Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003511.1 Kokia drynarioides strain JFW-HI SEQ_116347, 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: 5519
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37


Found at i:1816 original size:21 final size:21

Alignment explanation


    Indices: 1790--1832  Score: 61
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       1780 CTCGATGAAC

                            *     
       1790 TGTTCGTAT-AACGTTTGTTTA
          1 TGTTCGTATGAA-GTTCGTTTA

                                 
       1811 TGTTCGTATGAAGTTCGTTTA
          1 TGTTCGTATGAAGTTCGTTTA

             
       1832 T
          1 T

       1833 TTTTCGTGAA


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  21   18  0.90
  22    2  0.10

ACGTcount: A:0.19, C:0.09, G:0.21, T:0.51


Consensus pattern (21 bp):   
TGTTCGTATGAAGTTCGTTTA

Found at i:2336 original size:24 final size:25

Alignment explanation


    Indices: 2309--2360  Score: 61
    Period size: 25  Copynumber: 2.1  Consensus size: 25

       2299 AGATAATAAC

                              * *    
       2309 TTTAATAG-TTGAATTTTGATATGT
          1 TTTAATAGCTTGAATTTTCAAATGT

                *      *             
       2333 TTTAGTAGCTTTAATTTTCAAATGT
          1 TTTAATAGCTTGAATTTTCAAATGT

               
       2358 TTT
          1 TTT

       2361 GATATAATAA


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

Matches are distributed among these distances:
  24    7  0.30
  25   16  0.70

ACGTcount: A:0.27, C:0.04, G:0.13, T:0.56


Consensus pattern (25 bp):   
TTTAATAGCTTGAATTTTCAAATGT

Found at i:4362 original size:50 final size:51

Alignment explanation


    Indices: 4281--4812  Score: 525
    Period size: 50  Copynumber: 10.7  Consensus size: 51

       4271 GCTTTTTTTC

                        *        *   *          *       *      
       4281 TCTGCCCCTCTATAGCTTTAGAGGTGTAAGATTTGATTTC-GCAACTTCAA
          1 TCTGCCCCTCTACAGCTTTAGGGGTATAAGATTTGACTTCTGCAGCTTCAA

                *         *           *        *               
       4331 TCTGTCCCTCTACAACTTTAGGGGTACAAGATTTGCCTT-TGCAGCTTCAA
          1 TCTGCCCCTCTACAGCTTTAGGGGTATAAGATTTGACTTCTGCAGCTTCAA

               *        *                            *   *     
       4381 ---ACCCCTCTATAGCTTTAGGGGTATAAGATTTG-CTTCTACAGTTTCAA
          1 TCTGCCCCTCTACAGCTTTAGGGGTATAAGATTTGACTTCTGCAGCTTCAA

             *    *  *  *                                      
       4428 TTTGCCTCTTTATAGCTTTAGGGGTATAAGATTTG-CTTCTGCAGCTTCAA
          1 TCTGCCCCTCTACAGCTTTAGGGGTATAAGATTTGACTTCTGCAGCTTCAA

             *                    *      *       *  * *       *
       4478 TTTGCCCCTCTACAGCTTTAGGTGTATAAAATTT-ACCTCAGTAGCTTCAG
          1 TCTGCCCCTCTACAGCTTTAGGGGTATAAGATTTGACTTCTGCAGCTTCAA

                     *  *                             *        
       4528 TCTGCCCCTTTATAGCTTTAGGGGTATAAGATTTG-CTTCTGTAGCTTCAA
          1 TCTGCCCCTCTACAGCTTTAGGGGTATAAGATTTGACTTCTGCAGCTTCAA

             *  *   * * *                *         *  * *      
       4578 TTTGACCCACCAAAGCTTTAGGGGTATAAAATTTGA-TTTTGTAACTTCAA
          1 TCTGCCCCTCTACAGCTTTAGGGGTATAAGATTTGACTTCTGCAGCTTCAA

                                 *               *   *         
       4628 TCTGCCCCTCTACAGCTTTAGAGGTATAAGATTTG-CCTCTACAGCTTCAA
          1 TCTGCCCCTCTACAGCTTTAGGGGTATAAGATTTGACTTCTGCAGCTTCAA

                                   *               *        *  
       4678 TCTGCCCCTCTACAGCTTTAGGGATATAAGATTTGA-TTTTGCAGCTTTAA
          1 TCTGCCCCTCTACAGCTTTAGGGGTATAAGATTTGACTTCTGCAGCTTCAA

             *               *   *  *                          
       4728 TTTGCCCCTCTACAGCTCTAGAGGAATAAGATTTGACTT-TGCAGCTTCAA
          1 TCTGCCCCTCTACAGCTTTAGGGGTATAAGATTTGACTTCTGCAGCTTCAA

