Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008019.1 Kokia drynarioides strain JFW-HI SEQ_122673, 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: 7351
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32


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:2937 original size:21 final size:21

Alignment explanation


    Indices: 2913--2952  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       2903 CACATAGCAC

                 *               
       2913 ATTGTGGAAAACGACCACAAA
          1 ATTGTCGAAAACGACCACAAA

                         *     
       2934 ATTGTCGAAAACGGCCACA
          1 ATTGTCGAAAACGACCACA

       2953 TAATCACAGT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.42, C:0.23, G:0.20, T:0.15


Consensus pattern (21 bp):   
ATTGTCGAAAACGACCACAAA

Found at i:4022 original size:17 final size:18

Alignment explanation


    Indices: 4000--4039  Score: 55
    Period size: 20  Copynumber: 2.2  Consensus size: 18

       3990 TCACTGACGA

                              
       4000 TGACGA-CGATGGTGGTC
          1 TGACGAGCGATGGTGGTC

                                
       4017 TGACGATGGCGATGGTGGTC
          1 TGACGA--GCGATGGTGGTC

               
       4037 TGA
          1 TGA

       4040 TGACTCGAAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 3
        0.87            0.00        0.13

Matches are distributed among these distances:
  17    6  0.30
  20   14  0.70

ACGTcount: A:0.17, C:0.15, G:0.42, T:0.25


Consensus pattern (18 bp):   
TGACGAGCGATGGTGGTC

Found at i:6249 original size:25 final size:25

Alignment explanation


    Indices: 6220--6271  Score: 104
    Period size: 25  Copynumber: 2.1  Consensus size: 25

       6210 TAATAACTAA

                                     
       6220 AAAGTAATTGAAGGACCAATTATGT
          1 AAAGTAATTGAAGGACCAATTATGT

                                     
       6245 AAAGTAATTGAAGGACCAATTATGT
          1 AAAGTAATTGAAGGACCAATTATGT

              
       6270 AA
          1 AA

       6272 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.