Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013863.1 Kokia drynarioides strain JFW-HI SEQ_128891, 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: 7352
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35


Found at i:4325 original size:18 final size:18

Alignment explanation


    Indices: 4284--4325  Score: 50
    Period size: 18  Copynumber: 2.3  Consensus size: 18

       4274 TATTTTATCG

                            * 
       4284 AATTAATAAAATGTAATA
          1 AATTAATAAAATGTAACA

                               
       4302 AATTAACTAAAAT-TAACA
          1 AATTAA-TAAAATGTAACA

             *    
       4320 ACTTAA
          1 AATTAA

       4326 ATTTATATTT


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  18   15  0.71
  19    6  0.29

ACGTcount: A:0.60, C:0.07, G:0.02, T:0.31


Consensus pattern (18 bp):   
AATTAATAAAATGTAACA

Found at i:4784 original size:23 final size:22

Alignment explanation


    Indices: 4740--4784  Score: 54
    Period size: 23  Copynumber: 2.0  Consensus size: 22

       4730 TATGTTAAAG

                   *      *  *    
       4740 ACAATAACATATTTTAACAATA
          1 ACAATAAAATATTTAAAAAATA

                                   
       4762 ACAATAAAAATATTTAAAAAATA
          1 ACAAT-AAAATATTTAAAAAATA

       4785 TATTAAAAAT


Statistics
Matches: 19,  Mismatches: 3, Indels: 1
        0.83            0.13        0.04

Matches are distributed among these distances:
  22    5  0.26
  23   14  0.74

ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29


Consensus pattern (22 bp):   
ACAATAAAATATTTAAAAAATA

Found at i:5094 original size:24 final size:24

Alignment explanation


    Indices: 5061--5107  Score: 67
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       5051 TTAATTATAA

                 *                  
       5061 ATTTTTAAATATGAATATAAAAAC
          1 ATTTTCAAATATGAATATAAAAAC

                      * *          
       5085 ATTTTCAAATTTTAATATAAAAA
          1 ATTTTCAAATATGAATATAAAAA

       5108 AGAGATTGAA


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  24   20  1.00

ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40


Consensus pattern (24 bp):   
ATTTTCAAATATGAATATAAAAAC

Found at i:5310 original size:26 final size:25

Alignment explanation


    Indices: 5257--5320  Score: 74
    Period size: 26  Copynumber: 2.5  Consensus size: 25

       5247 TGAAGAGGTT

                   *   *   *       * 
       5257 TTATTTTCAATATAACTTTTACTCA
          1 TTATTTTAAATTTAAATTTTACTAA

                                      
       5282 TTATTTTAAATTTAAATTTATACTAA
          1 TTATTTTAAATTTAAATTT-TACTAA

                   *     
       5308 TTATTTTTAATTT
          1 TTATTTTAAATTT

       5321 TATGTCTCCT


Statistics
Matches: 33,  Mismatches: 5, Indels: 1
        0.85            0.13        0.03

Matches are distributed among these distances:
  25   16  0.48
  26   17  0.52

ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58


Consensus pattern (25 bp):   
TTATTTTAAATTTAAATTTTACTAA
Done.