Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01004358.1 Hibiscus syriacus cultivar Beakdansim tig00009547_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: 48238
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:4929 original size:15 final size:15

Alignment explanation


    Indices: 4911--4941  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       4901 AGAATGGGGT

                           
       4911 ACTAGTTGATGGAGC
          1 ACTAGTTGATGGAGC

                           
       4926 ACTAGTTGATGGAGC
          1 ACTAGTTGATGGAGC

             
       4941 A
          1 A

       4942 GGTGCAAGTG


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.29, C:0.13, G:0.32, T:0.26


Consensus pattern (15 bp):   
ACTAGTTGATGGAGC

Found at i:9735 original size:2 final size:2

Alignment explanation


    Indices: 9728--9774  Score: 94
    Period size: 2  Copynumber: 23.5  Consensus size: 2

       9718 GCCAACTACC

                                                                          
       9728 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                   
       9770 TA TA T
          1 TA TA T

       9775 CAATTAATTG


Statistics
Matches: 45,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   45  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:25567 original size:18 final size:18

Alignment explanation


    Indices: 25544--25578  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

      25534 TTCCATCCGG

                  *           
      25544 TCTTATTATTTAATTCAA
          1 TCTTATCATTTAATTCAA

                        *    
      25562 TCTTATCATTTACTTCA
          1 TCTTATCATTTAATTCA

      25579 GTCCTTTCGT


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   15  1.00

ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54


Consensus pattern (18 bp):   
TCTTATCATTTAATTCAA

Found at i:26878 original size:15 final size:17

Alignment explanation


    Indices: 26848--26881  Score: 54
    Period size: 15  Copynumber: 2.1  Consensus size: 17

      26838 TCAAAGTTTT

                             
      26848 GGTCAACAGTGGTCAAC
          1 GGTCAACAGTGGTCAAC

                             
      26865 GGTCAAC-G-GGTCAAC
          1 GGTCAACAGTGGTCAAC

              
      26880 GG
          1 GG

      26882 GTCGAGTCAA


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  15    9  0.53
  16    1  0.06
  17    7  0.41

ACGTcount: A:0.26, C:0.24, G:0.35, T:0.15


Consensus pattern (17 bp):   
GGTCAACAGTGGTCAAC

Found at i:26912 original size:13 final size:13

Alignment explanation


    Indices: 26871--26915  Score: 72
    Period size: 13  Copynumber: 3.5  Consensus size: 13

      26861 CAACGGTCAA

                         
      26871 CGGGTCAACGGGT
          1 CGGGTCAACGGGT

              *          
      26884 CGAGTCAACGGGT
          1 CGGGTCAACGGGT

                 *       
      26897 CGGGTAAACGGGT
          1 CGGGTCAACGGGT

                  
      26910 CGGGTC
          1 CGGGTC

      26916 GGTAAACGGG


Statistics
Matches: 28,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  13   28  1.00

ACGTcount: A:0.18, C:0.22, G:0.44, T:0.16


Consensus pattern (13 bp):   
CGGGTCAACGGGT

Found at i:26913 original size:18 final size:18

Alignment explanation


    Indices: 26892--26936  Score: 83
    Period size: 17  Copynumber: 2.6  Consensus size: 18

      26882 GTCGAGTCAA

                              
      26892 CGGGTCGGGTAAACGGGT
          1 CGGGTCGGGTAAACGGGT

                              
      26910 CGGGTC-GGTAAACGGGT
          1 CGGGTCGGGTAAACGGGT

                      
      26927 CGGGTCGGGT
          1 CGGGTCGGGT

      26937 TGTGACCGGT


Statistics
Matches: 26,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
  17   17  0.65
  18    9  0.35

ACGTcount: A:0.13, C:0.18, G:0.51, T:0.18


Consensus pattern (18 bp):   
CGGGTCGGGTAAACGGGT

Found at i:41062 original size:12 final size:12

Alignment explanation


    Indices: 41045--41074  Score: 60
    Period size: 12  Copynumber: 2.5  Consensus size: 12

      41035 CGAGACTCGA

                        
      41045 GCTCGATTTTGT
          1 GCTCGATTTTGT

                        
      41057 GCTCGATTTTGT
          1 GCTCGATTTTGT

                  
      41069 GCTCGA
          1 GCTCGA

      41075 ACTCGATTCA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   18  1.00

ACGTcount: A:0.10, C:0.20, G:0.27, T:0.43


Consensus pattern (12 bp):   
GCTCGATTTTGT

Found at i:41187 original size:14 final size:14

Alignment explanation


    Indices: 41168--41197  Score: 51
    Period size: 14  Copynumber: 2.1  Consensus size: 14

      41158 TATAATTGTC

                     *    
      41168 AATAATGTATTTTT
          1 AATAATGTAATTTT

                          
      41182 AATAATGTAATTTT
          1 AATAATGTAATTTT

              
      41196 AA
          1 AA

      41198 AAAATCTAAA


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

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50


Consensus pattern (14 bp):   
AATAATGTAATTTT
Done.