Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01001139.1 Hibiscus syriacus cultivar Beakdansim tig00002273_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: 129179
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34


File 2 of 2

Found at i:114925 original size:20 final size:22

Alignment explanation


    Indices: 114889--114936  Score: 64
    Period size: 20  Copynumber: 2.3  Consensus size: 22

     114879 ATTAAATTTA

                              *  *
     114889 ATATTTTGTGACTTTATACAAT
          1 ATATTTTGTGACTTTATAAAAC

                                  
     114911 ATATTTTGT-AC-TTATAAAAC
          1 ATATTTTGTGACTTTATAAAAC

                  
     114931 ATATTT
          1 ATATTT

     114937 AAACAATTTC


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  20   13  0.54
  21    2  0.08
  22    9  0.38

ACGTcount: A:0.35, C:0.08, G:0.06, T:0.50


Consensus pattern (22 bp):   
ATATTTTGTGACTTTATAAAAC

Found at i:115186 original size:14 final size:12

Alignment explanation


    Indices: 115161--115217  Score: 53
    Period size: 13  Copynumber: 4.5  Consensus size: 12

     115151 AAAACTTATC

                        
     115161 TTAAAAATATAT
          1 TTAAAAATATAT

                          
     115173 TATAAAATATATAT
          1 T-TAAAA-ATATAT

                  *     
     115187 TTAAAACT-TAT
          1 TTAAAAATATAT

                *        
     115198 CTTAGAAATATAT
          1 -TTAAAAATATAT

                   
     115211 TATAAAA
          1 T-TAAAA

     115218 TACATGTTAT


Statistics
Matches: 36,  Mismatches: 4, Indels: 9
        0.73            0.08        0.18

Matches are distributed among these distances:
  11    3  0.08
  12    9  0.25
  13   17  0.47
  14    7  0.19

ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40


Consensus pattern (12 bp):   
TTAAAAATATAT

Found at i:121807 original size:31 final size:31

Alignment explanation


    Indices: 121749--121808  Score: 84
    Period size: 31  Copynumber: 1.9  Consensus size: 31

     121739 AATTGAAGCT

                        *   * *            
     121749 CAACTTGAAAGCTCACGAGCTACTTGATATA
          1 CAACTTGAAAGCCCACAACCTACTTGATATA

                                  *      
     121780 CAACTTGAAAGCCCACAACCTATTTGATA
          1 CAACTTGAAAGCCCACAACCTACTTGATA

     121809 CCCGACTTGA


Statistics
Matches: 25,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  31   25  1.00

ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25


Consensus pattern (31 bp):   
CAACTTGAAAGCCCACAACCTACTTGATATA

Done.