Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01008109.1 Hibiscus syriacus cultivar Beakdansim tig00110645_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: 32259
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33


Found at i:4359 original size:16 final size:16

Alignment explanation


    Indices: 4334--4376  Score: 77
    Period size: 16  Copynumber: 2.7  Consensus size: 16

       4324 ATATGCTCTG

                 *          
       4334 ATTTGGTTGTAAAATA
          1 ATTTGATTGTAAAATA

                            
       4350 ATTTGATTGTAAAATA
          1 ATTTGATTGTAAAATA

                       
       4366 ATTTGATTGTA
          1 ATTTGATTGTA

       4377 TTTATTACTG


Statistics
Matches: 26,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  16   26  1.00

ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47


Consensus pattern (16 bp):   
ATTTGATTGTAAAATA

Found at i:6763 original size:17 final size:16

Alignment explanation


    Indices: 6741--6772  Score: 55
    Period size: 17  Copynumber: 1.9  Consensus size: 16

       6731 ATTTTTTAAA

                             
       6741 TATTTTAAAATAATATT
          1 TATTTTAAAA-AATATT

                           
       6758 TATTTTAAAAAATAT
          1 TATTTTAAAAAATAT

       6773 AAATGTGACA


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  16    5  0.33
  17   10  0.67

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (16 bp):   
TATTTTAAAAAATATT

Found at i:10649 original size:18 final size:18

Alignment explanation


    Indices: 10628--10697  Score: 70
    Period size: 18  Copynumber: 3.8  Consensus size: 18

      10618 AAACAAATTT

                              
      10628 GGTATCAATACCCATGGG
          1 GGTATCAATACCCATGGG

                  *     *     
      10646 GGTATCGATACCTA-GGG
          1 GGTATCAATACCCATGGG

                                 
      10663 TAGAGTATCAATACCCATGGG
          1 --G-GTATCAATACCCATGGG

            *     *       
      10684 AGTATCGATACCCA
          1 GGTATCAATACCCA

      10698 AGCATTTTTC


Statistics
Matches: 42,  Mismatches: 6, Indels: 8
        0.75            0.11        0.14

Matches are distributed among these distances:
  17    3  0.07
  18   24  0.57
  19    1  0.02
  20   11  0.26
  21    3  0.07

ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23


Consensus pattern (18 bp):   
GGTATCAATACCCATGGG

Found at i:12817 original size:2 final size:2

Alignment explanation


    Indices: 12812--12847  Score: 72
    Period size: 2  Copynumber: 18.0  Consensus size: 2

      12802 CACACATTTA

                                                                 
      12812 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      12848 TAATAACTAA


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   34  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:22332 original size:28 final size:28

Alignment explanation


    Indices: 22301--22355  Score: 110
    Period size: 28  Copynumber: 2.0  Consensus size: 28

      22291 ACATATATTT

                                        
      22301 CTTTATACTTATTCCATAATATTAAAAG
          1 CTTTATACTTATTCCATAATATTAAAAG

                                       
      22329 CTTTATACTTATTCCATAATATTAAAA
          1 CTTTATACTTATTCCATAATATTAAAA

      22356 AAATCTGATA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  28   27  1.00

ACGTcount: A:0.40, C:0.15, G:0.02, T:0.44


Consensus pattern (28 bp):   
CTTTATACTTATTCCATAATATTAAAAG
Done.