Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007987.1 Kokia drynarioides strain JFW-HI SEQ_122638, 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: 10562
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33


Found at i:2203 original size:21 final size:21

Alignment explanation


    Indices: 2148--2203  Score: 60
    Period size: 21  Copynumber: 2.7  Consensus size: 21

       2138 TTTGTGATGG

                        *        
       2148 TTCTACCGATACAAGTGTAAC
          1 TTCTACCGATACTAGTGTAAC

                   * *          * 
       2169 TTCTACCAAAACTAGT-TATGC
          1 TTCTACCGATACTAGTGTA-AC

                          
       2190 TTCTACCGATACTA
          1 TTCTACCGATACTA

       2204 AAAACTCTAG


Statistics
Matches: 28,  Mismatches: 6, Indels: 2
        0.78            0.17        0.06

Matches are distributed among these distances:
  20    2  0.07
  21   26  0.93

ACGTcount: A:0.32, C:0.25, G:0.11, T:0.32


Consensus pattern (21 bp):   
TTCTACCGATACTAGTGTAAC

Found at i:2910 original size:42 final size:42

Alignment explanation


    Indices: 2863--2996  Score: 137
    Period size: 42  Copynumber: 3.2  Consensus size: 42

       2853 TATATACTCA

                                **   *    *           
       2863 TTCCTTTAATCATAATCTCATTCTCTTCTCTAGACATGAGTC
          1 TTCCTTTAATCATAATCTCAACCTCATCTCGAGACATGAGTC

                            *                         
       2905 TTCCTTTAATCATAATTTCAACCTCATCTCGAGACATGAGTC
          1 TTCCTTTAATCATAATCTCAACCTCATCTCGAGACATGAGTC

                                   ***   * *             
       2947 TTCCATTT-ATACA-AATTCTCATGTTCAACCCGAGACATGAGTC
          1 TTCC-TTTAAT-CATAA-TCTCAACCTCATCTCGAGACATGAGTC

                   
       2990 TTCCTTT
          1 TTCCTTT

       2997 TTATACATAA


Statistics
Matches: 78,  Mismatches: 11, Indels: 6
        0.82            0.12        0.06

Matches are distributed among these distances:
  42   48  0.62
  43   30  0.38

ACGTcount: A:0.26, C:0.26, G:0.09, T:0.39


Consensus pattern (42 bp):   
TTCCTTTAATCATAATCTCAACCTCATCTCGAGACATGAGTC

Found at i:5549 original size:13 final size:13

Alignment explanation


    Indices: 5531--5555  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       5521 TAAATTGAAA

                         
       5531 GAATTTTCTGTAC
          1 GAATTTTCTGTAC

                        
       5544 GAATTTTCTGTA
          1 GAATTTTCTGTA

       5556 AAAATATAAT


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.24, C:0.12, G:0.16, T:0.48


Consensus pattern (13 bp):   
GAATTTTCTGTAC

Found at i:5910 original size:23 final size:23

Alignment explanation


    Indices: 5873--6005  Score: 196
    Period size: 23  Copynumber: 5.8  Consensus size: 23

       5863 TTACTGTTCA

                                  *
       5873 GCACTGT-TGTGCTTACTGATTC
          1 GCACTGTGTGTGCTTACTGATTT

                 * *               
       5895 GCACTATATGTGCTTACTGATTT
          1 GCACTGTGTGTGCTTACTGATTT

                                   
       5918 GCACTGTGTGTGCTTACTGATTT
          1 GCACTGTGTGTGCTTACTGATTT

                               *   
       5941 GCACTGTGTGTGCTTACTGTTTT
          1 GCACTGTGTGTGCTTACTGATTT

                  *      *  *      
       5964 GCACTGCGTGTGCCTATTGATTT
          1 GCACTGTGTGTGCTTACTGATTT

                               
       5987 GCACTGTGTGTGCTTACTG
          1 GCACTGTGTGTGCTTACTG

       6006 TTTCCCCAGC


Statistics
Matches: 98,  Mismatches: 12, Indels: 1
        0.88            0.11        0.01

Matches are distributed among these distances:
  22    6  0.06
  23   92  0.94

ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42


Consensus pattern (23 bp):   
GCACTGTGTGTGCTTACTGATTT

Found at i:6006 original size:46 final size:45

Alignment explanation


    Indices: 5861--6008  Score: 197
    Period size: 46  Copynumber: 3.2  Consensus size: 45

       5851 ACATTAGCGC

                      **      *              *     * *   
       5861 GCTTACTGTTCAGCACTGTTGTGCTTACTGATTCGCACTATATGT
          1 GCTTACTGTTTTGCACTGGTGTGCTTACTGATTTGCACTGTGTGT

                    *                                     
       5906 GCTTACTGATTTGCACTGTGTGTGCTTACTGATTTGCACTGTGTGT
          1 GCTTACTGTTTTGCACTG-GTGTGCTTACTGATTTGCACTGTGTGT

                                     *  *                 
       5952 GCTTACTGTTTTGCACTGCGTGTGCCTATTGATTTGCACTGTGTGT
          1 GCTTACTGTTTTGCACTG-GTGTGCTTACTGATTTGCACTGTGTGT

                       
       5998 GCTTACTGTTT
          1 GCTTACTGTTT

       6009 CCCCAGCACT


Statistics
Matches: 91,  Mismatches: 11, Indels: 1
        0.88            0.11        0.01

Matches are distributed among these distances:
  45   15  0.16
  46   76  0.84

ACGTcount: A:0.14, C:0.20, G:0.24, T:0.43


Consensus pattern (45 bp):   
GCTTACTGTTTTGCACTGGTGTGCTTACTGATTTGCACTGTGTGT
Done.