               *           *                    
       4778 TCTACCCCT-TCACAACTTTAGGGGTATAAGATTTG
          1 TCTGCCCCTCT-ACAGCTTTAGGGGTATAAGATTTG

       4813 CTAGTTCACT


Statistics
Matches: 393,  Mismatches: 77, Indels: 24
        0.80            0.16        0.05

Matches are distributed among these distances:
  46    3  0.01
  47   36  0.09
  49    1  0.00
  50  351  0.89
  51    2  0.01

ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36


Consensus pattern (51 bp):   
TCTGCCCCTCTACAGCTTTAGGGGTATAAGATTTGACTTCTGCAGCTTCAA

Found at i:4812 original size:150 final size:150

Alignment explanation


    Indices: 4283--4813  Score: 601
    Period size: 150  Copynumber: 3.6  Consensus size: 150

       4273 TTTTTTTCTC

                                   *                             *           
       4283 TGCCCCTCTATAGCTTTAGAGGTGTAAGATTTGA-TTTCGCAACTTCAATCTGTCCCTCTACAAC
          1 TGCCCCTCTATAGCTTTAGAGGTATAAGATTTGACTTT-GCAACTTCAATCTGCCCCTCTACAAC

                      *           * *            *                           
       4347 TTTAGGGGTACAAGATTTGCCTTTGCAGCTTCAA---ACCCCTCTATAGCTTTAGGGGTATAAGA
         65 TTTAGGGGTATAAGATTTGCCTCTACAGCTTCAATCTGCCCCTCTATAGCTTTAGGGGTATAAGA

                     *            
       4409 TTTGCTTCTACAG-TTTCAATT
        130 TTTGCTTCTGCAGCTTT-AATT

                *  *           *                      *       *            * 
       4430 TGCCTCTTTATAGCTTTAGGGGTATAAGATTTG-CTTCTGCAGCTTCAATTTGCCCCTCTACAGC
          1 TGCCCCTCTATAGCTTTAGAGGTATAAGATTTGACTT-TGCAACTTCAATCTGCCCCTCTACAAC

                  *      *    *       *       *         *                    
       4494 TTTAGGTGTATAAAATTTACCTC-AGTAGCTTCAGTCTGCCCCTTTATAGCTTTAGGGGTATAAG
         65 TTTAGGGGTATAAGATTTGCCTCTA-CAGCTTCAATCTGCCCCTCTATAGCTTTAGGGGTATAAG

                       *     *    
       4558 ATTTGCTTCTGTAGCTTCAATT
        129 ATTTGCTTCTGCAGCTTTAATT

              *   * * *        *       *      *    *                      *  
       4580 TGACCCACCAAAGCTTTAGGGGTATAAAATTTGATTTTGTAACTTCAATCTGCCCCTCTACAGCT
          1 TGCCCCTCTATAGCTTTAGAGGTATAAGATTTGACTTTGCAACTTCAATCTGCCCCTCTACAACT

                *                                        *          *        
       4645 TTAGAGGTATAAGATTTGCCTCTACAGCTTCAATCTGCCCCTCTACAGCTTTAGGGATATAAGAT
         66 TTAGGGGTATAAGATTTGCCTCTACAGCTTCAATCTGCCCCTCTATAGCTTTAGGGGTATAAGAT

               *  *             
       4710 TTGATTTTGCAGCTTTAATT
        131 TTGCTTCTGCAGCTTTAATT

                      *    *      *                  *         *             
       4730 TGCCCCTCTACAGCTCTAGAGGAATAAGATTTGACTTTGCAGCTTCAATCTACCCCT-TCACAAC
          1 TGCCCCTCTATAGCTTTAGAGGTATAAGATTTGACTTTGCAACTTCAATCTGCCCCTCT-ACAAC

                                
       4794 TTTAGGGGTATAAGATTTGC
         65 TTTAGGGGTATAAGATTTGC

       4814 TAGTTCACTG


Statistics
Matches: 315,  Mismatches: 59, Indels: 17
        0.81            0.15        0.04

Matches are distributed among these distances:
 147   78  0.25
 148    1  0.00
 149    1  0.00
 150  230  0.73
 151    5  0.02

ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36


Consensus pattern (150 bp):   
TGCCCCTCTATAGCTTTAGAGGTATAAGATTTGACTTTGCAACTTCAATCTGCCCCTCTACAACT
TTAGGGGTATAAGATTTGCCTCTACAGCTTCAATCTGCCCCTCTATAGCTTTAGGGGTATAAGAT
TTGCTTCTGCAGCTTTAATT
Done.