Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013624.1 Kokia drynarioides strain JFW-HI SEQ_128652, 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: 8007
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34


Found at i:5360 original size:23 final size:22

Alignment explanation


    Indices: 5330--5373  Score: 70
    Period size: 23  Copynumber: 2.0  Consensus size: 22

       5320 AAAGAAATAA

                       *          
       5330 AATTAACCCAATTTATTTAATT
          1 AATTAACCCAAATTATTTAATT

                                  
       5352 AATTCAACCCAAATTATTTAAT
          1 AATT-AACCCAAATTATTTAAT

       5374 GAAATATTTA


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  22    4  0.20
  23   16  0.80

ACGTcount: A:0.43, C:0.16, G:0.00, T:0.41


Consensus pattern (22 bp):   
AATTAACCCAAATTATTTAATT

Found at i:6319 original size:14 final size:14

Alignment explanation


    Indices: 6300--6335  Score: 54
    Period size: 14  Copynumber: 2.6  Consensus size: 14

       6290 TTGTTTGACT

                   *      
       6300 GAAAATGGTTTCCG
          1 GAAAATGATTTCCG

                        * 
       6314 GAAAATGATTTCTG
          1 GAAAATGATTTCCG

                    
       6328 GAAAATGA
          1 GAAAATGA

       6336 ATTACTTTTC


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  14   20  1.00

ACGTcount: A:0.39, C:0.08, G:0.25, T:0.28


Consensus pattern (14 bp):   
GAAAATGATTTCCG

Found at i:6788 original size:46 final size:46

Alignment explanation


    Indices: 6703--6804  Score: 125
    Period size: 46  Copynumber: 2.2  Consensus size: 46

       6693 TATTACAAAT

                 *         *     *  *  *  *               
       6703 TAGTAGTACACCACATGATAATTACAATATTTTTCATGTGCATAAC
          1 TAGTATTACACCACAAGATAACTAAAACATGTTTCATGTGCATAAC

                                                           
       6749 TAGTATTACACCACAAGATAACTAAAACATCGTTT-ATGTGCATAAC
          1 TAGTATTACACCACAAGATAACTAAAACAT-GTTTCATGTGCATAAC

              *       
       6795 TAATATTACA
          1 TAGTATTACA

       6805 AATTAGTAGT


Statistics
Matches: 48,  Mismatches: 7, Indels: 2
        0.84            0.12        0.04

Matches are distributed among these distances:
  46   45  0.94
  47    3  0.06

ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32


Consensus pattern (46 bp):   
TAGTATTACACCACAAGATAACTAAAACATGTTTCATGTGCATAAC

Found at i:6905 original size:109 final size:105

Alignment explanation


    Indices: 6690--6913  Score: 286
    Period size: 109  Copynumber: 2.1  Consensus size: 105

       6680 AAACCACAAT

                                              *              *  *           *
       6690 TAATATTACAAATTAGTAGTACACCACATGATAATTACAATATTTTTCATGTGCATAACTAGTAT
          1 TAATATTACAAATTAGTAGTACACCACATGATAACTACAATATTTTTCAAGTACATAACTAGTAG

                                       ** *         
       6755 TACACCACAAGATAACTAAAACATCGTTTATGTGCATAAC
         66 TACACCACAAGATAACTAAAACATCGTGCAAGTGCATAAC

                                                                          *  
       6795 TAATATTACAAATTAGTAGTACACCACATGATAACTACAAATAATATTTTCCAAGTACATAATTA
          1 TAATATTACAAATTAGTAGTACACCACATGATAACTAC-AAT-AT-TTTT-CAAGTACATAACTA

                    *    **          *  *               
       6860 GTAGTACATCACATTATAACTAAAATATTGTGCAAGTGCATAAC
         62 GTAGTACACCACAAGATAACTAAAACATCGTGCAAGTGCATAAC

              *       
       6904 TAGTATTACA
          1 TAATATTACA

       6914 CCATATAATT


Statistics
Matches: 101,  Mismatches: 14, Indels: 4
        0.85            0.12        0.03

Matches are distributed among these distances:
 105   37  0.37
 106    3  0.03
 107    2  0.02
 108    4  0.04
 109   55  0.54

ACGTcount: A:0.42, C:0.16, G:0.09, T:0.32


Consensus pattern (105 bp):   
TAATATTACAAATTAGTAGTACACCACATGATAACTACAATATTTTTCAAGTACATAACTAGTAG
TACACCACAAGATAACTAAAACATCGTGCAAGTGCATAAC

Found at i:6908 original size:46 final size:48

Alignment explanation


    Indices: 6808--6916  Score: 123
    Period size: 46  Copynumber: 2.3  Consensus size: 48

       6798 TATTACAAAT

                                               *             *
       6808 TAGTAGTACACCACATGATAACTACAAATAATATTTTCCAAGTACATAAT
          1 TAGTAGTACACCACATGATAACT--AAATAATATTGTCCAAGTACATAAC

                      *     *                  *     *      
       6858 TAGTAGTACATCACATTATAACT-AA-AATATTGTGCAAGTGCATAAC
          1 TAGTAGTACACCACATGATAACTAAATAATATTGTCCAAGTACATAAC

                 *       
       6904 TAGTATTACACCA
          1 TAGTAGTACACCA

       6917 TATAATTAGT


Statistics
Matches: 51,  Mismatches: 8, Indels: 4
        0.81            0.13        0.06

Matches are distributed among these distances:
  46   28  0.55
  47    2  0.04
  50   21  0.41

ACGTcount: A:0.42, C:0.17, G:0.10, T:0.30


Consensus pattern (48 bp):   
TAGTAGTACACCACATGATAACTAAATAATATTGTCCAAGTACATAAC
Done.