Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01007976.1 Hibiscus syriacus cultivar Beakdansim tig00110413_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: 428971
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33


File 3 of 3

Found at i:426948 original size:24 final size:24

Alignment explanation


    Indices: 426921--426996  Score: 74
    Period size: 24  Copynumber: 3.4  Consensus size: 24

     426911 TTGTGTATGA

                                    
     426921 TTATGTATTATGAGCTTTTAAACT
          1 TTATGTATTATGAGCTTTTAAACT

                         *    *  *   
     426945 TTATGTATT-T--TCTATGT-GA--
          1 TTATGTATTATGAGCT-TTTAAACT

                                    
     426964 TTATGTATTATGAGCTTTTAAACT
          1 TTATGTATTATGAGCTTTTAAACT

                     
     426988 TTATGTATT
          1 TTATGTATT

     426997 TTCTATGTGA


Statistics
Matches: 39,  Mismatches: 6, Indels: 14
        0.66            0.10        0.24

Matches are distributed among these distances:
  19    9  0.23
  20    1  0.03
  21    5  0.13
  22    5  0.13
  23    1  0.03
  24   18  0.46

ACGTcount: A:0.26, C:0.07, G:0.13, T:0.54


Consensus pattern (24 bp):   
TTATGTATTATGAGCTTTTAAACT

Found at i:426969 original size:43 final size:43

Alignment explanation


    Indices: 426918--427008  Score: 182
    Period size: 43  Copynumber: 2.1  Consensus size: 43

     426908 TTTTTGTGTA

                                                       
     426918 TGATTATGTATTATGAGCTTTTAAACTTTATGTATTTTCTATG
          1 TGATTATGTATTATGAGCTTTTAAACTTTATGTATTTTCTATG

                                                       
     426961 TGATTATGTATTATGAGCTTTTAAACTTTATGTATTTTCTATG
          1 TGATTATGTATTATGAGCTTTTAAACTTTATGTATTTTCTATG

                 
     427004 TGATT
          1 TGATT

     427009 TTTAAAAAGT


Statistics
Matches: 48,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  43   48  1.00

ACGTcount: A:0.25, C:0.07, G:0.14, T:0.54


Consensus pattern (43 bp):   
TGATTATGTATTATGAGCTTTTAAACTTTATGTATTTTCTATG

Found at i:428472 original size:28 final size:29

Alignment explanation


    Indices: 428398--428477  Score: 87
    Period size: 27  Copynumber: 2.9  Consensus size: 29

     428388 GAAAAAATTG

                 *      *           *    
     428398 AATACCTTATGTGCTTATTTTGACTAAAA
          1 AATACTTTATGTACTTATTTTGACCAAAA

                            *             
     428427 AATACTTTA-G-A-TAGATTTTGACCAAAA
          1 AATACTTTATGTACT-TATTTTGACCAAAA

                                     
     428454 AA-ACTTTATGTACTTATTTTGACC
          1 AATACTTTATGTACTTATTTTGACC

     428478 GAAATACTAT


Statistics
Matches: 42,  Mismatches: 5, Indels: 9
        0.75            0.09        0.16

Matches are distributed among these distances:
  26    7  0.17
  27   15  0.36
  28   11  0.26
  29    9  0.21

ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40


Consensus pattern (29 bp):   
AATACTTTATGTACTTATTTTGACCAAAA

Done.