Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008832.1 Kokia drynarioides strain JFW-HI SEQ_123516, 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: 8741
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34


Found at i:595 original size:17 final size:17

Alignment explanation


    Indices: 527--595  Score: 59
    Period size: 17  Copynumber: 4.1  Consensus size: 17

        517 CCAATTTTAA

                 *     *     
        527 ATTTTAAATTTTAATTT
          1 ATTTTGAATTTAAATTT

                           *  
        544 ATTTT-AAGTTTAAACTT
          1 ATTTTGAA-TTTAAATTT

               *   *     *   
        561 ATTCTGAGTTTAATTTT
          1 ATTTTGAATTTAAATTT

                      *      
        578 ATTTTGAATTCAAATTT
          1 ATTTTGAATTTAAATTT

             
        595 A
          1 A

        596 AAGTTTAAAT


Statistics
Matches: 40,  Mismatches: 10, Indels: 4
        0.74            0.19        0.07

Matches are distributed among these distances:
  16    2  0.05
  17   37  0.93
  18    1  0.03

ACGTcount: A:0.33, C:0.04, G:0.06, T:0.57


Consensus pattern (17 bp):   
ATTTTGAATTTAAATTT

Found at i:4290 original size:3 final size:3

Alignment explanation


    Indices: 4282--4310  Score: 58
    Period size: 3  Copynumber: 9.7  Consensus size: 3

       4272 CTATTTTTAT

                                                  
       4282 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA

       4311 GTTGATTAAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   26  1.00

ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34


Consensus pattern (3 bp):   
TAA

Found at i:5902 original size:18 final size:18

Alignment explanation


    Indices: 5879--5917  Score: 53
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       5869 CTGAGTTTTT

                               
       5879 ATTTAACAA-TTGTAATTA
          1 ATTTAA-AATTTGTAATTA

                       *      
       5897 ATTTAAAATTTTTAATTA
          1 ATTTAAAATTTGTAATTA

               
       5915 ATT
          1 ATT

       5918 AAATTTATTT


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  17    2  0.11
  18   17  0.89

ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51


Consensus pattern (18 bp):   
ATTTAAAATTTGTAATTA

Found at i:5928 original size:18 final size:18

Alignment explanation


    Indices: 5891--5942  Score: 65
    Period size: 18  Copynumber: 3.0  Consensus size: 18

       5881 TTAACAATTG

                         *     
       5891 TAATTAATTTAAAATT-TT
          1 TAATTAA-TTAAATTTATT

                              
       5909 TAATTAATTAAATTTATT
          1 TAATTAATTAAATTTATT

                              
       5927 TAATTAA--AAATTTATT
          1 TAATTAATTAAATTTATT

       5943 CTCATCTCAG


Statistics
Matches: 32,  Mismatches: 1, Indels: 4
        0.86            0.03        0.11

Matches are distributed among these distances:
  16    9  0.28
  17    7  0.22
  18   16  0.50

ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54


Consensus pattern (18 bp):   
TAATTAATTAAATTTATT

Found at i:6207 original size:2 final size:2

Alignment explanation


    Indices: 6200--6233  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       6190 AAATACCTCC

                                                              
       6200 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       6234 TAACACGTTT


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.