Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008020.1 Kokia drynarioides strain JFW-HI SEQ_122674, 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: 7385
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33


Found at i:1853 original size:15 final size:16

Alignment explanation


    Indices: 1833--1872  Score: 55
    Period size: 16  Copynumber: 2.5  Consensus size: 16

       1823 TATAGTTTCA

                            
       1833 TATAGTTTCACA-ATC
          1 TATAGTTTCACATATC

                          *  
       1848 TATAGTTTTCACATTTC
          1 TATAG-TTTCACATATC

                    
       1865 TATAGTTT
          1 TATAGTTT

       1873 TAAAGTTAAT


Statistics
Matches: 22,  Mismatches: 1, Indels: 3
        0.85            0.04        0.12

Matches are distributed among these distances:
  15    5  0.23
  16   10  0.45
  17    7  0.32

ACGTcount: A:0.28, C:0.15, G:0.07, T:0.50


Consensus pattern (16 bp):   
TATAGTTTCACATATC

Found at i:1868 original size:17 final size:17

Alignment explanation


    Indices: 1828--1873  Score: 60
    Period size: 17  Copynumber: 2.8  Consensus size: 17

       1818 TTAACTATAG

                              
       1828 TTTCATATAG-TTTCACA
          1 TTTC-TATAGTTTTCACA

             *               
       1845 -ATCTATAGTTTTCACA
          1 TTTCTATAGTTTTCACA

                         
       1861 TTTCTATAGTTTT
          1 TTTCTATAGTTTT

       1874 AAAGTTAATA


Statistics
Matches: 25,  Mismatches: 2, Indels: 4
        0.81            0.06        0.13

Matches are distributed among these distances:
  15    5  0.20
  16    9  0.36
  17   11  0.44

ACGTcount: A:0.26, C:0.15, G:0.07, T:0.52


Consensus pattern (17 bp):   
TTTCTATAGTTTTCACA

Found at i:2938 original size:21 final size:21

Alignment explanation


    Indices: 2913--2956  Score: 79
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       2903 CACATAGCAC

                 *               
       2913 ATTGTGGAAAACGGCCACATA
          1 ATTGTCGAAAACGGCCACATA

                                 
       2934 ATTGTCGAAAACGGCCACATA
          1 ATTGTCGAAAACGGCCACATA

              
       2955 AT
          1 AT

       2957 CACAGTTAAA


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  21   22  1.00

ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20


Consensus pattern (21 bp):   
ATTGTCGAAAACGGCCACATA

Found at i:3412 original size:3 final size:3

Alignment explanation


    Indices: 3404--3456  Score: 106
    Period size: 3  Copynumber: 17.7  Consensus size: 3

       3394 ATTTTGTTTC

                                                                           
       3404 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT

                  
       3452 AAT AA
          1 AAT AA

       3457 CTTCACTTAA


Statistics
Matches: 50,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   50  1.00

ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32


Consensus pattern (3 bp):   
AAT

Found at i:6283 original size:25 final size:25

Alignment explanation


    Indices: 6254--6305  Score: 104
    Period size: 25  Copynumber: 2.1  Consensus size: 25

       6244 TAATAACTAA

                                     
       6254 AAAGTAATTGAAGGACCAATTATGT
          1 AAAGTAATTGAAGGACCAATTATGT

                                     
       6279 AAAGTAATTGAAGGACCAATTATGT
          1 AAAGTAATTGAAGGACCAATTATGT

              
       6304 AA
          1 AA

       6306 TTGGACCCTC


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  25   27  1.00

ACGTcount: A:0.46, C:0.08, G:0.19, T:0.27


Consensus pattern (25 bp):   
AAAGTAATTGAAGGACCAATTATGT

Done.