Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013365.1 Kokia drynarioides strain JFW-HI SEQ_128388, 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: 4485
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.31

Warning! 50 characters in sequence are not A, C, G, or T


Found at i:2521 original size:96 final size:96

Alignment explanation


    Indices: 2347--2538  Score: 235
    Period size: 96  Copynumber: 2.0  Consensus size: 96

       2337 TTTTTGGGAA

                                           **                     *          
       2347 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAATAAGTTAAGGCGCAATATTTCA
          1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAATAAGTTAAGGCACAATATTTCA

                    *              *        
       2412 AAATCGAAGAT-AAAGAAACATTGCCTCGATT
         66 AAATCGAAAATAAAAG-AACATTACCTCGATT

                *           *                         * *               *   *
       2443 AAGGGTATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTCAGTTAAGGCACAAATTTTTG
          1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAATAAGTTAAGGCAC-AATATTTC

               *               *            
       2508 AAACTC-AAAATAAAAGAATATTACCTCGATT
         65 AAAATCGAAAATAAAAGAACATTACCTCGATT

       2539 TTAAAGTCTT


Statistics
Matches: 81,  Mismatches: 13, Indels: 4
        0.83            0.13        0.04

Matches are distributed among these distances:
  96   66  0.81
  97   15  0.19

ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30


Consensus pattern (96 bp):   
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAATAAGTTAAGGCACAATATTTCA
AAATCGAAAATAAAAGAACATTACCTCGATT

Found at i:2789 original size:29 final size:28

Alignment explanation


    Indices: 2757--2819  Score: 72
    Period size: 28  Copynumber: 2.2  Consensus size: 28

       2747 AAAATGAGGC

                         *               
       2757 TTTTCGGATACCCGGGGGCAAAATGGTAA
          1 TTTT-GGATACCCAGGGGCAAAATGGTAA

                    * *      **         
       2786 TTTTGGATTCTCAGGGGTGAAATGGTAA
          1 TTTTGGATACCCAGGGGCAAAATGGTAA

                  
       2814 TTTTGG
          1 TTTTGG

       2820 GAAAATTCGG


Statistics
Matches: 29,  Mismatches: 5, Indels: 1
        0.83            0.14        0.03

Matches are distributed among these distances:
  28   25  0.86
  29    4  0.14

ACGTcount: A:0.24, C:0.11, G:0.32, T:0.33


Consensus pattern (28 bp):   
TTTTGGATACCCAGGGGCAAAATGGTAA

Found at i:2948 original size:29 final size:30

Alignment explanation


    Indices: 2902--3110  Score: 110
    Period size: 29  Copynumber: 7.4  Consensus size: 30

       2892 GGAAATGGAG

                                           *
       2902 TTTTTGGACA-TTTGGGGG-C-AAAAGGGTAT
          1 TTTTTGGA-AGTTTGGGGGTCAAAAAGGG-AA

                         *           *    
       2931 TTTTTGGAAGTTTTGGGGTCAAAAATGGAA
          1 TTTTTGGAAGTTTGGGGGTCAAAAAGGGAA

                           *     *        
       2961 TTTTTGGAAGTTT-GAGG-C-TAAA---AA
          1 TTTTTGGAAGTTTGGGGGTCAAAAAGGGAA

                     *   *           *    
       2985 ----TGGAACTTTTGGGGTCAAAAATGGAA
          1 TTTTTGGAAGTTTGGGGGTCAAAAAGGGAA

                         *   *       *    
       3011 TTTTTGGAAGTTTAGGGAT-AAAAATGGAA
          1 TTTTTGGAAGTTTGGGGGTCAAAAAGGGAA

                        * *           *    
       3040 TTTTTGGAAGTTCGAGGGT-AAAAATAGG-A
          1 TTTTTGGAAGTTTGGGGGTCAAAAA-GGGAA

                 *       * *         *    
       3069 TTTTTAGAAGTTTTGAGGT-AAAAATGGAA
          1 TTTTTGGAAGTTTGGGGGTCAAAAAGGGAA

                         
       3098 TTTTTGGAAGTTT
          1 TTTTTGGAAGTTT

       3111 CGGGACCTCC


Statistics
Matches: 142,  Mismatches: 23, Indels: 30
        0.73            0.12        0.15

Matches are distributed among these distances:
  20    8  0.06
  21    3  0.02
  22    1  0.01
  23    3  0.02
  24    2  0.01
  26    2  0.01
  27    3  0.02
  28    4  0.03
  29   81  0.57
  30   29  0.20
  31    6  0.04

ACGTcount: A:0.32, C:0.03, G:0.29, T:0.36


Consensus pattern (30 bp):   
TTTTTGGAAGTTTGGGGGTCAAAAAGGGAA

Found at i:2995 original size:50 final size:50

Alignment explanation


    Indices: 2935--3046  Score: 181
    Period size: 50  Copynumber: 2.2  Consensus size: 50

       2925 GGGTATTTTT

                 *                                      *      
       2935 TGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTT-GAGGCTAAAAA
          1 TGGAACTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTAG-GGATAAAAA

                                                              
       2985 TGGAACTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTAGGGATAAAAA
          1 TGGAACTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTAGGGATAAAAA

                 *      
       3035 TGGAATTTTTGG
          1 TGGAACTTTTGG

       3047 AAGTTCGAGG


Statistics
Matches: 58,  Mismatches: 3, Indels: 2
        0.92            0.05        0.03

Matches are distributed among these distances:
  50   57  0.98
  51    1  0.02

ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34


Consensus pattern (50 bp):   
TGGAACTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTAGGGATAAAAA

Found at i:3072 original size:58 final size:59

Alignment explanation


    Indices: 2996--3109  Score: 171
    Period size: 58  Copynumber: 1.9  Consensus size: 59

       2986 GGAACTTTTG

                                *                                       
       2996 GGGTCAAAAATGGAATTTTTGGAAGTTTAG-GGATAAAAATGGAATTTTTGGAAGTTCGA
          1 GGGTCAAAAATGGAATTTTTAGAAGTTTAGAGG-TAAAAATGGAATTTTTGGAAGTTCGA

                                         *                           
       3055 GGGT-AAAAATAGG-ATTTTTAGAAGTTTTGAGGTAAAAATGGAATTTTTGGAAGTT
          1 GGGTCAAAAAT-GGAATTTTTAGAAGTTTAGAGGTAAAAATGGAATTTTTGGAAGTT

       3110 TCGGGACCTC


Statistics
Matches: 51,  Mismatches: 2, Indels: 5
        0.88            0.03        0.09

Matches are distributed among these distances:
  58   43  0.84
  59    8  0.16

ACGTcount: A:0.36, C:0.02, G:0.28, T:0.34


Consensus pattern (59 bp):   
GGGTCAAAAATGGAATTTTTAGAAGTTTAGAGGTAAAAATGGAATTTTTGGAAGTTCGA
Done.