Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010832.1 Kokia drynarioides strain JFW-HI SEQ_125799, 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: 10338
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35

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


Found at i:5622 original size:90 final size:91

Alignment explanation


    Indices: 5436--5644  Score: 244
    Period size: 90  Copynumber: 2.3  Consensus size: 91

       5426 TTAGGGGTTA

                   *                                               * *  *    
       5436 TTCAAGTGCCCAATTGAGTGC-AAA-AAAATCAAGGGCTTAATTGCTTTTTTTTTTTTAAGTTTG
          1 TTCAAGTACCCAATTGAGTGCAAAATAAAATCAAGGGCTTAATTGCTTTTTTTTTATGAAATTTG

               *              *       
       5499 AGGGCATTTTTGATGAATTTTAAAAG
         66 AGGACATTTTTGATGAATGTTAAAAG

              *                            * *                               
       5525 TTTAAGTACCCAATTGAGTGCAAAATAAAATGATGGGCTTAATTGC-TTTTTTTTATGAAATTTG
          1 TTCAAGTACCCAATTGAGTGCAAAATAAAATCAAGGGCTTAATTGCTTTTTTTTTATGAAATTTG

                *      *   *     *    
       5589 AGGATATTTTTTATGCATGTTGAAAG
         66 AGGACATTTTTGATGAATGTTAAAAG

                    **   *     *          
       5615 TTCAAGTATTCAAGTGAGTTCAAAATAAAA
          1 TTCAAGTACCCAATTGAGTGCAAAATAAAA

       5645 GCATGTGTTC


Statistics
Matches: 100,  Mismatches: 18, Indels: 3
        0.83            0.15        0.02

Matches are distributed among these distances:
  89   19  0.19
  90   63  0.63
  91   18  0.18

ACGTcount: A:0.33, C:0.09, G:0.18, T:0.39


Consensus pattern (91 bp):   
TTCAAGTACCCAATTGAGTGCAAAATAAAATCAAGGGCTTAATTGCTTTTTTTTTATGAAATTTG
AGGACATTTTTGATGAATGTTAAAAG

Found at i:5679 original size:90 final size:91

Alignment explanation


    Indices: 5436--5679  Score: 212
    Period size: 90  Copynumber: 2.7  Consensus size: 91

       5426 TTAGGGGTTA

                   *     *                 * *          *        ** **       
       5436 TTCAAGTGCCCAATTGAGTGC-AAA-AAAATCAAGGGCTTAATTGCTTTTTTTTTTTTAAGTTTG
          1 TTCAAGTACCCAAGTGAGTGCAAAATAAAATGATGGGCTTAATTACTTTTTTTGATAAAAGTTTG

               *              *       
       5499 AGGGCATTTTTGATGAATTTTAAAAG
         66 AGGACATTTTTGATGAATGTTAAAAG

              *          *                              *        *  *        
       5525 TTTAAGTACCCAATTGAGTGCAAAATAAAATGATGGGCTTAATTGCTTTTTTTTATGAAA-TTTG
          1 TTCAAGTACCCAAGTGAGTGCAAAATAAAATGATGGGCTTAATTACTTTTTTTGATAAAAGTTTG

                *      *   *     *    
       5589 AGGATATTTTTTATGCATGTTGAAAG
         66 AGGACATTTTTGATGAATGTTAAAAG

                    **         *                *                            
       5615 TTCAAGTATTCAAGTGAGTTCAAAATAAAA-GCATGTG-TTCAATTACTTTTTTTGA-AAAAGTT
          1 TTCAAGTACCCAAGTGAGTGCAAAATAAAATG-ATGGGCTT-AATTACTTTTTTTGATAAAAGTT

               
       5677 TGA
         64 TGA

       5680 AGGCTTTTTA


Statistics
Matches: 128,  Mismatches: 22, Indels: 9
        0.81            0.14        0.06

Matches are distributed among these distances:
  89   25  0.20
  90   74  0.58
  91   29  0.23

ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40


Consensus pattern (91 bp):   
TTCAAGTACCCAAGTGAGTGCAAAATAAAATGATGGGCTTAATTACTTTTTTTGATAAAAGTTTG
AGGACATTTTTGATGAATGTTAAAAG

Found at i:6025 original size:22 final size:22

Alignment explanation


    Indices: 5999--6040  Score: 59
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       5989 AACTTTAATG

                                   
       5999 AAATA-AAAATATAAAAATTATT
          1 AAATATAAAAT-TAAAAATTATT

                  *             
       6021 AAATATCAAATTAAAAATTA
          1 AAATATAAAATTAAAAATTA

       6041 AAATTCCTAT


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  22   14  0.78
  23    4  0.22

ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31


Consensus pattern (22 bp):   
AAATATAAAATTAAAAATTATT

Found at i:6076 original size:15 final size:16

Alignment explanation


    Indices: 6049--6088  Score: 64
    Period size: 15  Copynumber: 2.5  Consensus size: 16

       6039 TAAAATTCCT

                            
       6049 ATATAATATTTTTAAA
          1 ATATAATATTTTTAAA

                            
       6065 ATATAA-ATTTTTAAA
          1 ATATAATATTTTTAAA

                     
       6080 ATATGAATA
          1 ATAT-AATA

       6089 AACTTAAAAC


Statistics
Matches: 22,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  15   13  0.59
  16    8  0.36
  17    1  0.05

ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45


Consensus pattern (16 bp):   
ATATAATATTTTTAAA

Found at i:8460 original size:31 final size:30

Alignment explanation


    Indices: 8394--8465  Score: 83
    Period size: 30  Copynumber: 2.4  Consensus size: 30

       8384 GTTACGTGTA

                          *            *  
       8394 ACAAAACAGTCACTCAACTTTGAAAATGTG
          1 ACAAAACAGTCACTAAACTTTGAAAATATG

                             *              
       8424 ACAAAACAGTCACTAAAGTTATCGAAAA-ATG
          1 ACAAAACAGTCACTAAACTT-T-GAAAATATG

                  *    
       8455 ACAAAATAGTC
          1 ACAAAACAGTC

       8466 CTCTTGTTAT


Statistics
Matches: 36,  Mismatches: 4, Indels: 3
        0.84            0.09        0.07

Matches are distributed among these distances:
  30   18  0.50
  31   13  0.36
  32    5  0.14

ACGTcount: A:0.49, C:0.18, G:0.12, T:0.21


Consensus pattern (30 bp):   
ACAAAACAGTCACTAAACTTTGAAAATATG
Done.