Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001971.1 Kokia drynarioides strain JFW-HI SEQ_113812, 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: 2006
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27


Found at i:1256 original size:47 final size:48

Alignment explanation


    Indices: 1187--1367  Score: 199
    Period size: 47  Copynumber: 3.8  Consensus size: 48

       1177 GTACTATCAG

                                   * *                      
       1187 GCAGATTGAAGCCATCACATCCAGTTTTATACCCCAAATCTA-AAGGA
          1 GCAGATTGAAGCCATCACATCCAATCTTATACCCCAAATCTAGAAGGA

                    *    *                                  
       1234 GCAGATTGGAGCCTTCACATCCAATCTTATACCCCAAATCTAGAA-G-
          1 GCAGATTGAAGCCATCACATCCAATCTTATACCCCAAATCTAGAAGGA

                    *            *            **          *  
       1280 GCTAGATTTAAGCCATCACATTCAATCTTATACCTTAAATCTAGAAAG-
          1 GC-AGATTGAAGCCATCACATCCAATCTTATACCCCAAATCTAGAAGGA

             *     *    *      * *                  
       1328 GTAGATTAAAGCTATCACAGCTAATCTTATACCCCAAATC
          1 GCAGATTGAAGCCATCACATCCAATCTTATACCCCAAATC

       1368 CAAAGAGGCG


Statistics
Matches: 113,  Mismatches: 18, Indels: 6
        0.82            0.13        0.04

Matches are distributed among these distances:
  46    2  0.02
  47  107  0.95
  48    4  0.04

ACGTcount: A:0.36, C:0.25, G:0.13, T:0.27


Consensus pattern (48 bp):   
GCAGATTGAAGCCATCACATCCAATCTTATACCCCAAATCTAGAAGGA

Found at i:1792 original size:17 final size:17

Alignment explanation


    Indices: 1751--1794  Score: 63
    Period size: 17  Copynumber: 2.6  Consensus size: 17

       1741 GTTTGGGCCC

                             
       1751 AAATAAAAACCAAAACA
          1 AAATAAAAACCAAAACA

               *             
       1768 AAAAAAAAACCAAAA-A
          1 AAATAAAAACCAAAACA

                       
       1784 TAAATAAAAAC
          1 -AAATAAAAAC

       1795 ATTAAAATTA


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  16    1  0.04
  17   23  0.96

ACGTcount: A:0.80, C:0.14, G:0.00, T:0.07


Consensus pattern (17 bp):   
AAATAAAAACCAAAACA
Done.