Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008216.1 Kokia drynarioides strain JFW-HI SEQ_122880, 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: 15438
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34


Found at i:2902 original size:23 final size:21

Alignment explanation


    Indices: 2868--2915  Score: 53
    Period size: 23  Copynumber: 2.2  Consensus size: 21

       2858 ATTCGACTCC

                                  
       2868 AATTTATATCAAATAATTCAAA
          1 AATTTATATCAAATAATT-AAA

                          *        
       2890 TAATTTA-ATTCAAGTAATTAAA
          1 -AATTTATA-TCAAATAATTAAA

                
       2912 AATT
          1 AATT

       2916 CAAAATATTT


Statistics
Matches: 23,  Mismatches: 1, Indels: 4
        0.82            0.04        0.14

Matches are distributed among these distances:
  21    4  0.17
  22    4  0.17
  23   15  0.65

ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40


Consensus pattern (21 bp):   
AATTTATATCAAATAATTAAA

Found at i:9115 original size:31 final size:32

Alignment explanation


    Indices: 9055--9123  Score: 106
    Period size: 32  Copynumber: 2.2  Consensus size: 32

       9045 CATAATAATC

                                            
       9055 CAACAAACTTAAACCATAAAACTTTCAATAGT
          1 CAACAAACTTAAACCATAAAACTTTCAATAGT

                                           * 
       9087 CAACAAACTTAAA-CATTAAAA-TTTCAATATT
          1 CAACAAACTTAAACCA-TAAAACTTTCAATAGT

                  
       9118 CAACAA
          1 CAACAA

       9124 TTTCAAAACA


Statistics
Matches: 35,  Mismatches: 1, Indels: 3
        0.90            0.03        0.08

Matches are distributed among these distances:
  31   17  0.49
  32   18  0.51

ACGTcount: A:0.52, C:0.20, G:0.01, T:0.26


Consensus pattern (32 bp):   
CAACAAACTTAAACCATAAAACTTTCAATAGT

Found at i:9138 original size:31 final size:30

Alignment explanation


    Indices: 9055--9200  Score: 111
    Period size: 31  Copynumber: 4.7  Consensus size: 30

       9045 CATAATAATC

                                            
       9055 CAACAAACTTAAACCATAAAACTTTCAATAGT
          1 CAACAAACTTAAA-CATAAAA-TTTCAATAGT

                                         * 
       9087 CAACAAACTTAAACATTAAAATTTCAATATT
          1 CAACAAACTTAAACA-TAAAATTTCAATAGT

                   *                 * *    
       9118 CAAC-AATTTCAAAACATAAAATTTTATTA-T
          1 CAACAAACTT--AAACATAAAATTTCAATAGT

               *   *                         
       9148 CTAGCAAGCTTAAAACATAAAATTTTCAATA-T
          1 C-AACAAACTT-AAACATAAAA-TTTCAATAGT

                    *  *          
       9180 CCAA-AAAATTTAACATAAAAT
          1 -CAACAAACTTAAACATAAAAT

       9201 ACTCTACCTA


Statistics
Matches: 94,  Mismatches: 13, Indels: 17
        0.76            0.10        0.14

Matches are distributed among these distances:
  29    1  0.01
  30   15  0.16
  31   43  0.46
  32   34  0.36
  33    1  0.01

ACGTcount: A:0.51, C:0.16, G:0.02, T:0.30


Consensus pattern (30 bp):   
CAACAAACTTAAACATAAAATTTCAATAGT

Found at i:11215 original size:21 final size:21

Alignment explanation


    Indices: 11186--11238  Score: 88
    Period size: 21  Copynumber: 2.5  Consensus size: 21

      11176 GAAGCCTGAG

                             *   
      11186 GTCTCGAGACACAATATGCAT
          1 GTCTCGAGACACAATATACAT

                *                
      11207 GTCTAGAGACACAATATACAT
          1 GTCTCGAGACACAATATACAT

                       
      11228 GTCTCGAGACA
          1 GTCTCGAGACA

      11239 AGGCTCCTCT


Statistics
Matches: 29,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  21   29  1.00

ACGTcount: A:0.36, C:0.23, G:0.19, T:0.23


Consensus pattern (21 bp):   
GTCTCGAGACACAATATACAT

Found at i:15273 original size:3 final size:3

Alignment explanation


    Indices: 15265--15306  Score: 75
    Period size: 3  Copynumber: 14.0  Consensus size: 3

      15255 TGCTAGCTAC

                                                        *          
      15265 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT CAT AAT AAT
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT

      15307 TTATACTATT


Statistics
Matches: 37,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   3   37  1.00

ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33


Consensus pattern (3 bp):   
AAT

Found at i:15389 original size:17 final size:18

Alignment explanation


    Indices: 15355--15390  Score: 56
    Period size: 18  Copynumber: 2.1  Consensus size: 18

      15345 TGAATTTCTG

                              
      15355 TCCAATTTATACCCTAAT
          1 TCCAATTTATACCCTAAT

                       *      
      15373 TCCAATTTA-ATCCTAAT
          1 TCCAATTTATACCCTAAT

             
      15390 T
          1 T

      15391 AACTCATTTA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  17    8  0.47
  18    9  0.53

ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42


Consensus pattern (18 bp):   
TCCAATTTATACCCTAAT
Done.