Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006130.1 Kokia drynarioides strain JFW-HI SEQ_120652, 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: 10754
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:3807 original size:16 final size:16

Alignment explanation


    Indices: 3775--3829  Score: 58
    Period size: 16  Copynumber: 3.3  Consensus size: 16

       3765 ATTATTTTTA

                             
       3775 AAAATATATAAA-ATAT
          1 AAAAT-TATAAATATAT

                              
       3791 AAAATTATAAATTTATAT
          1 AAAATTATAAA--TATAT

             *     *        
       3809 ACAATTAAAAATATAT
          1 AAAATTATAAATATAT

                 
       3825 AAAAT
          1 AAAAT

       3830 ACTTATAATA


Statistics
Matches: 33,  Mismatches: 3, Indels: 6
        0.79            0.07        0.14

Matches are distributed among these distances:
  15    6  0.18
  16   14  0.42
  18   13  0.39

ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35


Consensus pattern (16 bp):   
AAAATTATAAATATAT

Found at i:3814 original size:18 final size:18

Alignment explanation


    Indices: 3787--3825  Score: 51
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       3777 AATATATAAA

                       *    * 
       3787 ATATAAAATTATAAATTT
          1 ATATAAAATTAAAAATAT

                 *            
       3805 ATATACAATTAAAAATAT
          1 ATATAAAATTAAAAATAT

               
       3823 ATA
          1 ATA

       3826 AAATACTTAT


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38


Consensus pattern (18 bp):   
ATATAAAATTAAAAATAT

Found at i:5678 original size:27 final size:27

Alignment explanation


    Indices: 5628--5721  Score: 120
    Period size: 27  Copynumber: 3.4  Consensus size: 27

       5618 AAATTTAGAG

                                         
       5628 AGCAAAATATATATTATTTTTTTATAATT
          1 AGCAAAATATATATTA--TTTTTATAATT

                                     * 
       5657 AGCAAAATATATATTATTTTTATAACT
          1 AGCAAAATATATATTATTTTTATAATT

                 *                       
       5684 AGGTCCAAA-ATATA-TATTTTTATAATT
          1 A-G-CAAAATATATATTATTTTTATAATT

                       
       5711 AGCAAAATATA
          1 AGCAAAATATA

       5722 CATTGTTTGA


Statistics
Matches: 58,  Mismatches: 4, Indels: 9
        0.82            0.06        0.13

Matches are distributed among these distances:
  25    4  0.07
  26    4  0.07
  27   24  0.41
  28    6  0.10
  29   20  0.34

ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44


Consensus pattern (27 bp):   
AGCAAAATATATATTATTTTTATAATT
Done.