Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001584.1 Kokia drynarioides strain JFW-HI SEQ_113194, 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: 7839
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34

Warning! 29 characters in sequence are not A, C, G, or T


Found at i:746 original size:17 final size:17

Alignment explanation


    Indices: 721--814  Score: 82
    Period size: 17  Copynumber: 5.4  Consensus size: 17

        711 GGACTTTTAA

                *        **  
        721 TTAAGTTTTAAATCCAT
          1 TTAAATTTTAAATAAAT

                       *     
        738 TTAAATTTTAATTAAAT
          1 TTAAATTTTAAATAAAT

                         *    
        755 TTAAA-TTTAAAGCAAAT
          1 TTAAATTTTAAA-TAAAT

                     *         
        772 TTAAATTTAAAAGATAAAT
          1 TTAAATTT-TAA-ATAAAT

                     *        
        791 TTAAATTTAAAAATAAAT
          1 TTAAATTT-TAAATAAAT

                  
        809 TTAAAT
          1 TTAAAT

        815 CAATTTAAAC


Statistics
Matches: 65,  Mismatches: 8, Indels: 7
        0.81            0.10        0.09

Matches are distributed among these distances:
  16    5  0.08
  17   27  0.42
  18   14  0.22
  19   18  0.28
  20    1  0.02

ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43


Consensus pattern (17 bp):   
TTAAATTTTAAATAAAT

Found at i:750 original size:6 final size:6

Alignment explanation


    Indices: 736--814  Score: 72
    Period size: 6  Copynumber: 13.3  Consensus size: 6

        726 TTTTAAATCC

                       *                         **                 
        736 ATTTAA ATTTTA A-TTAA ATTTAA ATTTAA A-GCAA ATTTAA ATTTAAA
          1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA

             **                   **             
        783 AGATAA ATTTAA ATTTAA AAATAA ATTTAA AT
          1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT

        815 CAATTTAAAC


Statistics
Matches: 56,  Mismatches: 14, Indels: 6
        0.74            0.18        0.08

Matches are distributed among these distances:
   5    7  0.12
   6   45  0.80
   7    4  0.07

ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42


Consensus pattern (6 bp):   
ATTTAA

Found at i:6966 original size:97 final size:97

Alignment explanation


    Indices: 6777--6970  Score: 264
    Period size: 97  Copynumber: 2.0  Consensus size: 97

       6767 CACTTTTGAA

                  *                                           *   *          
       6777 AAGGATGTTCGATTATCTCGATTTGAAGAAAAAGTCGCACCTAGTAAGTTTAGGTACAAATTTTC
          1 AAGGATATTCGATTATCTCGATTTGAAGAAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTTC

                     ** * *       *         
       6842 AAAATTCGAGGTGAGAAACATTTCCTCGATTT
         66 AAAATTCGAAATAAAAAACATTGCCTCGATTT

                            *                    **                          
       6874 AAGGATATTCGATTATTTCGATTTGAAGAAAAA-TCGTGCCTAGTAAGTTAAGGCACAAATTTTC
          1 AAGGATATTCGATTATCTCGATTTGAAGAAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTTC

                               *             
       6938 AAAATTCGAAATAAAAGAATATTGCCTCGATTT
         66 AAAATTCGAAATAAAA-AACATTGCCTCGATTT

       6971 TAAAGTTTTT


Statistics
Matches: 84,  Mismatches: 12, Indels: 2
        0.86            0.12        0.02

Matches are distributed among these distances:
  96   39  0.46
  97   45  0.54

ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32


Consensus pattern (97 bp):   
AAGGATATTCGATTATCTCGATTTGAAGAAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTTC
AAAATTCGAAATAAAAAACATTGCCTCGATTT

Found at i:7326 original size:29 final size:29

Alignment explanation


    Indices: 7284--7447  Score: 129
    Period size: 29  Copynumber: 5.6  Consensus size: 29

       7274 ATTGGGATAA

                   * *                    
       7284 AAAAATGGAGTTTTTGGACA-TTTGGGGGT
          1 AAAAATGTAATTTTTGGA-AGTTTGGGGGT

                           *       ** *  
       7313 AAAAATGTAATTTTTAGAAGTTTCAGAGT
          1 AAAAATGTAATTTTTGGAAGTTTGGGGGT

                *   *        *             
       7342 CAAATATGGAATTTTT-AAAGGTTTGGGGGT
          1 -AAAAATGTAATTTTTGGAA-GTTTGGGGGT

                                        * 
       7372 AAAAATGT-ATTTTTGGAAGTTTCGGGGTT
          1 AAAAATGTAATTTTTGGAAGTTT-GGGGGT

                             *     * *    
       7401 AAAAATAG-AATTTTTGAAAGTTCGAGGGT
          1 AAAAAT-GTAATTTTTGGAAGTTTGGGGGT

                  *           
       7430 AAAAATATAATTTTTGGA
          1 AAAAATGTAATTTTTGGA

       7448 TACTTTAGGG


Statistics
Matches: 105,  Mismatches: 22, Indels: 16
        0.73            0.15        0.11

Matches are distributed among these distances:
  28   11  0.10
  29   61  0.58
  30   33  0.31

ACGTcount: A:0.35, C:0.03, G:0.25, T:0.37


Consensus pattern (29 bp):   
AAAAATGTAATTTTTGGAAGTTTGGGGGT

Found at i:7412 original size:58 final size:59

Alignment explanation


    Indices: 7304--7447  Score: 184
    Period size: 58  Copynumber: 2.5  Consensus size: 59

       7294 TTTTTGGACA

                                    *                 *  *              
       7304 TTTGGGGGTAAAAATGTAATTTTTAGAAGTTTCAGAGTCAAATATGGAATTTTT-AAAGG
          1 TTTGGGGGTAAAAATGTAATTTTTGGAAGTTTCAGAGTCAAAAATAGAATTTTTGAAA-G

                                             * *  *                    
       7363 TTTGGGGGTAAAAATGT-ATTTTTGGAAGTTTCGGGGTTAAAAATAGAATTTTTGAAAG
          1 TTTGGGGGTAAAAATGTAATTTTTGGAAGTTTCAGAGTCAAAAATAGAATTTTTGAAAG

              * *          *           
       7421 TTCGAGGGTAAAAATATAATTTTTGGA
          1 TTTGGGGGTAAAAATGTAATTTTTGGA

       7448 TACTTTAGGG


Statistics
Matches: 74,  Mismatches: 9, Indels: 4
        0.85            0.10        0.05

Matches are distributed among these distances:
  58   45  0.61
  59   29  0.39

ACGTcount: A:0.35, C:0.03, G:0.25, T:0.38


Consensus pattern (59 bp):   
TTTGGGGGTAAAAATGTAATTTTTGGAAGTTTCAGAGTCAAAAATAGAATTTTTGAAAG

Done.