Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000612.1 Kokia drynarioides strain JFW-HI SEQ_111564, 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: 7135
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32

Warning! 10 characters in sequence are not A, C, G, or T


Found at i:2051 original size:30 final size:30

Alignment explanation


    Indices: 2017--2180  Score: 134
    Period size: 30  Copynumber: 5.5  Consensus size: 30

       2007 AGTAAATTTA

                                **       *
       2017 GAAAGTTTAGGGGTTAAAATGCAATTTTTT
          1 GAAAGTTTAGGGGTTAAAATATAATTTTTG

                   * *   *      * *      *
       2047 GAAAGTTAAAGGGCTAAAATGTGATTTTTA
          1 GAAAGTTTAGGGGTTAAAATATAATTTTTG

                         * * *        *     
       2077 GAAAGTTT-GGGAATCATAATCA-AAGTTTTG
          1 GAAAGTTTAGGG-GTTAAAAT-ATAATTTTTG

                        *                 
       2107 GAAAGTTTAGGGTTTAAAATATAATTTTTG
          1 GAAAGTTTAGGGGTTAAAATATAATTTTTG

                     *   *                
       2137 GAAAGTTTAAGGGATAAAATATAATTTTTG
          1 GAAAGTTTAGGGGTTAAAATATAATTTTTG

                *   *     
       2167 GAAAATTTGGGGGT
          1 GAAAGTTTAGGGGT

       2181 CGAAATTGAA


Statistics
Matches: 103,  Mismatches: 27, Indels: 8
        0.75            0.20        0.06

Matches are distributed among these distances:
  29    3  0.03
  30   97  0.94
  31    3  0.03

ACGTcount: A:0.37, C:0.02, G:0.24, T:0.37


Consensus pattern (30 bp):   
GAAAGTTTAGGGGTTAAAATATAATTTTTG

Found at i:2193 original size:90 final size:90

Alignment explanation


    Indices: 2013--2203  Score: 231
    Period size: 90  Copynumber: 2.1  Consensus size: 90

       2003 AAAAAGTAAA

                                    *        *             *      * *        
       2013 TTTAGAAAGTTTAGGGGTTAAAATGCAATTTTTTGAAAGTTAAAGGGCTAAAATGTGATTTTTAG
          1 TTTAGAAAGTTTAGGGGTTAAAATACAATTTTTGGAAAGTTAAAGGGATAAAATATAATTTTTAG

               *                     
       2078 AAAGTTTGGGAATCATAATCAAAGT
         66 AAAATTTGGGAATCATAATCAAAGT

               *            *        *               *                     * 
       2103 TTTGGAAAGTTTAGGGTTTAAAATATAATTTTTGGAAAGTTTAAGGGATAAAATATAATTTTTGG
          1 TTTAGAAAGTTTAGGGGTTAAAATACAATTTTTGGAAAGTTAAAGGGATAAAATATAATTTTTAG

                      **        **    
       2168 AAAATTTGGGGGTCGA-AATTGAAGT
         66 AAAATTTGGGAATC-ATAATCAAAGT

                       
       2193 TTTAGAAAGTT
          1 TTTAGAAAGTT

       2204 CGAGGTTAAA


Statistics
Matches: 84,  Mismatches: 16, Indels: 2
        0.82            0.16        0.02

Matches are distributed among these distances:
  90   83  0.99
  91    1  0.01

ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37


Consensus pattern (90 bp):   
TTTAGAAAGTTTAGGGGTTAAAATACAATTTTTGGAAAGTTAAAGGGATAAAATATAATTTTTAG
AAAATTTGGGAATCATAATCAAAGT

Found at i:2591 original size:22 final size:22

Alignment explanation


    Indices: 2534--2580  Score: 87
    Period size: 22  Copynumber: 2.2  Consensus size: 22

       2524 CGATCTGAGG

                                  
       2534 AAAAATAAAAG-AAACATAATT
          1 AAAAATAAAAGAAAACATAATT

                                  
       2555 AAAAATAAAAGAAAACATAATT
          1 AAAAATAAAAGAAAACATAATT

                
       2577 AAAA
          1 AAAA

       2581 GAAATAGAAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  21   11  0.44
  22   14  0.56

ACGTcount: A:0.74, C:0.04, G:0.04, T:0.17


Consensus pattern (22 bp):   
AAAAATAAAAGAAAACATAATT

Found at i:4186 original size:29 final size:29

Alignment explanation


    Indices: 4144--4308  Score: 154
    Period size: 29  Copynumber: 5.6  Consensus size: 29

       4134 GGTAAAATTT

                                          
       4144 GGGGTAAAAAATGGGATTTTTAGAAGTTCG
          1 GGGGT-AAAAATGGGATTTTTAGAAGTTCG

                            *            **
       4174 GGGGTAAAAAT-GGACCTTTT-GAAAGTTTT
          1 GGGGTAAAAATGGGA-TTTTTAG-AAGTTCG

                 *              * *      
       4203 GGGGTTAAAATGGGATTTTTGGTAGTTCG
          1 GGGGTAAAAATGGGATTTTTAGAAGTTCG

                         *      *         
       4232 GGGGTAAAAATGGAATTTTTGGAAGTTTCG
          1 GGGGTAAAAATGGGATTTTTAGAAG-TTCG

               *     *       *   *        
       4262 GGGTTAAAATTGGGATTATTAAAAGCTTCG
          1 GGGGTAAAAATGGGATTTTTAGAAG-TTCG

               *             
       4292 GGGTTAAAAATGGGATT
          1 GGGGTAAAAATGGGATT

       4309 GTTTCCTAAC


Statistics
Matches: 111,  Mismatches: 19, Indels: 10
        0.79            0.14        0.07

Matches are distributed among these distances:
  28    4  0.04
  29   55  0.50
  30   52  0.47

ACGTcount: A:0.30, C:0.04, G:0.32, T:0.33


Consensus pattern (29 bp):   
GGGGTAAAAATGGGATTTTTAGAAGTTCG

Found at i:4217 original size:58 final size:58

Alignment explanation


    Indices: 4141--4304  Score: 211
    Period size: 58  Copynumber: 2.8  Consensus size: 58

       4131 TTTGGTAAAA

                     *                                     *           
       4141 TTTGGGGTAAAAAATGGGATTTTTAGAAGTTCGGGGGTAAAAATGGACCTTTTGAAAGT
          1 TTTGGGGT-TAAAATGGGATTTTTAGAAGTTCGGGGGTAAAAATGGAACTTTTGAAAGT

                                   * *                     *     *    
       4200 TTTGGGGTTAAAATGGGATTTTTGGTAGTTCGGGGGTAAAAATGGAATTTTTGGAAGT
          1 TTTGGGGTTAAAATGGGATTTTTAGAAGTTCGGGGGTAAAAATGGAACTTTTGAAAGT

              *                  *   *           *         
       4258 TTCGGGGTTAAAATTGGGATTATTAAAAGCTTCGGGGTTAAAAATGG
          1 TTTGGGGTTAAAA-TGGGATTTTTAGAAG-TTCGGGGGTAAAAATGG

       4305 GATTGTTTCC


Statistics
Matches: 91,  Mismatches: 12, Indels: 3
        0.86            0.11        0.03

Matches are distributed among these distances:
  58   56  0.62
  59   19  0.21
  60   16  0.18

ACGTcount: A:0.30, C:0.04, G:0.32, T:0.34


Consensus pattern (58 bp):   
TTTGGGGTTAAAATGGGATTTTTAGAAGTTCGGGGGTAAAAATGGAACTTTTGAAAGT
Done.