Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01007198.1 Hibiscus syriacus cultivar Beakdansim tig00018991_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: 64476
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32


Found at i:14386 original size:16 final size:16

Alignment explanation


    Indices: 14365--14404  Score: 80
    Period size: 16  Copynumber: 2.5  Consensus size: 16

      14355 TTTAGGAGTA

                            
      14365 AGGTTTTGTCTAATAC
          1 AGGTTTTGTCTAATAC

                            
      14381 AGGTTTTGTCTAATAC
          1 AGGTTTTGTCTAATAC

                    
      14397 AGGTTTTG
          1 AGGTTTTG

      14405 GAACTACAAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   24  1.00

ACGTcount: A:0.23, C:0.10, G:0.23, T:0.45


Consensus pattern (16 bp):   
AGGTTTTGTCTAATAC

Found at i:18212 original size:22 final size:21

Alignment explanation


    Indices: 18160--18214  Score: 58
    Period size: 22  Copynumber: 2.5  Consensus size: 21

      18150 CTTATAATAT

                   *             
      18160 TTTTTATATTTTTAATATGAA
          1 TTTTTATTTTTTTAATATGAA

                 *                  
      18181 TATTTAATTTTTTTAAACTAT-AA
          1 T-TTTTATTTTTTT-AA-TATGAA

                       
      18204 TTTTTATTTTT
          1 TTTTTATTTTT

      18215 AGTGTTTTTC


Statistics
Matches: 28,  Mismatches: 3, Indels: 5
        0.78            0.08        0.14

Matches are distributed among these distances:
  21    1  0.04
  22   19  0.68
  23    5  0.18
  24    3  0.11

ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65


Consensus pattern (21 bp):   
TTTTTATTTTTTTAATATGAA

Found at i:19170 original size:16 final size:16

Alignment explanation


    Indices: 19149--19187  Score: 53
    Period size: 16  Copynumber: 2.4  Consensus size: 16

      19139 TTCCTATTCG

                             
      19149 TTTATTTACT-TTCAAA
          1 TTTATTTA-TATTCAAA

                            
      19165 TTTATTTATATTCAAA
          1 TTTATTTATATTCAAA

                   
      19181 TTATATT
          1 TT-TATT

      19188 CATTAACATT


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  15    1  0.05
  16   16  0.76
  17    4  0.19

ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59


Consensus pattern (16 bp):   
TTTATTTATATTCAAA

Found at i:37026 original size:13 final size:14

Alignment explanation


    Indices: 36999--37027  Score: 51
    Period size: 14  Copynumber: 2.1  Consensus size: 14

      36989 AATAAATGAA

                          
      36999 CTCACTTTGTATGC
          1 CTCACTTTGTATGC

                          
      37013 CTCACTTT-TATGC
          1 CTCACTTTGTATGC

              
      37026 CT
          1 CT

      37028 TACTAACGAT


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

Matches are distributed among these distances:
  13    7  0.47
  14    8  0.53

ACGTcount: A:0.14, C:0.31, G:0.10, T:0.45


Consensus pattern (14 bp):   
CTCACTTTGTATGC

Found at i:53570 original size:13 final size:14

Alignment explanation


    Indices: 53543--53571  Score: 51
    Period size: 14  Copynumber: 2.1  Consensus size: 14

      53533 AATAAATGAA

                          
      53543 CTCACTTTGTATGC
          1 CTCACTTTGTATGC

                          
      53557 CTCACTTT-TATGC
          1 CTCACTTTGTATGC

              
      53570 CT
          1 CT

      53572 TACTAACGAT


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

Matches are distributed among these distances:
  13    7  0.47
  14    8  0.53

ACGTcount: A:0.14, C:0.31, G:0.10, T:0.45


Consensus pattern (14 bp):   
CTCACTTTGTATGC
Done.