Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01008919.1 Hibiscus syriacus cultivar Beakdansim tig00112223_pilon, 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: 1453011
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


File 5 of 5

Found at i:1443553 original size:19 final size:20

Alignment explanation


    Indices: 1443524--1443574  Score: 61
    Period size: 21  Copynumber: 2.5  Consensus size: 20

    1443514 GGCCAAGAGC

                  *             
    1443524 ATGTATCTTCA-TT-AAAAT
          1 ATGTATTTTCATTTAAAAAT

                                 
    1443542 ATTGTATTTTCATTTAAAAAT
          1 A-TGTATTTTCATTTAAAAAT

                        
    1443563 CATGTATTTTCA
          1 -ATGTATTTTCA

    1443575 AAGGGGTTTC


Statistics
Matches: 28,  Mismatches: 1, Indels: 5
        0.82            0.03        0.15

Matches are distributed among these distances:
  18    1  0.04
  19    9  0.32
  20    2  0.07
  21   15  0.54
  22    1  0.04

ACGTcount: A:0.35, C:0.10, G:0.06, T:0.49


Consensus pattern (20 bp):   
ATGTATTTTCATTTAAAAAT

Found at i:1445974 original size:15 final size:16

Alignment explanation


    Indices: 1445934--1445977  Score: 54
    Period size: 15  Copynumber: 2.8  Consensus size: 16

    1445924 TAATATAATT

                    *       
    1445934 ATGAAATGAAAAGTAA
          1 ATGAAATGGAAAGTAA

               *            
    1445950 ATGGAATGGAAAG-AA
          1 ATGAAATGGAAAGTAA

            *            
    1445965 TTGAAATGGAAAG
          1 ATGAAATGGAAAG

    1445978 GAATGTTATC


Statistics
Matches: 24,  Mismatches: 4, Indels: 1
        0.83            0.14        0.03

Matches are distributed among these distances:
  15   13  0.54
  16   11  0.46

ACGTcount: A:0.55, C:0.00, G:0.27, T:0.18


Consensus pattern (16 bp):   
ATGAAATGGAAAGTAA

Found at i:1447180 original size:19 final size:21

Alignment explanation


    Indices: 1447156--1447207  Score: 81
    Period size: 21  Copynumber: 2.6  Consensus size: 21

    1447146 CAGCCAAGAG

                   *             
    1447156 CATGTATCTTCA-TT-AAAAT
          1 CATGTATTTTCATTTAAAAAT

                                 
    1447175 CATGTATTTTCATTTAAAAAT
          1 CATGTATTTTCATTTAAAAAT

                        
    1447196 CATGTATTTTCA
          1 CATGTATTTTCA

    1447208 AAGGGGTTTC


Statistics
Matches: 30,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
  19   11  0.37
  20    2  0.07
  21   17  0.57

ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46


Consensus pattern (21 bp):   
CATGTATTTTCATTTAAAAAT

Found at i:1449689 original size:7 final size:6

Alignment explanation


    Indices: 1449674--1449732  Score: 54
    Period size: 6  Copynumber: 10.3  Consensus size: 6

    1449664 GTGAAAAAAG

                                   *            *      *            
    1449674 AAAGAA AAAGACA AAAG-A AGAGAA AAAGAA GAA-AA GAAG-A AAAG-A
          1 AAAGAA AAAGA-A AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA

                            
    1449719 AAAGAA AAAGAA AA
          1 AAAGAA AAAGAA AA

    1449733 TTTCAAAAAG


Statistics
Matches: 45,  Mismatches: 4, Indels: 8
        0.79            0.07        0.14

Matches are distributed among these distances:
   5   18  0.40
   6   22  0.49
   7    5  0.11

ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00


Consensus pattern (6 bp):   
AAAGAA

Found at i:1449699 original size:27 final size:28

Alignment explanation


    Indices: 1449668--1449731  Score: 87
    Period size: 27  Copynumber: 2.3  Consensus size: 28

    1449658 ATTGGAGTGA

                                      *  
    1449668 AAAAAGAAAGAAAA-AGACAAAAGAAGAG
          1 AAAAAGAAAGAAAAGA-ACAAAAGAAAAG

                             *          
    1449696 AAAAAG-AAGAAAAGAAGAAAAGAAAAG
          1 AAAAAGAAAGAAAAGAACAAAAGAAAAG

                     
    1449723 AAAAAGAAA
          1 AAAAAGAAA

    1449732 ATTTCAAAAA


Statistics
Matches: 32,  Mismatches: 2, Indels: 4
        0.84            0.05        0.11

Matches are distributed among these distances:
  27   23  0.72
  28    9  0.28

ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00


Consensus pattern (28 bp):   
AAAAAGAAAGAAAAGAACAAAAGAAAAG

Done.