Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013973.1 Kokia drynarioides strain JFW-HI SEQ_129004, 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: 7784
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35

Warning! 5 characters in sequence are not A, C, G, or T


Found at i:5755 original size:21 final size:22

Alignment explanation


    Indices: 5713--5755  Score: 52
    Period size: 21  Copynumber: 2.0  Consensus size: 22

       5703 AAAAAGGGTC

                            **    
       5713 AAATGCAAGATTTATTTTTTTA
          1 AAATGCAAGATTTATTAATTTA

                 *                
       5735 AAATGGAA-ATTTATTAATTTA
          1 AAATGCAAGATTTATTAATTTA

       5756 CTAAATAAAT


Statistics
Matches: 18,  Mismatches: 3, Indels: 1
        0.82            0.14        0.05

Matches are distributed among these distances:
  21   11  0.61
  22    7  0.39

ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47


Consensus pattern (22 bp):   
AAATGCAAGATTTATTAATTTA

Found at i:6876 original size:4 final size:4

Alignment explanation


    Indices: 6867--6946  Score: 63
    Period size: 4  Copynumber: 19.2  Consensus size: 4

       6857 AAATAAACGG

                                                 *      *     *          
       6867 GAAA GAAA GAAA GGAAA GAAA GAAA GAAA GGAA GAAG GAGAG GAAA GAAA
          1 GAAA GAAA GAAA -GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA

                **                   *            
       6917 GGAGGG GAAA GAAA G-AA GAAG GAAA GAAA G
          1 -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA G

       6947 GTAATGTGTT


Statistics
Matches: 61,  Mismatches: 10, Indels: 10
        0.75            0.12        0.12

Matches are distributed among these distances:
   3    3  0.05
   4   46  0.75
   5   12  0.20

ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00


Consensus pattern (4 bp):   
GAAA

Found at i:6889 original size:17 final size:18

Alignment explanation


    Indices: 6867--6946  Score: 74
    Period size: 17  Copynumber: 4.3  Consensus size: 18

       6857 AAATAAACGG

                              
       6867 GAAAGAAAGAAAGGA-AA
          1 GAAAGAAAGAAAGGAGAA

                               
       6884 GAAAGAAAGAAAGGAAGAA
          1 GAAAGAAAGAAAGG-AGAA

                 *            **
       6903 GGAGAGGAAAGAAAGGAGGG
          1 -GA-AAGAAAGAAAGGAGAA

                                
       6923 GAAAGAAAGAAGAAGGA-AA
          1 GAAAGAAAG-A-AAGGAGAA

                 
       6942 GAAAG
          1 GAAAG

       6947 GTAATGTGTT


Statistics
Matches: 51,  Mismatches: 6, Indels: 10
        0.76            0.09        0.15

Matches are distributed among these distances:
  17   14  0.27
  18    7  0.14
  19   10  0.20
  20    9  0.18
  21   11  0.22

ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00


Consensus pattern (18 bp):   
GAAAGAAAGAAAGGAGAA
Done.