Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009472.1 Kokia drynarioides strain JFW-HI SEQ_124180, 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: 9573
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33


Found at i:1490 original size:18 final size:18

Alignment explanation


    Indices: 1450--1490  Score: 55
    Period size: 18  Copynumber: 2.3  Consensus size: 18

       1440 TTTCCAAAAA

                          *   
       1450 GCCAACTTTCCATCTTCT
          1 GCCAACTTTCCATCGTCT

            *            *    
       1468 ACCAACTTTCCATGGTCT
          1 GCCAACTTTCCATCGTCT

                 
       1486 GCCAA
          1 GCCAA

       1491 GTGAAAATCC


Statistics
Matches: 19,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  18   19  1.00

ACGTcount: A:0.22, C:0.37, G:0.10, T:0.32


Consensus pattern (18 bp):   
GCCAACTTTCCATCGTCT

Found at i:4522 original size:15 final size:16

Alignment explanation


    Indices: 4504--4533  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       4494 TTTTGGTATT

                            
       4504 TTAA-ATTTTTATTTA
          1 TTAATATTTTTATTTA

                           
       4519 TTAATATTTTTATTT
          1 TTAATATTTTTATTT

       4534 CAGACTCAAA


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    4  0.29
  16   10  0.71

ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70


Consensus pattern (16 bp):   
TTAATATTTTTATTTA

Found at i:5364 original size:14 final size:14

Alignment explanation


    Indices: 5347--5376  Score: 60
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       5337 AAGGAGTTCG

                          
       5347 AATAAAGAAGAAAA
          1 AATAAAGAAGAAAA

                          
       5361 AATAAAGAAGAAAA
          1 AATAAAGAAGAAAA

              
       5375 AA
          1 AA

       5377 AGAGAATAGC


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   16  1.00

ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07


Consensus pattern (14 bp):   
AATAAAGAAGAAAA

Found at i:5459 original size:5 final size:5

Alignment explanation


    Indices: 5449--5484  Score: 56
    Period size: 5  Copynumber: 7.2  Consensus size: 5

       5439 TAAAAGGTTC

                                                        
       5449 GAAAA GAAAA GAAAA GAAAA GAAAA GAGAAA -AAAA G
          1 GAAAA GAAAA GAAAA GAAAA GAAAA GA-AAA GAAAA G

       5485 GAGAAAAAGA


Statistics
Matches: 29,  Mismatches: 0, Indels: 4
        0.88            0.00        0.12

Matches are distributed among these distances:
   4    3  0.10
   5   23  0.79
   6    3  0.10

ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00


Consensus pattern (5 bp):   
GAAAA

Found at i:5492 original size:12 final size:11

Alignment explanation


    Indices: 5453--5503  Score: 52
    Period size: 11  Copynumber: 4.7  Consensus size: 11

       5443 AGGTTCGAAA

                        
       5453 AGAAAAGAAAAG
          1 AGAAAA-AAAAG

                 *     
       5465 A-AAAGAAAAG
          1 AGAAAAAAAAG

                     * 
       5475 AGAAAAAAAGG
          1 AGAAAAAAAAG

                   *   
       5486 AGAAAAAGAAG
          1 AGAAAAAAAAG

                    
       5497 A-AAAAAA
          1 AGAAAAAA

       5504 TGATTGCTTG


Statistics
Matches: 32,  Mismatches: 6, Indels: 4
        0.76            0.14        0.10

Matches are distributed among these distances:
  10   11  0.34
  11   20  0.62
  12    1  0.03

ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00


Consensus pattern (11 bp):   
AGAAAAAAAAG

Found at i:9243 original size:22 final size:23

Alignment explanation


    Indices: 9206--9259  Score: 83
    Period size: 22  Copynumber: 2.4  Consensus size: 23

       9196 TCCGTCCTTA

                  *                
       9206 CTGACTAGACCTTCTAGAAGCTG
          1 CTGACTGGACCTTCTAGAAGCTG

                              *    
       9229 CTGACTGGA-CTTCTAGATGCTG
          1 CTGACTGGACCTTCTAGAAGCTG

                     
       9251 CTGACTGGA
          1 CTGACTGGA

       9260 TGCCACGTCA


Statistics
Matches: 29,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  22   21  0.72
  23    8  0.28

ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28


Consensus pattern (23 bp):   
CTGACTGGACCTTCTAGAAGCTG
Done.