Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005834.1 Kokia drynarioides strain JFW-HI SEQ_120125, 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: 44324
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34


Found at i:8920 original size:22 final size:23

Alignment explanation


    Indices: 8886--8939  Score: 58
    Period size: 22  Copynumber: 2.4  Consensus size: 23

       8876 AGAGAAGCAG

                     *         *   
       8886 AAAAAA-AATAGAAAATAATA-A
          1 AAAAAATAAAAGAAAATAAAAGA

                 *        *        
       8907 AAAAATTAAAAGAACATAAAAGA
          1 AAAAAATAAAAGAAAATAAAAGA

                      
       8930 AAAAAATAAA
          1 AAAAAATAAA

       8940 TTGCTTAAAG


Statistics
Matches: 26,  Mismatches: 5, Indels: 2
        0.79            0.15        0.06

Matches are distributed among these distances:
  21    5  0.19
  22   11  0.42
  23   10  0.38

ACGTcount: A:0.80, C:0.02, G:0.06, T:0.13


Consensus pattern (23 bp):   
AAAAAATAAAAGAAAATAAAAGA

Found at i:15556 original size:7 final size:7

Alignment explanation


    Indices: 15544--15572  Score: 58
    Period size: 7  Copynumber: 4.1  Consensus size: 7

      15534 CTGTCCTATT

                   
      15544 CAACTTC
          1 CAACTTC

                   
      15551 CAACTTC
          1 CAACTTC

                   
      15558 CAACTTC
          1 CAACTTC

                   
      15565 CAACTTC
          1 CAACTTC

             
      15572 C
          1 C

      15573 CGACAATTCT


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   22  1.00

ACGTcount: A:0.28, C:0.45, G:0.00, T:0.28


Consensus pattern (7 bp):   
CAACTTC

Found at i:16453 original size:17 final size:17

Alignment explanation


    Indices: 16431--16485  Score: 58
    Period size: 17  Copynumber: 3.2  Consensus size: 17

      16421 ATATTTTTGT

                             
      16431 AATATATTTTTATAAAA
          1 AATATATTTTTATAAAA

                  **     *   
      16448 AATATAAGTTTA-CAAA
          1 AATATATTTTTATAAAA

                        *     
      16464 AATATAATTTTTGTAAAA
          1 AATAT-ATTTTTATAAAA

                
      16482 AATA
          1 AATA

      16486 CTTTATATAA


Statistics
Matches: 29,  Mismatches: 7, Indels: 3
        0.74            0.18        0.08

Matches are distributed among these distances:
  16    8  0.28
  17   14  0.48
  18    7  0.24

ACGTcount: A:0.55, C:0.02, G:0.04, T:0.40


Consensus pattern (17 bp):   
AATATATTTTTATAAAA

Found at i:22200 original size:18 final size:19

Alignment explanation


    Indices: 22160--22203  Score: 56
    Period size: 18  Copynumber: 2.4  Consensus size: 19

      22150 AATTCATATA

                           * * 
      22160 ATATTTCTTCTTCAGGATC
          1 ATATTTCTTCTTCAGAAAC

                               
      22179 -TATTTCTTCTTC-GAAAC
          1 ATATTTCTTCTTCAGAAAC

                    
      22196 ATATTTCT
          1 ATATTTCT

      22204 AGATTTTATT


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

Matches are distributed among these distances:
  17    3  0.14
  18   19  0.86

ACGTcount: A:0.23, C:0.20, G:0.07, T:0.50


Consensus pattern (19 bp):   
ATATTTCTTCTTCAGAAAC

Found at i:23320 original size:23 final size:23

Alignment explanation


    Indices: 23269--23313  Score: 81
    Period size: 23  Copynumber: 2.0  Consensus size: 23

      23259 TAAAATTATT

                                   
      23269 GTCTGTCTCGTTGACACGCGCTC
          1 GTCTGTCTCGTTGACACGCGCTC

                    *             
      23292 GTCTGTCTTGTTGACACGCGCT
          1 GTCTGTCTCGTTGACACGCGCT

      23314 TCTCTGTATT


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  23   21  1.00

ACGTcount: A:0.09, C:0.31, G:0.27, T:0.33


Consensus pattern (23 bp):   
GTCTGTCTCGTTGACACGCGCTC

Found at i:40832 original size:6 final size:6

Alignment explanation


    Indices: 40823--40852  Score: 60
    Period size: 6  Copynumber: 5.0  Consensus size: 6

      40813 TTCACGTTTC

                                              
      40823 TTGCTT TTGCTT TTGCTT TTGCTT TTGCTT
          1 TTGCTT TTGCTT TTGCTT TTGCTT TTGCTT

      40853 GCTACAATTC


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   24  1.00

ACGTcount: A:0.00, C:0.17, G:0.17, T:0.67


Consensus pattern (6 bp):   
TTGCTT

Done.