Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011948.1 Kokia drynarioides strain JFW-HI SEQ_126946, 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: 1950
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.36


Found at i:905 original size:33 final size:32

Alignment explanation


    Indices: 863--976  Score: 101
    Period size: 33  Copynumber: 3.6  Consensus size: 32

        853 TGTTAATTTA

                                  *          
        863 TTATTTTTTATTTTATTTTATTTTATTTATCAT
          1 TTATTTTTTATTTTATTTTA-TCTATTTATCAT

                                     *     *  
        896 TTATTTTTTATTTCCT-TTTTATCTGTTTATTAT
          1 TTATTTTTTATTT--TATTTTATCTATTTATCAT

               *                   * *      
        929 TTAATTTTTATTTTATTTT-TCTCTCTAT-AT
          1 TTATTTTTTATTTTATTTTATCTATTTATCAT

            *                  
        959 AT-TTTTTTATATTTATTT
          1 TTATTTTTTAT-TTTATTT

        977 CTTTATTATT


Statistics
Matches: 69,  Mismatches: 8, Indels: 11
        0.78            0.09        0.12

Matches are distributed among these distances:
  29    7  0.10
  30   10  0.14
  31    8  0.12
  32    4  0.06
  33   34  0.49
  34    5  0.07
  35    1  0.01

ACGTcount: A:0.19, C:0.06, G:0.01, T:0.74


Consensus pattern (32 bp):   
TTATTTTTTATTTTATTTTATCTATTTATCAT

Found at i:908 original size:11 final size:11

Alignment explanation


    Indices: 859--948  Score: 67
    Period size: 11  Copynumber: 8.2  Consensus size: 11

        849 CTTTTGTTAA

                       
        859 TTTA-TTATTT
          1 TTTATTTATTT

                     * 
        869 TTTATTT-TAT
          1 TTTATTTATTT

                        
        879 TTTATTTTATTT
          1 TTTA-TTTATTT

            * *        
        891 ATCATTTATTT
          1 TTTATTTATTT

                   **  
        902 TTTATTTCCTT
          1 TTTATTTATTT

                 * *   
        913 TTTATCTGTTT
          1 TTTATTTATTT

            *       *  
        924 ATTATTTAATT
          1 TTTATTTATTT

                        
        935 TTTATTTTATTT
          1 TTTA-TTTATTT

              
        947 TT
          1 TT

        949 CTCTCTATAT


Statistics
Matches: 59,  Mismatches: 17, Indels: 6
        0.72            0.21        0.07

Matches are distributed among these distances:
  10   10  0.17
  11   37  0.63
  12   12  0.20

ACGTcount: A:0.19, C:0.04, G:0.01, T:0.76


Consensus pattern (11 bp):   
TTTATTTATTT

Found at i:1090 original size:10 final size:10

Alignment explanation


    Indices: 1071--1114  Score: 54
    Period size: 10  Copynumber: 4.4  Consensus size: 10

       1061 TATTTCTATT

                      
       1071 ATTTATTTTC
          1 ATTTATTTTC

                 *    
       1081 ATTTAATTTC
          1 ATTTATTTTC

                  *    
       1091 -TTTCACTTTC
          1 ATTT-ATTTTC

                      
       1101 ATTTATTTTC
          1 ATTTATTTTC

                
       1111 ATTT
          1 ATTT

       1115 TTATCTATTG


Statistics
Matches: 29,  Mismatches: 3, Indels: 4
        0.81            0.08        0.11

Matches are distributed among these distances:
   9    3  0.10
  10   23  0.79
  11    3  0.10

ACGTcount: A:0.20, C:0.14, G:0.00, T:0.66


Consensus pattern (10 bp):   
ATTTATTTTC
Done.