Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01000972.1 Hibiscus syriacus cultivar Beakdansim tig00001941_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: 104210
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.34


File 2 of 2

Found at i:103644 original size:6 final size:6

Alignment explanation


    Indices: 103633--103702  Score: 52
    Period size: 6  Copynumber: 11.0  Consensus size: 6

     103623 TATCAAATTC

                                                             *        **
     103633 TTTCTT TTTCTTT TTTCAGTTT TTTCTT TTTCTT TTTCTT TTTTTCT TTTCAC
          1 TTTCTT TTTC-TT TTTC---TT TTTCTT TTTCTT TTTCTT TTTCT-T TTTCTT

                 *              
     103686 TTTCTC TTT-TT TTTCTT
          1 TTTCTT TTTCTT TTTCTT

     103703 CAGGCGAAGT


Statistics
Matches: 53,  Mismatches: 6, Indels: 10
        0.77            0.09        0.14

Matches are distributed among these distances:
   5    4  0.08
   6   32  0.60
   7   10  0.19
   9    7  0.13

ACGTcount: A:0.03, C:0.17, G:0.01, T:0.79


Consensus pattern (6 bp):   
TTTCTT

Found at i:103658 original size:22 final size:20

Alignment explanation


    Indices: 103633--103682  Score: 73
    Period size: 20  Copynumber: 2.4  Consensus size: 20

     103623 TATCAAATTC

                                  
     103633 TTTCTTTTTCTTTTTTCAGTTT
          1 TTTCTTTTTC-TTTTTC-GTTT

                            *   
     103655 TTTCTTTTTCTTTTTCTTTT
          1 TTTCTTTTTCTTTTTCGTTT

                    
     103675 TTTCTTTT
          1 TTTCTTTT

     103683 CACTTTCTCT


Statistics
Matches: 27,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  20   11  0.41
  21    6  0.22
  22   10  0.37

ACGTcount: A:0.02, C:0.14, G:0.02, T:0.82


Consensus pattern (20 bp):   
TTTCTTTTTCTTTTTCGTTT

Found at i:103688 original size:21 final size:20

Alignment explanation


    Indices: 103652--103698  Score: 67
    Period size: 21  Copynumber: 2.3  Consensus size: 20

     103642 CTTTTTTCAG

                       *    *   
     103652 TTTTTTCTTTTTCTTTTTCT
          1 TTTTTTCTTTTACTTTCTCT

                                 
     103672 TTTTTTCTTTTCACTTTCTCT
          1 TTTTTTCTTTT-ACTTTCTCT

                  
     103693 TTTTTT
          1 TTTTTT

     103699 TCTTCAGGCG


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  20   11  0.46
  21   13  0.54

ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81


Consensus pattern (20 bp):   
TTTTTTCTTTTACTTTCTCT

Done.