Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011910.1 Kokia drynarioides strain JFW-HI SEQ_126908, 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: 4043
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.34


Found at i:2861 original size:18 final size:18

Alignment explanation


    Indices: 2840--2898  Score: 50
    Period size: 18  Copynumber: 3.3  Consensus size: 18

       2830 CACCGGAGAA

                              
       2840 AGGAGGGATCTTGGGCAG
          1 AGGAGGGATCTTGGGCAG

                        *   *  
       2858 AGGAGCGG-TCTCGGGGAG
          1 AGGAG-GGATCTTGGGCAG

                * *            
       2876 A-GAAGCAGTCTTGGGCAG
          1 AGGAGGGA-TCTTGGGCAG

                 
       2894 AGGAG
          1 AGGAG

       2899 CGGTCAATAG


Statistics
Matches: 30,  Mismatches: 7, Indels: 7
        0.68            0.16        0.16

Matches are distributed among these distances:
  16    1  0.03
  17    2  0.07
  18   23  0.77
  19    4  0.13

ACGTcount: A:0.24, C:0.14, G:0.49, T:0.14


Consensus pattern (18 bp):   
AGGAGGGATCTTGGGCAG

Found at i:2947 original size:11 final size:11

Alignment explanation


    Indices: 2931--2975  Score: 54
    Period size: 11  Copynumber: 4.1  Consensus size: 11

       2921 GGGTCACATG

                       
       2931 GCTGACGTGGC
          1 GCTGACGTGGC

                    *  
       2942 GCTGACGTAGC
          1 GCTGACGTGGC

             *   *     
       2953 GATGAAGTGGC
          1 GCTGACGTGGC

                 *     
       2964 GCTGATGTGGC
          1 GCTGACGTGGC

             
       2975 G
          1 G

       2976 AAGCTGATGT


Statistics
Matches: 28,  Mismatches: 6, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  11   28  1.00

ACGTcount: A:0.16, C:0.20, G:0.44, T:0.20


Consensus pattern (11 bp):   
GCTGACGTGGC

Found at i:3352 original size:48 final size:49

Alignment explanation


    Indices: 3311--3468  Score: 128
    Period size: 49  Copynumber: 3.2  Consensus size: 49

       3301 GCTTATATTT

                       *  *    *  *                          
       3311 TTCCCTTCAT-TTTTTGAGGTATAAGGTTCACCGTTGCGGCTTAAATCG
          1 TTCCCTTCATGCTTCTGAGATACAAGGTTCACCGTTGCGGCTTAAATCG

                                            *      *        *
       3359 TTCCCTTCATGCTTCTGAGATACAAGGTTCACTGTTGCGACTTAAA-CC
          1 TTCCCTTCATGCTTCTGAGATACAAGGTTCACCGTTGCGGCTTAAATCG

                   *     *              *                     *  *
       3407 TTCCTCTCCATTATCTTCGTG-G-TAC-TGGATTCACCGTTGCGGCTTAATTCT
          1 TTCC-CTTCA-T-GCTTC-TGAGATACAAGG-TTCACCGTTGCGGCTTAAATCG

                       
       3458 TTCCCTTCATG
          1 TTCCCTTCATG

       3469 TTTTCATGGT


Statistics
Matches: 87,  Mismatches: 16, Indels: 14
        0.74            0.14        0.12

Matches are distributed among these distances:
  48   15  0.17
  49   36  0.41
  50   24  0.28
  51   10  0.11
  52    2  0.02

ACGTcount: A:0.18, C:0.26, G:0.18, T:0.39


Consensus pattern (49 bp):   
TTCCCTTCATGCTTCTGAGATACAAGGTTCACCGTTGCGGCTTAAATCG

Done.