Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001453.1 Kokia drynarioides strain JFW-HI SEQ_112971, 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: 12322
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35


Found at i:2987 original size:13 final size:13

Alignment explanation


    Indices: 2969--2995  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

       2959 TACAAAATTG

                         
       2969 TTACTTTAAACTA
          1 TTACTTTAAACTA

                         
       2982 TTACTTTAAACTA
          1 TTACTTTAAACTA

             
       2995 T
          1 T

       2996 GTCTAAATAT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.37, C:0.15, G:0.00, T:0.48


Consensus pattern (13 bp):   
TTACTTTAAACTA

Found at i:8048 original size:42 final size:42

Alignment explanation


    Indices: 8001--8080  Score: 151
    Period size: 42  Copynumber: 1.9  Consensus size: 42

       7991 TGGGATGATT

                                                      
       8001 CCACTTGCTCATATATATTGATTTCATACATGTTGATTTATA
          1 CCACTTGCTCATATATATTGATTTCATACATGTTGATTTATA

                          *                       
       8043 CCACTTGCTCATATGTATTGATTTCATACATGTTGATT
          1 CCACTTGCTCATATATATTGATTTCATACATGTTGATT

       8081 CATAAATACA


Statistics
Matches: 37,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  42   37  1.00

ACGTcount: A:0.26, C:0.17, G:0.11, T:0.45


Consensus pattern (42 bp):   
CCACTTGCTCATATATATTGATTTCATACATGTTGATTTATA

Found at i:8425 original size:28 final size:28

Alignment explanation


    Indices: 8225--8452  Score: 205
    Period size: 28  Copynumber: 8.1  Consensus size: 28

       8215 ATACGAACTT

                               * **    *
       8225 TTGCTTGAAAGATAGTCCACGTGGACTA
          1 TTGCTTGAAAGATAGTCCATGCAGACTC

                      *            *    
       8253 TTGCTTGAAAAATAGTCCATGCAAACTC
          1 TTGCTTGAAAGATAGTCCATGCAGACTC

                                 *  *    
       8281 TTTGCTTGAAAGATAGTCCATTCAAACTC
          1 -TTGCTTGAAAGATAGTCCATGCAGACTC

                      *      *    **  *  
       8310 TTTGCTTGAAGGATAGTGCATGTGGATTC
          1 -TTGCTTGAAAGATAGTCCATGCAGACTC

                                        * 
       8339 TTGCTTGAAAGATAG-CCTATGC-GAACAC
          1 TTGCTTGAAAGATAGTCC-ATGCAG-ACTC

                           *      *      
       8367 TTGCTTG-AAGAATAATCCATGTAGACTC
          1 TTGCTTGAAAG-ATAGTCCATGCAGACTC

                          *             
       8395 TTGCTTGAAAGATAATCCATGCAGACTC
          1 TTGCTTGAAAGATAGTCCATGCAGACTC

                                          
       8423 TTG-TTCG-AAGAATAGTCCATGCAGACTC
          1 TTGCTT-GAAAG-ATAGTCCATGCAGACTC

              
       8451 TT
          1 TT

       8453 ACATGAAGAT


Statistics
Matches: 166,  Mismatches: 25, Indels: 18
        0.79            0.12        0.09

Matches are distributed among these distances:
  27   10  0.06
  28  102  0.61
  29   54  0.33

ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31


Consensus pattern (28 bp):   
TTGCTTGAAAGATAGTCCATGCAGACTC

Done.