Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01007267.1 Hibiscus syriacus cultivar Beakdansim tig00019267_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: 245752
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


File 2 of 2

Found at i:232482 original size:17 final size:16

Alignment explanation


    Indices: 232444--232496  Score: 54
    Period size: 17  Copynumber: 3.1  Consensus size: 16

     232434 ATTATATAGT

                             
     232444 TTATAATATAAA-TATA
          1 TTAT-ATATAAATTATA

                               
     232460 GTTTATATATAAACTTATA
          1 --TTATATATAAA-TTATA

                     *      
     232479 TTATATATATATTATA
          1 TTATATATAAATTATA

              
     232495 TT
          1 TT

     232497 TTTTTCAATT


Statistics
Matches: 32,  Mismatches: 1, Indels: 6
        0.82            0.03        0.15

Matches are distributed among these distances:
  16    7  0.22
  17   17  0.53
  18    4  0.12
  19    4  0.12

ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51


Consensus pattern (16 bp):   
TTATATATAAATTATA

Found at i:232607 original size:16 final size:16

Alignment explanation


    Indices: 232586--232635  Score: 50
    Period size: 15  Copynumber: 3.2  Consensus size: 16

     232576 TTTTTGTGTT

                   *        
     232586 TTTTAATTTATTTCAA
          1 TTTTAATATATTTCAA

                           *
     232602 TTTTAA-ATATTTCAC
          1 TTTTAATATATTTCAA

                     *       
     232617 TTTT-ATATGTATTCAA
          1 TTTTAATATAT-TTCAA

               
     232633 TTT
          1 TTT

     232636 AGTCCTTAAA


Statistics
Matches: 28,  Mismatches: 4, Indels: 4
        0.78            0.11        0.11

Matches are distributed among these distances:
  14    1  0.04
  15   14  0.50
  16   13  0.46

ACGTcount: A:0.30, C:0.08, G:0.02, T:0.60


Consensus pattern (16 bp):   
TTTTAATATATTTCAA

Found at i:237228 original size:14 final size:14

Alignment explanation


    Indices: 237195--237231  Score: 56
    Period size: 14  Copynumber: 2.6  Consensus size: 14

     237185 ATTTTAGTCT

                 *    *   
     237195 TTATTGTGATCAAA
          1 TTATTTTGATAAAA

                          
     237209 TTATTTTGATAAAA
          1 TTATTTTGATAAAA

                     
     237223 TTATTTTGA
          1 TTATTTTGA

     237232 GAAGGAATTT


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  14   21  1.00

ACGTcount: A:0.35, C:0.03, G:0.11, T:0.51


Consensus pattern (14 bp):   
TTATTTTGATAAAA

Found at i:239089 original size:48 final size:48

Alignment explanation


    Indices: 239018--239127  Score: 220
    Period size: 48  Copynumber: 2.3  Consensus size: 48

     239008 ATTTGTTAAT

                                                            
     239018 TCTCAGCATTAAAACAGAGATTGTTGTGTGACCAATGTAGATGCCTTA
          1 TCTCAGCATTAAAACAGAGATTGTTGTGTGACCAATGTAGATGCCTTA

                                                            
     239066 TCTCAGCATTAAAACAGAGATTGTTGTGTGACCAATGTAGATGCCTTA
          1 TCTCAGCATTAAAACAGAGATTGTTGTGTGACCAATGTAGATGCCTTA

                          
     239114 TCTCAGCATTAAAA
          1 TCTCAGCATTAAAA

     239128 TTTAATTCTC


Statistics
Matches: 62,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  48   62  1.00

ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31


Consensus pattern (48 bp):   
TCTCAGCATTAAAACAGAGATTGTTGTGTGACCAATGTAGATGCCTTA

Done.