score: 420
    Period size: 97  Copynumber: 3.3  Consensus size: 98

      12918 GGTTTACCAT

                                     *                                       
      12928 GAAGACATGAAGGGAAAGATTTAAGTCGCAACGACGAATCCAGTACCGTAAAGATATAAAGGGAA
          1 GAAG-CATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCGTAAAGATATAAAGGG-A

                        *                    * 
      12993 AAGGTTTAAGTCACAACGGCGAA-CTTGTACCTGA
         64 AAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCA

                                                                             
      13027 GAAGCATGAAGGGAAA-ATTTTAAGCCGCAACGACGAATCCAGTACCGTAAAGATATAAAGGGAA
          1 GAAGCATGAAGGGAAAGA-TTTAAGCCGCAACGACGAATCCAGTACCGTAAAGATATAAAGGGAA

             *               * *              
      13091 ATGTTTAAGTCGCAACGACAAACCTTGTACCTCA
         65 AGGTTTAAGTCGCAACGGCGAACCTTGTACCTCA

                      *            *        * *     *     **      **         
      13125 GAAGCATGAAAGGAAA-ATTTAATCCGCAACGGCAAATCCGGTACCACAAAGATGCAAAGGGAAA
          1 GAAGCATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCGTAAAGATATAAAGGGAAA

                          *            * *   
      13189 GGTTTAAGTCGCAATGGCGAACCTTGTGCTTCA
         66 GGTTTAAGTCGCAACGGCGAACCTTGTACCTCA

            *                        *    
      13222 AAAGCATGAAGGGAAAGATTTAAGCTGCAA
          1 GAAGCATGAAGGGAAAGATTTAAGCCGCAA

      13252 TGGCGATTTA


Statistics
Matches: 197,  Mismatches: 25, Indels: 7
        0.86            0.11        0.03

Matches are distributed among these distances:
  97  101  0.51
  98   92  0.47
  99    4  0.02

ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19


Consensus pattern (98 bp):   
GAAGCATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCGTAAAGATATAAAGGGAAA
GGTTTAAGTCGCAACGGCGAACCTTGTACCTCA

Found at i:15510 original size:21 final size:19

Alignment explanation


    Indices: 15481--15525  Score: 54
    Period size: 21  Copynumber: 2.3  Consensus size: 19

      15471 TTCTTTTTTT

                               
      15481 TTAAACTTTGAATTTCACC
          1 TTAAACTTTGAATTTCACC

                       * *       
      15500 TCTAAATCTTTTATTTTCACC
          1 T-TAAA-CTTTGAATTTCACC

                 
      15521 TTAAA
          1 TTAAA

      15526 ATTTTGTTAA


Statistics
Matches: 22,  Mismatches: 2, Indels: 3
        0.81            0.07        0.11

Matches are distributed among these distances:
  19    1  0.05
  20    8  0.36
  21   13  0.59

ACGTcount: A:0.31, C:0.20, G:0.02, T:0.47


Consensus pattern (19 bp):   
TTAAACTTTGAATTTCACC
Done.