Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009883.1 Kokia drynarioides strain JFW-HI SEQ_124618, 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: 7741
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:73 original size:23 final size:23

Alignment explanation


    Indices: 47--194  Score: 136
    Period size: 23  Copynumber: 6.3  Consensus size: 23

         37 ACACTAGCGC

                                   
         47 GCTCTCTGATTAGCACTGTGTGT
          1 GCTCTCTGATTAGCACTGTGTGT

                    *       *  *    
         70 GCTCTCTGTTTAGCA-AGTCTCGT
          1 GCTCTCTGATTAGCACTGTGT-GT

                                     
         93 GCTCTCTGTTATTAGCACTGTGTGT
          1 GCTCTCTG--ATTAGCACTGTGTGT

            *           *  * *     
        118 ACTCTCTGATTATCATTTTGTGT
          1 GCTCTCTGATTAGCACTGTGTGT

               *     *   *   * *   
        141 GCTTTCTGACTAGTACTTTCTGT
          1 GCTCTCTGATTAGCACTGTGTGT

            *       *              
        164 ACTCTCTGTTTAGCACTGTGTGT
          1 GCTCTCTGATTAGCACTGTGTGT

                    
        187 GCTCTCTG
          1 GCTCTCTG

        195 TTTCCCAGCA


Statistics
Matches: 96,  Mismatches: 25, Indels: 8
        0.74            0.19        0.06

Matches are distributed among these distances:
  22    3  0.03
  23   75  0.78
  25   15  0.16
  26    3  0.03

ACGTcount: A:0.13, C:0.22, G:0.21, T:0.44


Consensus pattern (23 bp):   
GCTCTCTGATTAGCACTGTGTGT

Found at i:3586 original size:21 final size:22

Alignment explanation


    Indices: 3562--3604  Score: 61
    Period size: 21  Copynumber: 2.0  Consensus size: 22

       3552 ACTTTCATCA

                                  
       3562 TTAAGCTTAATTAA-CCCATTT
          1 TTAAGCTTAATTAAGCCCATTT

                *   *             
       3583 TTAATCTTGATTAAGCCCATTT
          1 TTAAGCTTAATTAAGCCCATTT

       3605 ATACTTAATT


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  21   12  0.63
  22    7  0.37

ACGTcount: A:0.30, C:0.19, G:0.07, T:0.44


Consensus pattern (22 bp):   
TTAAGCTTAATTAAGCCCATTT

Found at i:5210 original size:43 final size:43

Alignment explanation


    Indices: 5139--5237  Score: 144
    Period size: 43  Copynumber: 2.3  Consensus size: 43

       5129 CAATTTTTTG

                *                             *     *  
       5139 ACCTTTGTCGATATCTATCTCACAAAAATATTGATACCCGTGA
          1 ACCTGTGTCGATATCTATCTCACAAAAATATTGAGACCCGCGA

                     *                            *    
       5182 ACCTGTGTCTATATCTATCTCACAAAAATATTGAGACCTGCGA
          1 ACCTGTGTCGATATCTATCTCACAAAAATATTGAGACCCGCGA

              *          
       5225 ACTTGTGTCGATA
          1 ACCTGTGTCGATA

       5238 CCTACGTTGT


Statistics
Matches: 49,  Mismatches: 7, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  43   49  1.00

ACGTcount: A:0.31, C:0.22, G:0.14, T:0.32


Consensus pattern (43 bp):   
ACCTGTGTCGATATCTATCTCACAAAAATATTGAGACCCGCGA

Found at i:6377 original size:30 final size:30

Alignment explanation


    Indices: 6341--6409  Score: 129
    Period size: 30  Copynumber: 2.3  Consensus size: 30

       6331 AATCTCATTG

                   *                      
       6341 ATTCATTTTATGATGTTTTGTGCCTCAATT
          1 ATTCATTCTATGATGTTTTGTGCCTCAATT

                                          
       6371 ATTCATTCTATGATGTTTTGTGCCTCAATT
          1 ATTCATTCTATGATGTTTTGTGCCTCAATT

                     
       6401 ATTCATTCT
          1 ATTCATTCT

       6410 TCCAATTAAA


Statistics
Matches: 38,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  30   38  1.00

ACGTcount: A:0.20, C:0.16, G:0.12, T:0.52


Consensus pattern (30 bp):   
ATTCATTCTATGATGTTTTGTGCCTCAATT
Done.