Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012668.1 Kokia drynarioides strain JFW-HI SEQ_127679, 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: 6989
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33


Found at i:1889 original size:15 final size:15

Alignment explanation


    Indices: 1869--1900  Score: 64
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       1859 GAAGAAAATG

                           
       1869 CAAGACCAGTTCAGC
          1 CAAGACCAGTTCAGC

                           
       1884 CAAGACCAGTTCAGC
          1 CAAGACCAGTTCAGC

              
       1899 CA
          1 CA

       1901 CTCAATCAAA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.34, C:0.34, G:0.19, T:0.12


Consensus pattern (15 bp):   
CAAGACCAGTTCAGC

Found at i:2003 original size:33 final size:33

Alignment explanation


    Indices: 1966--2041  Score: 125
    Period size: 33  Copynumber: 2.3  Consensus size: 33

       1956 TCGTATTTTT

                                    *        
       1966 TACACCATTTAATGTATAAAAATATTATATTTA
          1 TACACCATTTAATGTATAAAAATAATATATTTA

                      *               *      
       1999 TACACCATTTTATGTATAAAAATAATGTATTTA
          1 TACACCATTTAATGTATAAAAATAATATATTTA

                      
       2032 TACACCATTT
          1 TACACCATTT

       2042 GACATATATT


Statistics
Matches: 40,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  33   40  1.00

ACGTcount: A:0.42, C:0.12, G:0.04, T:0.42


Consensus pattern (33 bp):   
TACACCATTTAATGTATAAAAATAATATATTTA

Found at i:3051 original size:29 final size:28

Alignment explanation


    Indices: 2993--3391  Score: 194
    Period size: 30  Copynumber: 13.2  Consensus size: 28

       2983 AAATAAAAAA

                                            
       2993 TAGGGTCAAAAAATG-AATTTTTGGAGAA-TT
          1 TAGGGTC--AAAATGTAA-TTTTGGA-AAGTT

                                      *  
       3023 TAGGGTCAAAATGTAATTTTGGAAAAATT
          1 TAGGGTCAAAATGTAATTTTGG-AAAGTT

                                          
       3052 T-GGTGTCAAAATGTAATTTTAGGAAAGTT
          1 TAGG-GTCAAAATGTAATTTT-GGAAAGTT

                *  *     *   *             
       3081 T-GATGTTAAAATATGATTTTTAGGAAAGTT
          1 TAG-GGTCAAAATGT-AATTTT-GGAAAGTT

                         * *       *     
       3111 TAGGGGTCAAAATATGATTTTGGGAAGTT
          1 TA-GGGTCAAAATGTAATTTTGGAAAGTT

                         * *              
       3140 TAGGGGTCAAAATTTGATTTTGGAAAAGTT
          1 TA-GGGTCAAAATGTAATTTTGG-AAAGTT

                   *     * *               
       3170 TAGAGGTGAAAATATGATTTTGAGAAAGTTT
          1 TAG-GGTCAAAATGTAATTTTG-GAAAG-TT

              *   *       *           *  
       3201 TACGGTTAAAATGTGATTTTGGGAAATTT
          1 TAGGGTCAAAATGTAATTTT-GGAAAGTT

             *     *       *              
       3230 TTGGGTTTAAAATGTGATTTTAGGAAAGTT
          1 TAGGG-TCAAAATGTAATTTT-GGAAAGTT

                 **                               
       3260 TAGGGGGAAAAGTGTAATTTTGGAAAAATTTATGAGTT
          1 TAGGGTCAAAA-TGTAATTTTGG----A---A--AGTT

                 **                    *  
       3298 TAGGGGGAAAAGTGTAATTTTGGAAAAATT
          1 TAGGGTCAAAA-TGTAATTTTGG-AAAGTT

                   * *            *      
       3328 TATGGGTGAGAATGTAATTTTGAAAAGTT
          1 TA-GGGTCAAAATGTAATTTTGGAAAGTT

                         *   *            
       3357 TGAGGGTCAAAATATGATTTTTGGAAAGTT
          1 T-AGGGTCAAAATGT-AATTTTGGAAAGTT

                 
       3387 TAGGG
          1 TAGGG

       3392 ACCTTTTGGG


Statistics
Matches: 305,  Mismatches: 36, Indels: 57
        0.77            0.09        0.14

Matches are distributed among these distances:
  28   16  0.05
  29   97  0.32
  30  137  0.45
  31   22  0.07
  32    2  0.01
  33    1  0.00
  35    2  0.01
  36    1  0.00
  38   27  0.09

ACGTcount: A:0.35, C:0.02, G:0.26, T:0.37


Consensus pattern (28 bp):   
TAGGGTCAAAATGTAATTTTGGAAAGTT

Found at i:3307 original size:38 final size:38

Alignment explanation


    Indices: 3256--3331  Score: 152
    Period size: 38  Copynumber: 2.0  Consensus size: 38

       3246 ATTTTAGGAA

                                                  
       3256 AGTTTAGGGGGAAAAGTGTAATTTTGGAAAAATTTATG
          1 AGTTTAGGGGGAAAAGTGTAATTTTGGAAAAATTTATG

                                                  
       3294 AGTTTAGGGGGAAAAGTGTAATTTTGGAAAAATTTATG
          1 AGTTTAGGGGGAAAAGTGTAATTTTGGAAAAATTTATG

       3332 GGTGAGAATG


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  38   38  1.00

ACGTcount: A:0.37, C:0.00, G:0.29, T:0.34


Consensus pattern (38 bp):   
AGTTTAGGGGGAAAAGTGTAATTTTGGAAAAATTTATG

Found at i:5741 original size:20 final size:20

Alignment explanation


    Indices: 5718--5757  Score: 62
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       5708 AAAAAAATAG

                 *   *          
       5718 ATAAAGGAAGAAAATAAAAA
          1 ATAAAAGAACAAAATAAAAA

                                
       5738 ATAAAAGAACAAAATAAAAA
          1 ATAAAAGAACAAAATAAAAA

       5758 CAAACAATAA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.78, C:0.03, G:0.10, T:0.10


Consensus pattern (20 bp):   
ATAAAAGAACAAAATAAAAA
Done.