Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001295.1 Kokia drynarioides strain JFW-HI SEQ_112694, 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: 3315
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36

Warning! 2 characters in sequence are not A, C, G, or T


Found at i:1701 original size:13 final size:13

Alignment explanation


    Indices: 1683--1708  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       1673 TTGGGCTTGA

                         
       1683 TTTGTAATTGGAC
          1 TTTGTAATTGGAC

                         
       1696 TTTGTAATTGGAC
          1 TTTGTAATTGGAC

       1709 ATTATTTAAA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46


Consensus pattern (13 bp):   
TTTGTAATTGGAC

Found at i:1730 original size:6 final size:6

Alignment explanation


    Indices: 1719--1804  Score: 74
    Period size: 6  Copynumber: 15.0  Consensus size: 6

       1709 ATTATTTAAA

                                   *                        *       
       1719 TAAATT TAAATT TAAATT TCTAA-- TAAATT TAAATT TAAA-A TAAATT
          1 TAAATT TAAATT TAAATT T-AAATT TAAATT TAAATT TAAATT TAAATT

                        *     *     *        *              
       1765 TAAATT TAAA-A TAAACT TAATTT TAAA-A TAAATT TAAATT
          1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT

       1805 CTGTTGGGCC


Statistics
Matches: 63,  Mismatches: 11, Indels: 12
        0.73            0.13        0.14

Matches are distributed among these distances:
   4    2  0.03
   5   13  0.21
   6   46  0.73
   7    2  0.03

ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44


Consensus pattern (6 bp):   
TAAATT

Found at i:1747 original size:17 final size:17

Alignment explanation


    Indices: 1725--1804  Score: 124
    Period size: 17  Copynumber: 4.7  Consensus size: 17

       1715 TAAATAAATT

                         **  
       1725 TAAATTTAAATTTCTAA
          1 TAAATTTAAATTTAAAA

                             
       1742 TAAATTTAAATTTAAAA
          1 TAAATTTAAATTTAAAA

                             
       1759 TAAATTTAAATTTAAAA
          1 TAAATTTAAATTTAAAA

                *    *       
       1776 TAAACTTAATTTTAAAA
          1 TAAATTTAAATTTAAAA

                        
       1793 TAAATTTAAATT
          1 TAAATTTAAATT

       1805 CTGTTGGGCC


Statistics
Matches: 57,  Mismatches: 6, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  17   57  1.00

ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44


Consensus pattern (17 bp):   
TAAATTTAAATTTAAAA

Found at i:1768 original size:23 final size:22

Alignment explanation


    Indices: 1712--1774  Score: 74
    Period size: 23  Copynumber: 2.8  Consensus size: 22

       1702 ATTGGACATT

                                  
       1712 ATTTAAATAAATTTAAATTTAA
          1 ATTTAAATAAATTTAAATTTAA

                 *                 
       1734 ATTTCTAATAAATTTAAATTTAA
          1 ATTT-AAATAAATTTAAATTTAA

              *                
       1757 A-ATAAATTTAAATTTAAA
          1 ATTTAAA--TAAATTTAAA

       1775 ATAAACTTAA


Statistics
Matches: 35,  Mismatches: 3, Indels: 5
        0.81            0.07        0.12

Matches are distributed among these distances:
  21    2  0.06
  22    5  0.14
  23   28  0.80

ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44


Consensus pattern (22 bp):   
ATTTAAATAAATTTAAATTTAA
Done.