Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011515.1 Kokia drynarioides strain JFW-HI SEQ_126500, 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: 12399
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.36


Found at i:3872 original size:16 final size:17

Alignment explanation


    Indices: 3851--3882  Score: 57
    Period size: 16  Copynumber: 1.9  Consensus size: 17

       3841 ATGATGCGTA

                             
       3851 AATATAATAA-ATATAT
          1 AATATAATAAGATATAT

                            
       3867 AATATAATAAGATATA
          1 AATATAATAAGATATA

       3883 AGCAAATAAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  16   10  0.67
  17    5  0.33

ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34


Consensus pattern (17 bp):   
AATATAATAAGATATAT

Found at i:5352 original size:49 final size:49

Alignment explanation


    Indices: 5299--5394  Score: 176
    Period size: 49  Copynumber: 2.0  Consensus size: 49

       5289 TCCTCTATTA

                                                              
       5299 TTTTTTTGCTTAAAAATACCATAAACATATCTTTCAG-AGTCCACTACTC
          1 TTTTTTTGCTTAAAAATACCATAAACATATCTTTC-GCAGTCCACTACTC

                                                           
       5348 TTTTTTTGCTTAAAAATACCATAAACATATCTTTCGCAGTCCACTAC
          1 TTTTTTTGCTTAAAAATACCATAAACATATCTTTCGCAGTCCACTAC

       5395 AATCTGACCA


Statistics
Matches: 46,  Mismatches: 0, Indels: 2
        0.96            0.00        0.04

Matches are distributed among these distances:
  48    1  0.02
  49   45  0.98

ACGTcount: A:0.32, C:0.23, G:0.06, T:0.39


Consensus pattern (49 bp):   
TTTTTTTGCTTAAAAATACCATAAACATATCTTTCGCAGTCCACTACTC

Found at i:6503 original size:25 final size:26

Alignment explanation


    Indices: 6466--6519  Score: 83
    Period size: 25  Copynumber: 2.1  Consensus size: 26

       6456 ATTACCGTAA

                           *        * 
       6466 AAAGAAAAAGAAAATGACTAAAACTT
          1 AAAGAAAAAGAAAATAACTAAAACCT

                                      
       6492 AAAG-AAAAGAAAATAACTAAAACCT
          1 AAAGAAAAAGAAAATAACTAAAACCT

               
       6517 AAA
          1 AAA

       6520 TTACAGGATA


Statistics
Matches: 26,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
  25   22  0.85
  26    4  0.15

ACGTcount: A:0.69, C:0.09, G:0.09, T:0.13


Consensus pattern (26 bp):   
AAAGAAAAAGAAAATAACTAAAACCT

Found at i:9956 original size:12 final size:12

Alignment explanation


    Indices: 9939--9970  Score: 55
    Period size: 12  Copynumber: 2.7  Consensus size: 12

       9929 AGCACACGAC

                  *     
       9939 AAACAAGAAAAA
          1 AAACAAAAAAAA

                        
       9951 AAACAAAAAAAA
          1 AAACAAAAAAAA

                    
       9963 AAACAAAA
          1 AAACAAAA

       9971 TTTCTATGTT


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  12   19  1.00

ACGTcount: A:0.88, C:0.09, G:0.03, T:0.00


Consensus pattern (12 bp):   
AAACAAAAAAAA
Done.