Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006490.1 Kokia drynarioides strain JFW-HI SEQ_121074, 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: 7434
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35


Found at i:5895 original size:19 final size:17

Alignment explanation


    Indices: 5865--5914  Score: 64
    Period size: 19  Copynumber: 2.8  Consensus size: 17

       5855 ATTAAAATGG

                   *         
       5865 TAAAAAATTATAAATAA
          1 TAAAAAAATATAAATAA

                *              
       5882 TTATTAAAAATATAAATAA
          1 -TA-AAAAAATATAAATAA

                          
       5901 TAAAAAAATATAAA
          1 TAAAAAAATATAAA

       5915 ATCCTTAAAA


Statistics
Matches: 28,  Mismatches: 3, Indels: 3
        0.82            0.09        0.09

Matches are distributed among these distances:
  17   11  0.39
  18    4  0.14
  19   13  0.46

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


Consensus pattern (17 bp):   
TAAAAAAATATAAATAA

Found at i:5910 original size:8 final size:9

Alignment explanation


    Indices: 5865--5915  Score: 50
    Period size: 9  Copynumber: 5.6  Consensus size: 9

       5855 ATTAAAATGG

                      
       5865 TAAAAAATTA
          1 TAAAAAA-TA

                   *  
       5875 TAAATAATTA
          1 TAAA-AAATA

             *       
       5885 TTAAAAATA
          1 TAAAAAATA

                *    
       5894 TAAATAATA
          1 TAAAAAATA

                     
       5903 -AAAAAATA
          1 TAAAAAATA

                 
       5911 TAAAA
          1 TAAAA

       5916 TCCTTAAAAT


Statistics
Matches: 33,  Mismatches: 6, Indels: 5
        0.75            0.14        0.11

Matches are distributed among these distances:
   8    7  0.21
   9   15  0.45
  10    9  0.27
  11    2  0.06

ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29


Consensus pattern (9 bp):   
TAAAAAATA

Found at i:6507 original size:22 final size:22

Alignment explanation


    Indices: 6456--6508  Score: 63
    Period size: 22  Copynumber: 2.4  Consensus size: 22

       6446 TTTTTTTTTA

                   *         *    
       6456 GATTTTTCAAATAATTATTTAT
          1 GATTTTTTAAATAATTAGTTAT

                *                  
       6478 -ATAATTTTAAATAATTAGTTAT
          1 GAT-TTTTTAAATAATTAGTTAT

                     
       6500 GATTTTTTA
          1 GATTTTTTA

       6509 TATTTTTATA


Statistics
Matches: 25,  Mismatches: 4, Indels: 4
        0.76            0.12        0.12

Matches are distributed among these distances:
  21    2  0.08
  22   21  0.84
  23    2  0.08

ACGTcount: A:0.38, C:0.02, G:0.06, T:0.55


Consensus pattern (22 bp):   
GATTTTTTAAATAATTAGTTAT
Done.