Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012335.1 Kokia drynarioides strain JFW-HI SEQ_127337, 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: 7677
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.35

Warning! 87 characters in sequence are not A, C, G, or T


Found at i:515 original size:19 final size:19

Alignment explanation


    Indices: 491--563  Score: 119
    Period size: 19  Copynumber: 3.8  Consensus size: 19

        481 CAGAAGGAAT

                   *           
        491 AGCATTACTGGCTCGTTTG
          1 AGCATTATTGGCTCGTTTG

                               
        510 AGCATTATTGGCTCGTTTG
          1 AGCATTATTGGCTCGTTTG

                          *    
        529 AGCATTATTGGCTCATTTG
          1 AGCATTATTGGCTCGTTTG

                *           
        548 AGCAGTATTGGCTCGT
          1 AGCATTATTGGCTCGT

        564 AAAAGCATAA


Statistics
Matches: 50,  Mismatches: 4, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  19   50  1.00

ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38


Consensus pattern (19 bp):   
AGCATTATTGGCTCGTTTG

Found at i:1537 original size:2 final size:2

Alignment explanation


    Indices: 1530--1555  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       1520 AGTAAATGAG

                                                  
       1530 TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA

       1556 AGCCTTTGTG


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:4019 original size:15 final size:15

Alignment explanation


    Indices: 3986--4043  Score: 55
    Period size: 15  Copynumber: 3.9  Consensus size: 15

       3976 GTAGGAAATT

                            
       3986 ATATGATATG-TCTCG
          1 ATATGATATGATCT-G

                          *
       4001 ATATGATATGATCTT
          1 ATATGATATGATCTG

                 *   *  *  
       4016 ATATGTTATTATGTG
          1 ATATGATATGATCTG

                *        
       4031 ATATAATATGATC
          1 ATATGATATGATC

       4044 CAATATGTTA


Statistics
Matches: 33,  Mismatches: 9, Indels: 2
        0.75            0.20        0.05

Matches are distributed among these distances:
  15   30  0.91
  16    3  0.09

ACGTcount: A:0.33, C:0.07, G:0.16, T:0.45


Consensus pattern (15 bp):   
ATATGATATGATCTG

Found at i:4034 original size:30 final size:30

Alignment explanation


    Indices: 4000--4063  Score: 83
    Period size: 30  Copynumber: 2.1  Consensus size: 30

       3990 GATATGTCTC

                 *        **         *  * 
       4000 GATATGATATGATCTTATATGTTATTATGT
          1 GATATAATATGATCCAATATGTTATAATAT

                                          
       4030 GATATAATATGATCCAATATGTTATAATAT
          1 GATATAATATGATCCAATATGTTATAATAT

                
       4060 GATA
          1 GATA

       4064 AGTTATGTTC


Statistics
Matches: 29,  Mismatches: 5, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  30   29  1.00

ACGTcount: A:0.38, C:0.05, G:0.14, T:0.44


Consensus pattern (30 bp):   
GATATAATATGATCCAATATGTTATAATAT

Found at i:5048 original size:17 final size:17

Alignment explanation


    Indices: 5026--5066  Score: 64
    Period size: 17  Copynumber: 2.4  Consensus size: 17

       5016 ACTATAAGTG

                             
       5026 CAAAAGAACAAAGAGTA
          1 CAAAAGAACAAAGAGTA

                     * *     
       5043 CAAAAGAACGAGGAGTA
          1 CAAAAGAACAAAGAGTA

                   
       5060 CAAAAGA
          1 CAAAAGA

       5067 TGAAAATAAA


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  17   22  1.00

ACGTcount: A:0.61, C:0.12, G:0.22, T:0.05


Consensus pattern (17 bp):   
CAAAAGAACAAAGAGTA
Done.