Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011196.1 Kokia drynarioides strain JFW-HI SEQ_126173, 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: 4166
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34


Found at i:34 original size:24 final size:24

Alignment explanation


    Indices: 2--48  Score: 69
    Period size: 24  Copynumber: 2.0  Consensus size: 24

          1 T

                      *              
          2 AATTTTAAACTTAAA-TTAAATTTA
          1 AATTTTAAA-ATAAATTTAAATTTA

                                   
         26 AATTTTAAAATAAATTTAAATTT
          1 AATTTTAAAATAAATTTAAATTT

         49 TTAAACAAAT


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  23    4  0.19
  24   17  0.81

ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47


Consensus pattern (24 bp):   
AATTTTAAAATAAATTTAAATTTA

Found at i:66 original size:17 final size:18

Alignment explanation


    Indices: 12--80  Score: 104
    Period size: 18  Copynumber: 3.9  Consensus size: 18

          2 AATTTTAAAC

                 *            
         12 TTAAATTAAATTTAAATT
          1 TTAAAATAAATTTAAATT

                              
         30 TTAAAATAAATTTAAATT
          1 TTAAAATAAATTTAAATT

              *   *           
         48 TTTAAACAAATTT-AATT
          1 TTAAAATAAATTTAAATT

                            
         65 TTAAAATAAATTTAAA
          1 TTAAAATAAATTTAAA

         81 GGGAGTATGA


Statistics
Matches: 45,  Mismatches: 5, Indels: 2
        0.87            0.10        0.04

Matches are distributed among these distances:
  17   15  0.33
  18   30  0.67

ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45


Consensus pattern (18 bp):   
TTAAAATAAATTTAAATT

Found at i:839 original size:198 final size:198

Alignment explanation


    Indices: 480--1020  Score: 717
    Period size: 198  Copynumber: 2.7  Consensus size: 198

        470 TTCCATCAGG

                 *          **            *         * *   *    *   *       **
        480 ATTTGATTCACTTCTCTGTATCTCATCAGGGAGCTAACCACTTTATCACTTTGACTTGCTTCTTA
          1 ATTTGGTTCACTTCTCCATATCTCATCAGGAAGCTAACC-GTCTATTACTTCGACCTGCTTCTCG

               *                  *   *    *      * **         * *           
        545 GTGCCTCATCAGGAAG-TTGGGATTCAAAG-CTTCGCTTACATCGAGCGTGAGTTTGGTTTGGTC
         65 GTGTCTCATCAGGAAGCTTGGGGTTCGAAGATTTCGCTCATTTCGAGCGTGGGCTTGGTTTGG--

                                                                             
        608 TTCTTCTTAGTATCTCATCAGGAAGATGATCACATCGCTGTTTCAATCCACTTCTCTGTATCTCA
        128 -TCTTC----T-TCTCATCAGGAAGATGATCACATCGCTGTTTCAATCCACTTCTCTGTATCTCA

                        
        673 TCAGGAAGACGA
        187 TCAGGAAGACGA

                                                              *              
        685 ATTTGGTTCACTTCTCCATATCTCATCAGGAAGCTAACCGTCTATTACTTTGACCTGCTTCTCGG
          1 ATTTGGTTCACTTCTCCATATCTCATCAGGAAGCTAACCGTCTATTACTTCGACCTGCTTCTCGG

               *                                  *                          
        750 TGTTTCATCAGGAAGCTTGGGGTTCGAAGATTTCGCTCGTTTCGAGCGTGGGCTTGGTTTGGTCT
         66 TGTCTCATCAGGAAGCTTGGGGTTCGAAGATTTCGCTCATTTCGAGCGTGGGCTTGGTTTGGTCT

                                                    *                        
        815 TCTTCTCATCAGGAAGATGATCACATCGCTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGA
        131 TCTTCTCATCAGGAAGATGATCACATCGCTGTTTCAATCCACTTCTCTGTATCTCATCAGGAAGA

               
        880 CGA
        196 CGA

                             *        *                   *                  
        883 ATTTGGTTCACTTCTCCGTATCTCATTAGGAAGCTAACCGTCTATTGCTTCGACCTGCTTCTCGG
          1 ATTTGGTTCACTTCTCCATATCTCATCAGGAAGCTAACCGTCTATTACTTCGACCTGCTTCTCGG

                                             **       *                      
        948 TGTCTCATCAGGAAGCTTGGGGTTCGAAGATTTTTCTCATTTTGAGCGTGGGCTTGGTTTGGTCT
         66 TGTCTCATCAGGAAGCTTGGGGTTCGAAGATTTCGCTCATTTCGAGCGTGGGCTTGGTTTGGTCT

                    
       1013 TCTTCTCA
        131 TCTTCTCA

       1021 GTATCTCATC


Statistics
Matches: 303,  Mismatches: 31, Indels: 11
        0.88            0.09        0.03

Matches are distributed among these distances:
 198  193  0.64
 199    1  0.00
 203    5  0.02
 204   33  0.11
 205   46  0.15
 206   25  0.08

ACGTcount: A:0.19, C:0.23, G:0.21, T:0.36


Consensus pattern (198 bp):   
ATTTGGTTCACTTCTCCATATCTCATCAGGAAGCTAACCGTCTATTACTTCGACCTGCTTCTCGG
TGTCTCATCAGGAAGCTTGGGGTTCGAAGATTTCGCTCATTTCGAGCGTGGGCTTGGTTTGGTCT
TCTTCTCATCAGGAAGATGATCACATCGCTGTTTCAATCCACTTCTCTGTATCTCATCAGGAAGA
CGA
Done.