Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01002904.1 Hibiscus syriacus cultivar Beakdansim tig00005995_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: 150632
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


File 2 of 2

Found at i:144724 original size:23 final size:23

Alignment explanation


    Indices: 144674--144718  Score: 72
    Period size: 23  Copynumber: 2.0  Consensus size: 23

     144664 TGCCTATTTT

                               *   
     144674 ATTATATAAGCGCTACATATTAC
          1 ATTATATAAGCGCTACATAATAC

                            *     
     144697 ATTATATAAGCGCTACCTAATA
          1 ATTATATAAGCGCTACATAATA

     144719 TGTTATTGTA


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  23   20  1.00

ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33


Consensus pattern (23 bp):   
ATTATATAAGCGCTACATAATAC

Found at i:145227 original size:72 final size:71

Alignment explanation


    Indices: 145086--145228  Score: 214
    Period size: 72  Copynumber: 2.0  Consensus size: 71

     145076 ATTTTAAGTT

                                              *  *   *    *    *   *         
     145086 TAATAATTAAAAAATATTTTTAAACATATTTTTTTTTCAAACACTCGAAAATATGGTAATTCAAT
          1 TAATAATTAAAAAATATTTTTAAACATATTTTTTATTAAAAAACTCAAAAACATGATAATTCAAT

                  
     145151 GGGCCC
         66 GGGCCC

                                                                            *
     145157 TAATAATTAAAAAATATTTTTAAACATAATTTTTTATTAAAAAACTCAAAAACATGATAATTCAG
          1 TAATAATTAAAAAATATTTTTAAACAT-ATTTTTTATTAAAAAACTCAAAAACATGATAATTCAA

                   
     145222 TGGGCCC
         65 TGGGCCC

     145229 CATTTTAATG


Statistics
Matches: 64,  Mismatches: 7, Indels: 1
        0.89            0.10        0.01

Matches are distributed among these distances:
  71   27  0.42
  72   37  0.58

ACGTcount: A:0.44, C:0.12, G:0.08, T:0.36


Consensus pattern (71 bp):   
TAATAATTAAAAAATATTTTTAAACATATTTTTTATTAAAAAACTCAAAAACATGATAATTCAAT
GGGCCC

Found at i:146921 original size:22 final size:22

Alignment explanation


    Indices: 146896--146938  Score: 59
    Period size: 22  Copynumber: 2.0  Consensus size: 22

     146886 TCACTTTCAT

                 *   *   *        
     146896 TGTTTTTCTTTTTTCTTTGTAG
          1 TGTTTGTCTGTTTACTTTGTAG

                                 
     146918 TGTTTGTCTGTTTACTTTGTA
          1 TGTTTGTCTGTTTACTTTGTA

     146939 TCAAATGTTA


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  22   18  1.00

ACGTcount: A:0.07, C:0.09, G:0.16, T:0.67


Consensus pattern (22 bp):   
TGTTTGTCTGTTTACTTTGTAG

Found at i:148732 original size:28 final size:28

Alignment explanation


    Indices: 148690--148753  Score: 110
    Period size: 28  Copynumber: 2.3  Consensus size: 28

     148680 CTTTTATTAA

                   *  *                 
     148690 ATCAAATTGCCTACTTTATACAATTTAT
          1 ATCAAATAGCATACTTTATACAATTTAT

                                        
     148718 ATCAAATAGCATACTTTATACAATTTAT
          1 ATCAAATAGCATACTTTATACAATTTAT

                    
     148746 ATCAAATA
          1 ATCAAATA

     148754 ATTTACAAAA


Statistics
Matches: 34,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  28   34  1.00

ACGTcount: A:0.42, C:0.16, G:0.03, T:0.39


Consensus pattern (28 bp):   
ATCAAATAGCATACTTTATACAATTTAT

Done.