Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01015101.1 Kokia drynarioides strain JFW-HI SEQ_130145, 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: 9428
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.31


Found at i:1725 original size:174 final size:175

Alignment explanation


    Indices: 1435--1781  Score: 626
    Period size: 174  Copynumber: 2.0  Consensus size: 175

       1425 ATCTATTTTC

                                                                             
       1435 CTTTTGCCAATTATCTATGGAGCTTCCAAATTGTGCTCCAATGCATAAACCATAACCAATAAGAA
          1 CTTTTGCCAATTATCTATGGAGCTTCCAAATTGTGCTCCAATGCATAAACCATAACCAATAAGAA

                                       *          *                 *        
       1500 TCTCAAATTTCCCCCACTCTCATTTTTTTATAAAGCCAGAAGCCCACAGATTCCAACTGATACAG
         66 TCTCAAATTTCCCCCACTCTCATTTTTCTATAAAGCCAAAAGCCCACAGATTCCAAATGATACA-

                                                          
       1565 TT-CAAGCACAATGAAGTGAAGTAATTGGGGC-ACAGGCTTTGCAG
        130 TTACAAGCACAATGAAGTGAAGTAATTGGGGCAACAGGCTTTGCAG

                                                                             
       1609 CTTTTGCCAATTATCTATGGAGCTTCCAAATTGTGCTCCAATGCATAAACCATAACCAATAAGAA
          1 CTTTTGCCAATTATCTATGGAGCTTCCAAATTGTGCTCCAATGCATAAACCATAACCAATAAGAA

                *                           *                                
       1674 TCTCGAATTTCCCCCACTCTCATTTTTCTATAGAGCCAAAAGCCCACAGATTCCAAATGATACAT
         66 TCTCAAATTTCCCCCACTCTCATTTTTCTATAAAGCCAAAAGCCCACAGATTCCAAATGATACAT

                                                       
       1739 TACAAGCACAATGAAGTGAAGTAATTGGGGCAACAGGCTTTGC
        131 TACAAGCACAATGAAGTGAAGTAATTGGGGCAACAGGCTTTGC

       1782 GCCTTTTCAG


Statistics
Matches: 166,  Mismatches: 5, Indels: 3
        0.95            0.03        0.02

Matches are distributed among these distances:
 173    2  0.01
 174  153  0.92
 175   11  0.07

ACGTcount: A:0.33, C:0.24, G:0.15, T:0.27


Consensus pattern (175 bp):   
CTTTTGCCAATTATCTATGGAGCTTCCAAATTGTGCTCCAATGCATAAACCATAACCAATAAGAA
TCTCAAATTTCCCCCACTCTCATTTTTCTATAAAGCCAAAAGCCCACAGATTCCAAATGATACAT
TACAAGCACAATGAAGTGAAGTAATTGGGGCAACAGGCTTTGCAG

Found at i:3673 original size:30 final size:30

Alignment explanation


    Indices: 3630--3702  Score: 85
    Period size: 30  Copynumber: 2.4  Consensus size: 30

       3620 GTTACATTTA

                 *        *  *             
       3630 ACAAAGCAATCACTCAACTTA-GAAAATGTG
          1 ACAAAACAATCACTAAAATTATGAAAA-GTG

                    *                      
       3660 ACAAAACAGTCACTAAAATTATTGAAAAGTG
          1 ACAAAACAATCACTAAAATTA-TGAAAAGTG

                        
       3691 ACAAAACAATCA
          1 ACAAAACAATCA

       3703 TCTACTTACT


Statistics
Matches: 36,  Mismatches: 5, Indels: 3
        0.82            0.11        0.07

Matches are distributed among these distances:
  30   17  0.47
  31   14  0.39
  32    5  0.14

ACGTcount: A:0.52, C:0.18, G:0.11, T:0.19


Consensus pattern (30 bp):   
ACAAAACAATCACTAAAATTATGAAAAGTG

Found at i:4554 original size:30 final size:31

Alignment explanation


    Indices: 4490--4561  Score: 103
    Period size: 30  Copynumber: 2.4  Consensus size: 31

       4480 AAGCCAAGAG

                                       *   
       4490 GACTGTTTTGTCACTTTTCGATAACTTTAGT
          1 GACTGTTTTGTCACTTTTCGATAACTTGAGT

                                     *      
       4521 GACTGTTTTGTCACATTTTC-A-AAGTTGAGT
          1 GACTGTTTTGTCAC-TTTTCGATAACTTGAGT

                       
       4551 GACTGTTTTGT
          1 GACTGTTTTGT

       4562 TAAATATAAC


Statistics
Matches: 38,  Mismatches: 2, Indels: 3
        0.88            0.05        0.07

Matches are distributed among these distances:
  30   18  0.47
  31   15  0.39
  32    5  0.13

ACGTcount: A:0.19, C:0.14, G:0.19, T:0.47


Consensus pattern (31 bp):   
GACTGTTTTGTCACTTTTCGATAACTTGAGT

Found at i:6815 original size:2 final size:2

Alignment explanation


    Indices: 6810--6839  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       6800 GAGAGAGAGA

                                                        
       6810 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
          1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT

       6840 TGGCTTTTTT


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

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


Consensus pattern (2 bp):   
CT

Done.