Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01009269.1 Hibiscus syriacus cultivar Beakdansim tig00112928_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: 362859
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


File 2 of 2

Found at i:344961 original size:30 final size:29

Alignment explanation


    Indices: 344918--345066  Score: 165
    Period size: 29  Copynumber: 5.1  Consensus size: 29

     344908 TGAGTAATAT

                                *        
     344918 TTTTGGGAATTAATTCGAAATGGGTGCTA
          1 TTTTGGGAATTAATTCGAAAAGGGTGCTA

                *                  *   *  
     344947 TTTTAGGAATTTAATTCGAAAA-TGTGTTA
          1 TTTTGGGAA-TTAATTCGAAAAGGGTGCTA

                                  *       
     344976 TTTTGGGAATTTAATTCGAAAAAGGTGCTA
          1 TTTTGGGAA-TTAATTCGAAAAGGGTGCTA

                 *          *            
     345006 TTTTGAGAATTAATTCAAAAAGGGTGCTA
          1 TTTTGGGAATTAATTCGAAAAGGGTGCTA

                  *     *  **         *  
     345035 TTTTGGTAATTATTTAAAAAAGGGTGTTA
          1 TTTTGGGAATTAATTCGAAAAGGGTGCTA

               
     345064 TTT
          1 TTT

     345067 CTGTAAAATG


Statistics
Matches: 103,  Mismatches: 15, Indels: 4
        0.84            0.12        0.03

Matches are distributed among these distances:
  29   79  0.77
  30   24  0.23

ACGTcount: A:0.33, C:0.05, G:0.21, T:0.41


Consensus pattern (29 bp):   
TTTTGGGAATTAATTCGAAAAGGGTGCTA

Found at i:345007 original size:59 final size:59

Alignment explanation


    Indices: 344918--345045  Score: 163
    Period size: 59  Copynumber: 2.2  Consensus size: 59

     344908 TGAGTAATAT

                                 **                         *     *   *  
     344918 TTTTGGGAA-TTAATTCGAAATGGGTGCTATTTT-AGGAATTTAATTCGAAAA-TGTGTTA
          1 TTTTGGGAATTTAATTCGAAAAAGGTGCTATTTTGA-GAA-TTAATTCAAAAAGGGTGCTA

                                                                       
     344976 TTTTGGGAATTTAATTCGAAAAAGGTGCTATTTTGAGAATTAATTCAAAAAGGGTGCTA
          1 TTTTGGGAATTTAATTCGAAAAAGGTGCTATTTTGAGAATTAATTCAAAAAGGGTGCTA

                  *    
     345035 TTTTGGTAATT
          1 TTTTGGGAATT

     345046 ATTTAAAAAA


Statistics
Matches: 61,  Mismatches: 6, Indels: 5
        0.85            0.08        0.07

Matches are distributed among these distances:
  58   20  0.33
  59   40  0.66
  60    1  0.02

ACGTcount: A:0.32, C:0.05, G:0.22, T:0.41


Consensus pattern (59 bp):   
TTTTGGGAATTTAATTCGAAAAAGGTGCTATTTTGAGAATTAATTCAAAAAGGGTGCTA

Found at i:353108 original size:21 final size:21

Alignment explanation


    Indices: 353082--353121  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

     353072 CTTCCTCGCT

                   *   *         
     353082 TTGGTTCGCTGTTTTTTCAAC
          1 TTGGTTCACTGCTTTTTCAAC

                               
     353103 TTGGTTCACTGCTTTTTCA
          1 TTGGTTCACTGCTTTTTCA

     353122 TTTTTGGCCA


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

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.10, C:0.20, G:0.17, T:0.53


Consensus pattern (21 bp):   
TTGGTTCACTGCTTTTTCAAC


Done.