Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013052.1 Kokia drynarioides strain JFW-HI SEQ_128070, 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: 4177
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32


Found at i:3143 original size:28 final size:29

Alignment explanation


    Indices: 3108--3250  Score: 148
    Period size: 28  Copynumber: 4.9  Consensus size: 29

       3098 GTTCAAAGTC

                                         
       3108 AAAAATGGGATTTTTGGAAGTTTAGGGGT
          1 AAAAATGGGATTTTTGGAAGTTTAGGGGT

              *     * *         *  * * * 
       3137 -AGAATGGTAATTTTGGAAGGTTCGAGAT
          1 AAAAATGGGATTTTTGGAAGTTTAGGGGT

                                   *      
       3165 CAAAAATGGGATTTTTGGAAGTTCAGGGGT
          1 -AAAAATGGGATTTTTGGAAGTTTAGGGGT

                     *              *      
       3195 -AAAATGGTAATTTTTGGAAG-TTCGGGGTT
          1 AAAAATGG-GATTTTTGGAAGTTTAGGGG-T

                                       
       3224 AAAAATGGGATTTTTGGAAGTTTAGGG
          1 AAAAATGGGATTTTTGGAAGTTTAGGG

       3251 ACCTTCGGGG


Statistics
Matches: 88,  Mismatches: 20, Indels: 11
        0.74            0.17        0.09

Matches are distributed among these distances:
  28   33  0.38
  29   23  0.26
  30   32  0.36

ACGTcount: A:0.31, C:0.03, G:0.33, T:0.34


Consensus pattern (29 bp):   
AAAAATGGGATTTTTGGAAGTTTAGGGGT

Found at i:3171 original size:58 final size:58

Alignment explanation


    Indices: 3072--3250  Score: 236
    Period size: 58  Copynumber: 3.1  Consensus size: 58

       3062 CGGATGCACG

                *         *                 *                            
       3072 GGGGCAAAATGGTAGTTTTGGGGAAGGTTC-AAAGTCAAAAATGGGATTTTTGGAAGTTTA
          1 GGGGTAAAATGGTAATTTT--GGAAGGTTCGAGA-TCAAAAATGGGATTTTTGGAAGTTTA

                  *                                                 * 
       3132 GGGGTAGAATGGTAATTTTGGAAGGTTCGAGATCAAAAATGGGATTTTTGGAAGTTCA
          1 GGGGTAAAATGGTAATTTTGGAAGGTTCGAGATCAAAAATGGGATTTTTGGAAGTTTA

                                          * * *                        
       3190 GGGGTAAAATGGTAATTTTTGGAA-GTTCGGGGTTAAAAATGGGATTTTTGGAAGTTTA
          1 GGGGTAAAATGGTAA-TTTTGGAAGGTTCGAGATCAAAAATGGGATTTTTGGAAGTTTA

               
       3248 GGG
          1 GGG

       3251 ACCTTCGGGG


Statistics
Matches: 107,  Mismatches: 10, Indels: 6
        0.87            0.08        0.05

Matches are distributed among these distances:
  58   81  0.76
  59   10  0.09
  60   16  0.15

ACGTcount: A:0.30, C:0.04, G:0.34, T:0.32


Consensus pattern (58 bp):   
GGGGTAAAATGGTAATTTTGGAAGGTTCGAGATCAAAAATGGGATTTTTGGAAGTTTA

Found at i:3188 original size:29 final size:28

Alignment explanation


    Indices: 3108--3245  Score: 145
    Period size: 29  Copynumber: 4.8  Consensus size: 28

       3098 GTTCAAAGTC

                                   *     
       3108 AAAAATGGGATTTTTGGAAGTTTAGGGGT
          1 AAAAATGGGATTTTTGGAAG-TTCGGGGT

              *     * *              * * 
       3137 -AGAATGGTAATTTTGGAAGGTTCGAGAT
          1 AAAAATGGGATTTTTGGAA-GTTCGGGGT

                                          
       3165 CAAAAATGGGATTTTTGGAAGTTCAGGGGT
          1 -AAAAATGGGATTTTTGGAAGTTC-GGGGT

                     *                    
       3195 -AAAATGGTAATTTTTGGAAGTTCGGGGTT
          1 AAAAATGG-GATTTTTGGAAGTTCGGGG-T

                                  
       3224 AAAAATGGGATTTTTGGAAGTT
          1 AAAAATGGGATTTTTGGAAGTT

       3246 TAGGGACCTT


Statistics
Matches: 89,  Mismatches: 13, Indels: 14
        0.77            0.11        0.12

Matches are distributed among these distances:
  28   31  0.35
  29   33  0.37
  30   25  0.28

ACGTcount: A:0.31, C:0.03, G:0.32, T:0.34


Consensus pattern (28 bp):   
AAAAATGGGATTTTTGGAAGTTCGGGGT

Found at i:3888 original size:31 final size:28

Alignment explanation


    Indices: 3834--3892  Score: 82
    Period size: 31  Copynumber: 2.0  Consensus size: 28

       3824 TAACCCAGAT

                             *          
       3834 CTTCAAAAAAAAAAACTCTTTTTTATTC
          1 CTTCAAAAAAAAAAACTATTTTTTATTC

                                           
       3862 CTTCAAAGAAAAAAAATCTATCTTTTTATTC
          1 CTTCAAA-AAAAAAAA-CTAT-TTTTTATTC

       3893 TCAAATCTAT


Statistics
Matches: 27,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  28    7  0.26
  29    8  0.30
  30    3  0.11
  31    9  0.33

ACGTcount: A:0.42, C:0.17, G:0.02, T:0.39


Consensus pattern (28 bp):   
CTTCAAAAAAAAAAACTATTTTTTATTC

Found at i:4042 original size:19 final size:19

Alignment explanation


    Indices: 4020--4063  Score: 79
    Period size: 19  Copynumber: 2.3  Consensus size: 19

       4010 AAATATGTTA

                 *             
       4020 TTATTTTTAATATTATTGT
          1 TTATTGTTAATATTATTGT

                               
       4039 TTATTGTTAATATTATTGT
          1 TTATTGTTAATATTATTGT

                  
       4058 TTATTG
          1 TTATTG

       4064 AACTGGAGAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  19   24  1.00

ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66


Consensus pattern (19 bp):   
TTATTGTTAATATTATTGT
Done.