Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002445.1 Kokia drynarioides strain JFW-HI SEQ_114558, 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: 3782
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.31


Found at i:149 original size:12 final size:12

Alignment explanation


    Indices: 134--217  Score: 78
    Period size: 12  Copynumber: 6.8  Consensus size: 12

        124 TAGATGGAAG

                        
        134 TGATGATGATTT
          1 TGATGATGATTT

                     *  
        146 TGATGATGAGTT
          1 TGATGATGATTT

            *            
        158 CGATGATGAATTT
          1 TGATGATG-ATTT

               *       *  
        171 GATTATGATGAATT
          1 --TGATGATGATTT

                      **
        185 TGATGATGATGA
          1 TGATGATGATTT

            *           
        197 AGATGATGATTT
          1 TGATGATGATTT

                     
        209 TGATGATGA
          1 TGATGATGA

        218 GGAATTTGGT


Statistics
Matches: 55,  Mismatches: 14, Indels: 6
        0.73            0.19        0.08

Matches are distributed among these distances:
  12   43  0.78
  13    3  0.05
  14    3  0.05
  15    6  0.11

ACGTcount: A:0.31, C:0.01, G:0.27, T:0.40


Consensus pattern (12 bp):   
TGATGATGATTT

Found at i:225 original size:15 final size:15

Alignment explanation


    Indices: 159--225  Score: 74
    Period size: 15  Copynumber: 4.9  Consensus size: 15

        149 TGATGAGTTC

                           
        159 GATGATGAATTTGAT
          1 GATGATGAATTTGAT

            *              
        174 TATGATGAATTTGAT
          1 GATGATGAATTTGAT

                           
        189 GATGATGAA---GAT
          1 GATGATGAATTTGAT

                           
        201 GATGAT---TTTGAT
          1 GATGATGAATTTGAT

                 *       
        213 GATGAGGAATTTG
          1 GATGATGAATTTG

        226 GTCATGGACA


Statistics
Matches: 43,  Mismatches: 3, Indels: 12
        0.74            0.05        0.21

Matches are distributed among these distances:
  12   17  0.40
  15   26  0.60

ACGTcount: A:0.33, C:0.00, G:0.28, T:0.39


Consensus pattern (15 bp):   
GATGATGAATTTGAT

Found at i:885 original size:9 final size:9

Alignment explanation


    Indices: 873--902  Score: 51
    Period size: 9  Copynumber: 3.3  Consensus size: 9

        863 CCAAATGGGT

                     
        873 GGTCAGATG
          1 GGTCAGATG

                     
        882 GGTCAGATG
          1 GGTCAGATG

                 *   
        891 GGTCACATG
          1 GGTCAGATG

               
        900 GGT
          1 GGT

        903 GGTCAGATGG


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   9   20  1.00

ACGTcount: A:0.20, C:0.13, G:0.43, T:0.23


Consensus pattern (9 bp):   
GGTCAGATG

Found at i:889 original size:30 final size:30

Alignment explanation


    Indices: 849--914  Score: 105
    Period size: 30  Copynumber: 2.2  Consensus size: 30

        839 CGGTAAGAAT

                 *                        
        849 ATGGGGCAGATGGGCCAAATGGGTGGTCAG
          1 ATGGGTCAGATGGGCCAAATGGGTGGTCAG

                          *  *            
        879 ATGGGTCAGATGGGTCACATGGGTGGTCAG
          1 ATGGGTCAGATGGGCCAAATGGGTGGTCAG

                  
        909 ATGGGT
          1 ATGGGT

        915 TATAACATGG


Statistics
Matches: 33,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  30   33  1.00

ACGTcount: A:0.21, C:0.12, G:0.45, T:0.21


Consensus pattern (30 bp):   
ATGGGTCAGATGGGCCAAATGGGTGGTCAG

Found at i:3694 original size:15 final size:15

Alignment explanation


    Indices: 3671--3706  Score: 54
    Period size: 15  Copynumber: 2.4  Consensus size: 15

       3661 AAATTTAAAG

                           
       3671 AAAAATGAATCTTGT
          1 AAAAATGAATCTTGT

                *     *    
       3686 AAAATTGAATGTTGT
          1 AAAAATGAATCTTGT

                  
       3701 AAAAAT
          1 AAAAAT

       3707 CTTGGTTTTG


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  15   18  1.00

ACGTcount: A:0.50, C:0.03, G:0.14, T:0.33


Consensus pattern (15 bp):   
AAAAATGAATCTTGT
Done.