Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005019.1 Kokia drynarioides strain JFW-HI SEQ_118780, 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: 16630
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34


Found at i:2065 original size:30 final size:30

Alignment explanation


    Indices: 2029--2227  Score: 231
    Period size: 30  Copynumber: 6.7  Consensus size: 30

       2019 CGAGCCATCA

                      *  *               *
       2029 AAAGTGCGAGTCTATTAAAGACAGTAAGCT
          1 AAAGTGCGAGCCTGTTAAAGACAGTAAGCC

                                 *       *
       2059 AAAGTGCGAGCCTGTTAAAGATAGTAAGCT
          1 AAAGTGCGAGCCTGTTAAAGACAGTAAGCC

                *  *                       
       2089 AAAGAGCCAGCCTGTTAAAGACAAG-AAGCC
          1 AAAGTGCGAGCCTGTTAAAGAC-AGTAAGCC

                       *   *              
       2119 AAAGTGCGAGCTTGTCAAAGACAGTAAGCC
          1 AAAGTGCGAGCCTGTTAAAGACAGTAAGCC

                       *                  
       2149 AAAGTGCGAGCTTGTTAAAGACAGTAAGCC
          1 AAAGTGCGAGCCTGTTAAAGACAGTAAGCC

                         *  *       *     
       2179 AAAGTGCGAGCCTATTGAAGACAGCAAG-C
          1 AAAGTGCGAGCCTGTTAAAGACAGTAAGCC

                  *   *    *    
       2208 AAAGTGTGAGTCTGTCAAAG
          1 AAAGTGCGAGCCTGTTAAAG

       2228 TGTGAGCCTG


Statistics
Matches: 146,  Mismatches: 21, Indels: 5
        0.85            0.12        0.03

Matches are distributed among these distances:
  29   18  0.12
  30  126  0.86
  31    2  0.01

ACGTcount: A:0.38, C:0.17, G:0.26, T:0.19


Consensus pattern (30 bp):   
AAAGTGCGAGCCTGTTAAAGACAGTAAGCC

Found at i:2228 original size:16 final size:16

Alignment explanation


    Indices: 2207--2239  Score: 57
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       2197 AGACAGCAAG

                       *    
       2207 CAAAGTGTGAGTCTGT
          1 CAAAGTGTGAGCCTGT

                            
       2223 CAAAGTGTGAGCCTGT
          1 CAAAGTGTGAGCCTGT

             
       2239 C
          1 C

       2240 GAATTGCAAG


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.24, C:0.18, G:0.30, T:0.27


Consensus pattern (16 bp):   
CAAAGTGTGAGCCTGT

Found at i:2307 original size:44 final size:44

Alignment explanation


    Indices: 2259--2342  Score: 134
    Period size: 44  Copynumber: 1.9  Consensus size: 44

       2249 GTCGAGGTGG

                 *                                       
       2259 CGGACGGTCTAAATGCAA-ACCCGAGTGGGTGCAAGCCAAAGCGA
          1 CGGACAGTCTAAATGCAAGA-CCGAGTGGGTGCAAGCCAAAGCGA

                                *                   
       2303 CGGACAGTCTAAATGCAAGATCGAGTGGGTGCAAGCCAAA
          1 CGGACAGTCTAAATGCAAGACCGAGTGGGTGCAAGCCAAA

       2343 ATGGCAAACT


Statistics
Matches: 37,  Mismatches: 2, Indels: 2
        0.90            0.05        0.05

Matches are distributed among these distances:
  44   36  0.97
  45    1  0.03

ACGTcount: A:0.33, C:0.23, G:0.31, T:0.13


Consensus pattern (44 bp):   
CGGACAGTCTAAATGCAAGACCGAGTGGGTGCAAGCCAAAGCGA

Found at i:4541 original size:30 final size:30

Alignment explanation


    Indices: 4507--4571  Score: 121
    Period size: 30  Copynumber: 2.2  Consensus size: 30

       4497 CAACTTAACA

                    *                     
       4507 AACAAATGTCTCTAAAATAATAACAAAATT
          1 AACAAATGCCTCTAAAATAATAACAAAATT

                                          
       4537 AACAAATGCCTCTAAAATAATAACAAAATT
          1 AACAAATGCCTCTAAAATAATAACAAAATT

                 
       4567 AACAA
          1 AACAA

       4572 TAAAATAAGT


Statistics
Matches: 34,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  30   34  1.00

ACGTcount: A:0.58, C:0.15, G:0.03, T:0.23


Consensus pattern (30 bp):   
AACAAATGCCTCTAAAATAATAACAAAATT

Found at i:6461 original size:16 final size:16

Alignment explanation


    Indices: 6440--6470  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       6430 GTTCGAATTA

                            
       6440 TTTTAAACTCAAATCT
          1 TTTTAAACTCAAATCT

                      *    
       6456 TTTTAAACTCGAATC
          1 TTTTAAACTCAAATC

       6471 AATTCGAGTT


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

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.35, C:0.19, G:0.03, T:0.42


Consensus pattern (16 bp):   
TTTTAAACTCAAATCT

Found at i:7664 original size:17 final size:17

Alignment explanation


    Indices: 7620--7666  Score: 55
    Period size: 15  Copynumber: 2.9  Consensus size: 17

       7610 AAAATTCAAT

                             
       7620 AAATAAAA-AAATA-TA
          1 AAATAAAATAAATATTA

                 * *         
       7635 AAAT-TATTAAATATTA
          1 AAATAAAATAAATATTA

                            
       7651 AAATAAAATAAATATT
          1 AAATAAAATAAATATT

       7667 TTTCTAAAAA


Statistics
Matches: 25,  Mismatches: 4, Indels: 4
        0.76            0.12        0.12

Matches are distributed among these distances:
  14    1  0.04
  15    9  0.36
  16    6  0.24
  17    9  0.36

ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32


Consensus pattern (17 bp):   
AAATAAAATAAATATTA
Done.