Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002559.1 Kokia drynarioides strain JFW-HI SEQ_114756, 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: 2796
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.39


Found at i:46 original size:24 final size:24

Alignment explanation


    Indices: 19--102  Score: 105
    Period size: 24  Copynumber: 3.5  Consensus size: 24

          9 ATAAGCTAAT

                               *    
         19 GAGCATAAACGTGTGCAAGATGAC
          1 GAGCATAAACGTGTGCAAGCTGAC

                *             *  *  
         43 GAGCGTAAACGTGTGCAATCTAAC
          1 GAGCATAAACGTGTGCAAGCTGAC

                        * **        
         67 GAGCATAAACGTATATAAGCTGAC
          1 GAGCATAAACGTGTGCAAGCTGAC

                        
         91 GAGCATAAACGT
          1 GAGCATAAACGT

        103 AATGAATCTA


Statistics
Matches: 50,  Mismatches: 10, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  24   50  1.00

ACGTcount: A:0.38, C:0.18, G:0.25, T:0.19


Consensus pattern (24 bp):   
GAGCATAAACGTGTGCAAGCTGAC

Found at i:103 original size:24 final size:24

Alignment explanation


    Indices: 1--103  Score: 89
    Period size: 24  Copynumber: 4.3  Consensus size: 24

                   * *       *      
          1 AAACGTACATAAGCTAATGAGCAT
          1 AAACGTATACAAGCTAACGAGCAT

                  * *    * *      * 
         25 AAACGTGTGCAAGATGACGAGCGT
          1 AAACGTATACAAGCTAACGAGCAT

                  * *   *           
         49 AAACGTGTGCAATCTAACGAGCAT
          1 AAACGTATACAAGCTAACGAGCAT

                     *     *        
         73 AAACGTATATAAGCTGACGAGCAT
          1 AAACGTATACAAGCTAACGAGCAT

                   
         97 AAACGTA
          1 AAACGTA

        104 ATGAATCTAT


Statistics
Matches: 62,  Mismatches: 17, Indels: 0
        0.78            0.22        0.00

Matches are distributed among these distances:
  24   62  1.00

ACGTcount: A:0.41, C:0.17, G:0.22, T:0.19


Consensus pattern (24 bp):   
AAACGTATACAAGCTAACGAGCAT

Found at i:111 original size:48 final size:48

Alignment explanation


    Indices: 1--112  Score: 120
    Period size: 48  Copynumber: 2.3  Consensus size: 48

                         *    *            * *             * 
          1 AAACGTACAT-AAGCTAATGAGCATAAACGTGTGCAAGATGACGAGCGT
          1 AAACGTA-ATGAATCTAACGAGCATAAACGTATACAAGATGACGAGCAT

                   *                          *   *          
         49 AAACGT-GTGCAATCTAACGAGCATAAACGTATATAAGCTGACGAGCAT
          1 AAACGTAATG-AATCTAACGAGCATAAACGTATACAAGATGACGAGCAT

                            
         97 AAACGTAATGAATCTA
          1 AAACGTAATGAATCTA

        113 TTACTGATTT


Statistics
Matches: 52,  Mismatches: 9, Indels: 6
        0.78            0.13        0.09

Matches are distributed among these distances:
  46    1  0.02
  48   49  0.94
  49    2  0.04

ACGTcount: A:0.41, C:0.17, G:0.21, T:0.21


Consensus pattern (48 bp):   
AAACGTAATGAATCTAACGAGCATAAACGTATACAAGATGACGAGCAT

Found at i:686 original size:20 final size:19

Alignment explanation


    Indices: 661--698  Score: 58
    Period size: 20  Copynumber: 1.9  Consensus size: 19

        651 TACCTAGCTT

                   *            
        661 TTGGTATTGATAATTATTTG
          1 TTGGTATCGATAA-TATTTG

                              
        681 TTGGTATCGATAATATTT
          1 TTGGTATCGATAATATTT

        699 AACAGGTGAA


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

Matches are distributed among these distances:
  19    5  0.29
  20   12  0.71

ACGTcount: A:0.26, C:0.03, G:0.18, T:0.53


Consensus pattern (19 bp):   
TTGGTATCGATAATATTTG

Found at i:1776 original size:14 final size:15

Alignment explanation


    Indices: 1759--1787  Score: 51
    Period size: 14  Copynumber: 2.0  Consensus size: 15

       1749 TTCGAGTCAA

                           
       1759 TTTGAATTTT-ATTT
          1 TTTGAATTTTGATTT

                           
       1773 TTTGAATTTTGATTT
          1 TTTGAATTTTGATTT

       1788 CGAATCGAAT


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  14   10  0.71
  15    4  0.29

ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69


Consensus pattern (15 bp):   
TTTGAATTTTGATTT

Found at i:1825 original size:9 final size:9

Alignment explanation


    Indices: 1807--1845  Score: 53
    Period size: 9  Copynumber: 4.3  Consensus size: 9

       1797 TTGAGTTTTC

                 *   
       1807 TAATTTGAA
          1 TAATTCGAA

                      
       1816 TAACTT-GAA
          1 TAA-TTCGAA

                     
       1825 TAATTCGAA
          1 TAATTCGAA

                     
       1834 TAATTCGAA
          1 TAATTCGAA

               
       1843 TAA
          1 TAA

       1846 ACCGAATATT


Statistics
Matches: 28,  Mismatches: 0, Indels: 4
        0.88            0.00        0.12

Matches are distributed among these distances:
   8    2  0.07
   9   24  0.86
  10    2  0.07

ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36


Consensus pattern (9 bp):   
TAATTCGAA

Done.