Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007432.1 Kokia drynarioides strain JFW-HI SEQ_122053, 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: 22861
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32

Warning! 83 characters in sequence are not A, C, G, or T


Found at i:1930 original size:20 final size:23

Alignment explanation


    Indices: 1905--1954  Score: 63
    Period size: 20  Copynumber: 2.3  Consensus size: 23

       1895 AGAAGACCGG

                            *      
       1905 AGGAGGAGA-TGGAA-TTGGC-A
          1 AGGAGGAGAGTGGAAGGTGGCGA

                                   
       1925 AGGAGGA-AGTGGAAGGTGGCGA
          1 AGGAGGAGAGTGGAAGGTGGCGA

                    
       1947 AGGAGGAG
          1 AGGAGGAG

       1955 GAGGAGGAGG


Statistics
Matches: 25,  Mismatches: 1, Indels: 5
        0.81            0.03        0.16

Matches are distributed among these distances:
  19    1  0.04
  20   12  0.48
  21    4  0.16
  22    8  0.32

ACGTcount: A:0.34, C:0.04, G:0.52, T:0.10


Consensus pattern (23 bp):   
AGGAGGAGAGTGGAAGGTGGCGA

Found at i:14174 original size:30 final size:28

Alignment explanation


    Indices: 14137--14229  Score: 78
    Period size: 30  Copynumber: 3.1  Consensus size: 28

      14127 TTTAAGAATC

                                         
      14137 AAGATTAAATTGATAAAATGTATAAAGTT
          1 AAGATTAAATTGATAAAAT-TATAAAGTT

                          *         *    *  
      14166 AAGAATTAAATTTGTTGAACAATTTTAAATTT
          1 AAG-ATTAAA-TTGAT-AA-AATTATAAAGTT

                *        *                
      14198 AAGACTAAATTGACAAAATCTATAAAGATT
          1 AAGATTAAATTGATAAAAT-TATAAAG-TT

              
      14228 AA
          1 AA

      14230 AAGGTAAATT


Statistics
Matches: 50,  Mismatches: 8, Indels: 11
        0.72            0.12        0.16

Matches are distributed among these distances:
  28    3  0.06
  29   10  0.20
  30   13  0.26
  31    9  0.18
  32   12  0.24
  33    3  0.06

ACGTcount: A:0.51, C:0.04, G:0.11, T:0.34


Consensus pattern (28 bp):   
AAGATTAAATTGATAAAATTATAAAGTT

Found at i:22842 original size:2 final size:2

Alignment explanation


    Indices: 22835--22861  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

      22825 ACCGATTTCA

                                                    
      22835 AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT A


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.