Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004476.1 Kokia drynarioides strain JFW-HI SEQ_117896, 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: 9266
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32


Found at i:108 original size:8 final size:9

Alignment explanation


    Indices: 87--115  Score: 58
    Period size: 9  Copynumber: 3.2  Consensus size: 9

         77 AATTTCAATT

                     
         87 TTTTTTCGA
          1 TTTTTTCGA

                     
         96 TTTTTTCGA
          1 TTTTTTCGA

                     
        105 TTTTTTCGA
          1 TTTTTTCGA

              
        114 TT
          1 TT

        116 CGAATCGAAT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   20  1.00

ACGTcount: A:0.10, C:0.10, G:0.10, T:0.69


Consensus pattern (9 bp):   
TTTTTTCGA

Found at i:620 original size:31 final size:32

Alignment explanation


    Indices: 584--654  Score: 81
    Period size: 31  Copynumber: 2.2  Consensus size: 32

        574 TAGAATGAGG

                  * *               *     * 
        584 TTTTAGGTTTATTAAAAGTT-GGAGAAAAATT
          1 TTTTAGATATATTAAAAGTTAGGAAAAAAAAT

                      *           *         
        615 TTTTAGATATCTTAAAAGTTAGTAAAAAAAAT
          1 TTTTAGATATATTAAAAGTTAGGAAAAAAAAT

                    
        647 TTTTAGAT
          1 TTTTAGAT

        655 CCTTAAAAGC


Statistics
Matches: 33,  Mismatches: 6, Indels: 1
        0.82            0.15        0.03

Matches are distributed among these distances:
  31   17  0.52
  32   16  0.48

ACGTcount: A:0.42, C:0.01, G:0.14, T:0.42


Consensus pattern (32 bp):   
TTTTAGATATATTAAAAGTTAGGAAAAAAAAT

Found at i:660 original size:31 final size:31

Alignment explanation


    Indices: 595--663  Score: 86
    Period size: 31  Copynumber: 2.2  Consensus size: 31

        585 TTTAGGTTTA

                        *     *          * 
        595 TTAAAAGTTGGAGAAAAATTTTTTAGATATC
          1 TTAAAAGTTGGAAAAAAAATTTTTAGATACC

                       *                    
        626 TTAAAAGTTAGTAAAAAAAATTTTTAGAT-CC
          1 TTAAAAGTT-GGAAAAAAAATTTTTAGATACC

                   
        657 TTAAAAG
          1 TTAAAAG

        664 CTAAGTTTTT


Statistics
Matches: 33,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
  31   17  0.52
  32   16  0.48

ACGTcount: A:0.46, C:0.04, G:0.13, T:0.36


Consensus pattern (31 bp):   
TTAAAAGTTGGAAAAAAAATTTTTAGATACC

Found at i:4635 original size:20 final size:20

Alignment explanation


    Indices: 4610--4649  Score: 71
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       4600 AACTATCTAC

                           *    
       4610 CAATCAAATCTCTAATATTA
          1 CAATCAAATCTCTAAGATTA

                                
       4630 CAATCAAATCTCTAAGATTA
          1 CAATCAAATCTCTAAGATTA

       4650 TAAGAATCAT


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.45, C:0.20, G:0.03, T:0.33


Consensus pattern (20 bp):   
CAATCAAATCTCTAAGATTA
Done.