Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000091.1 Kokia drynarioides strain JFW-HI SEQ_110717, 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: 6571
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.33

Warning! 203 characters in sequence are not A, C, G, or T


Found at i:4407 original size:97 final size:96

Alignment explanation


    Indices: 4233--4409  Score: 207
    Period size: 97  Copynumber: 1.8  Consensus size: 96

       4223 ATGATATTTG

                                **  *                   *         *  *       
       4233 ATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGTAATATTTCGGAATCGAAGAT
          1 ATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCGAAATATTTCGAAACCGAAGAT

              *                            
       4298 AAGGAAACATTGCCTCGATTAAGGGTATTCA
         66 AAAGAAACATTGCCTCGATTAAGGGTATTCA

                 *                            *                              
       4329 ATTATTTCGATTTGAAGAAAAAATTACACCTAGTGAGTTAAGGCGCAAAT-TTTCGAAACCCGAA
          1 ATTATCTCGATTTGAAG-AAAAATTACACCTAGTAAGTTAAGGCG-AAATATTTCGAAA-CCGAA

                       *       
       4393 -ATGAAAG-AATATTGCCT
         63 GAT-AAAGAAACATTGCCT

       4410 TGATATTAAA


Statistics
Matches: 67,  Mismatches: 10, Indels: 7
        0.80            0.12        0.08

Matches are distributed among these distances:
  96   16  0.24
  97   41  0.61
  98   10  0.15

ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29


Consensus pattern (96 bp):   
ATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCGAAATATTTCGAAACCGAAGAT
AAAGAAACATTGCCTCGATTAAGGGTATTCA

Found at i:4790 original size:59 final size:57

Alignment explanation


    Indices: 4724--5006  Score: 336
    Period size: 59  Copynumber: 4.8  Consensus size: 57

       4714 ATTCGAGGTC

                                  *                *     *             
       4724 AAAAATGGAATTTTTAGAAGTTCGAGGGTAAAAATGGACCTTTTGAAAGTTTTGGGGTT
          1 AAAAATGG-ATTTTTAGAAGTTTGAGGGTAAAAATGGA-TTTTTGGAAGTTTTGGGGTT

                           * *      *                                  
       4783 AAAAATGGGATTTTTGGTAGTTTGGGGGTAAAAATGGAATTTTTGGAAGTTTT-GGGTT
          1 AAAAAT-GGATTTTTAGAAGTTTGAGGGTAAAAATGG-ATTTTTGGAAGTTTTGGGGTT

                 *          *                                            
       4841 AAAATTTGGATTTTTAAAAGCTTTG-GGGTTAAAAATGGGATTTTTGGAAGTTTTGGGGTT
          1 AAAA-ATGGATTTTTAGAAG-TTTGAGGG-TAAAAAT-GGATTTTTGGAAGTTTTGGGGTT

                           *        *           *                      
       4901 AAAAATTGGATTTTTTGAAGTTTGGGGGTAAAAATTAGATTTTTGGAAGTTTTGGGGTT
          1 AAAAA-TGGATTTTTAGAAGTTTGAGGGTAAAAA-TGGATTTTTGGAAGTTTTGGGGTT

                                  *                        
       4960 AAAAATTGGATTTTTAGAAGTTCGAGGGTAAAAATGGGATTTTTGGA
          1 AAAAA-TGGATTTTTAGAAGTTTGAGGGTAAAAAT-GGATTTTTGGA

       5007 CAATTTAGGG


Statistics
Matches: 195,  Mismatches: 18, Indels: 22
        0.83            0.08        0.09

Matches are distributed among these distances:
  58   23  0.12
  59  142  0.73
  60   30  0.15

ACGTcount: A:0.31, C:0.02, G:0.29, T:0.39


Consensus pattern (57 bp):   
AAAAATGGATTTTTAGAAGTTTGAGGGTAAAAATGGATTTTTGGAAGTTTTGGGGTT

Found at i:5016 original size:29 final size:29

Alignment explanation


    Indices: 4724--5006  Score: 293
    Period size: 29  Copynumber: 9.6  Consensus size: 29

       4714 ATTCGAGGTC

                    *      *      *       
       4724 AAAAATGGAATTTTTAGAAGTTCGAGGG-T
          1 AAAAATGGGATTTTTGGAAGTTTG-GGGTT

                       *     *             
       4753 AAAAAT-GGACCTTTTGAAAGTTTTGGGGTT
          1 AAAAATGGGA-TTTTTGGAAG-TTTGGGGTT

                             *         * 
       4783 AAAAATGGGATTTTTGGTAGTTTGGGGGT
          1 AAAAATGGGATTTTTGGAAGTTTGGGGTT

                    *              *     
       4812 AAAAATGGAATTTTTGGAAGTTTTGGGTT
          1 AAAAATGGGATTTTTGGAAGTTTGGGGTT

                * *        **             
       4841 AAAATTTGGATTTTTAAAAGCTTTGGGGTT
          1 AAAAATGGGATTTTTGGAAG-TTTGGGGTT

                                          
       4871 AAAAATGGGATTTTTGGAAGTTTTGGGGTT
          1 AAAAATGGGATTTTTGGAAG-TTTGGGGTT

                  *        *           * 
       4901 AAAAATTGGATTTTTTGAAGTTTGGGGGT
          1 AAAAATGGGATTTTTGGAAGTTTGGGGTT

                  **                      
       4930 AAAAATTAGATTTTTGGAAGTTTTGGGGTT
          1 AAAAATGGGATTTTTGGAAG-TTTGGGGTT

                  *        *      *       
       4960 AAAAATTGGATTTTTAGAAGTTCGAGGG-T
          1 AAAAATGGGATTTTTGGAAGTTTG-GGGTT

                              
       4989 AAAAATGGGATTTTTGGA
          1 AAAAATGGGATTTTTGGA

       5007 CAATTTAGGG


Statistics
Matches: 212,  Mismatches: 35, Indels: 14
        0.81            0.13        0.05

Matches are distributed among these distances:
  28    2  0.01
  29  110  0.52
  30   97  0.46
  31    3  0.01

ACGTcount: A:0.31, C:0.02, G:0.29, T:0.39


Consensus pattern (29 bp):   
AAAAATGGGATTTTTGGAAGTTTGGGGTT

Found at i:6090 original size:14 final size:14

Alignment explanation


    Indices: 6063--6099  Score: 51
    Period size: 14  Copynumber: 2.7  Consensus size: 14

       6053 TGGTTATTAT

                          
       6063 TAATATATTAATAA
          1 TAATATATTAATAA

                           
       6077 TAATACTATT-ATAA
          1 TAATA-TATTAATAA

                      
       6091 TAAT-TATTA
          1 TAATATATTA

       6100 TTGCCATTAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 5
        0.81            0.00        0.19

Matches are distributed among these distances:
  12    4  0.19
  14   13  0.62
  15    4  0.19

ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46


Consensus pattern (14 bp):   
TAATATATTAATAA

Done.