Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006507.1 Kokia drynarioides strain JFW-HI SEQ_121091, 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: 7856
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34


Found at i:2000 original size:53 final size:53

Alignment explanation


    Indices: 1920--2168  Score: 365
    Period size: 53  Copynumber: 4.7  Consensus size: 53

       1910 TTGTTCCAAA

                       *         *      *                        
       1920 GATTAAAGGTCTGATGACTCTATGTCATAGTGAGTTATATGAATCCTATCACG
          1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACG

                                                             * * 
       1973 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTATG
          1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACG

                               *                             *   
       2026 GATTAAAGGTCCGATGACTATGTGTCATCGTGAGTTATATGAATCCTATTACG
          1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACG

                  *     *      *                 *     *       * 
       2079 GATTAAGGGTCCAATGACTTTGTGTCATCGTGAGTTACATGAAGCC-ATCATG
          1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACG

                                 *                
       2131 GATTAAAGGTCCGATGACTCTATGTCATCGTGAGTTAT
          1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTAT

       2169 CAAATGTGAA


Statistics
Matches: 177,  Mismatches: 19, Indels: 1
        0.90            0.10        0.01

Matches are distributed among these distances:
  52   37  0.21
  53  140  0.79

ACGTcount: A:0.28, C:0.16, G:0.23, T:0.34


Consensus pattern (53 bp):   
GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACG

Found at i:5765 original size:39 final size:39

Alignment explanation


    Indices: 5722--5800  Score: 149
    Period size: 39  Copynumber: 2.0  Consensus size: 39

       5712 ATGGTTGTTT

                                          *        
       5722 TCCTTAACCCTAGGTCAATTGTCATTCCTCGTGTTTAAG
          1 TCCTTAACCCTAGGTCAATTGTCATTCCTCATGTTTAAG

                                                   
       5761 TCCTTAACCCTAGGTCAATTGTCATTCCTCATGTTTAAG
          1 TCCTTAACCCTAGGTCAATTGTCATTCCTCATGTTTAAG

             
       5800 T
          1 T

       5801 GTCATTGTAT


Statistics
Matches: 39,  Mismatches: 1, Indels: 0
        0.98            0.03        0.00

Matches are distributed among these distances:
  39   39  1.00

ACGTcount: A:0.22, C:0.25, G:0.14, T:0.39


Consensus pattern (39 bp):   
TCCTTAACCCTAGGTCAATTGTCATTCCTCATGTTTAAG

Found at i:7772 original size:2 final size:2

Alignment explanation


    Indices: 7765--7790  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       7755 TGGGGTGAAA

                                                  
       7765 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

       7791 TTAATAGTAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.