Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01004710.1 Hibiscus syriacus cultivar Beakdansim tig00010614_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: 177538
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32


File 2 of 2

Found at i:152804 original size:33 final size:33

Alignment explanation


    Indices: 152762--152832  Score: 115
    Period size: 33  Copynumber: 2.2  Consensus size: 33

     152752 AATACTAACT

                           *                 
     152762 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
          1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA

                                 * *         
     152795 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
          1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA

                 
     152828 TGAAA
          1 TGAAA

     152833 TCTAAGTGAA


Statistics
Matches: 35,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  33   35  1.00

ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11


Consensus pattern (33 bp):   
TGAAAATCGCAACGACAGAATAGCAACGCGAAA

Found at i:153065 original size:22 final size:22

Alignment explanation


    Indices: 153013--153067  Score: 74
    Period size: 22  Copynumber: 2.5  Consensus size: 22

     153003 TGGTTGTGAG

                   **             
     153013 GGATTTCGCCGGAGATGGGGAC
          1 GGATTTCTTCGGAGATGGGGAC

               **                 
     153035 GGAAATCTTCGGAGATGGGGAC
          1 GGATTTCTTCGGAGATGGGGAC

                       
     153057 GGATTTCTTCG
          1 GGATTTCTTCG

     153068 CCGTAGAGAG


Statistics
Matches: 27,  Mismatches: 6, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  22   27  1.00

ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24


Consensus pattern (22 bp):   
GGATTTCTTCGGAGATGGGGAC

Found at i:153243 original size:20 final size:20

Alignment explanation


    Indices: 153214--153407  Score: 212
    Period size: 20  Copynumber: 9.7  Consensus size: 20

     153204 CTTTAAATAT

                                
     153214 CGCGTTGCGATTTACGGATA
          1 CGCGTTGCGATTTACGGATA

               *           * *    
     153234 CGCATTGCGATTTTATGTATTA
          1 CGCGTTGCGA-TTTACGGA-TA

             *                  
     153256 -TCGTTGCGATTTACGGATA
          1 CGCGTTGCGATTTACGGATA

                       *        
     153275 CGCGTTGCGATATACGGATA
          1 CGCGTTGCGATTTACGGATA

               *           **   
     153295 CGCATTGCGATTTACCCATA
          1 CGCGTTGCGATTTACGGATA

                                
     153315 CGCGTTGCGATTTACGGATA
          1 CGCGTTGCGATTTACGGATA

             *                  
     153335 CACGTTGCGATTTACGGATA
          1 CGCGTTGCGATTTACGGATA

                          *     *
     153355 CGCGTTGCGATTTATGTG-TT
          1 CGCGTTGCGATTTACG-GATA

                         * **  *
     153375 CGCGTTGCGATTTTCATATT
          1 CGCGTTGCGATTTACGGATA

                         
     153395 CGCGTTGCGATTT
          1 CGCGTTGCGATTT

     153408 TCCAAAATCG


Statistics
Matches: 145,  Mismatches: 24, Indels: 10
        0.81            0.13        0.06

Matches are distributed among these distances:
  19    2  0.01
  20  127  0.88
  21   14  0.10
  22    2  0.01

ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36


Consensus pattern (20 bp):   
CGCGTTGCGATTTACGGATA

Found at i:153401 original size:60 final size:60

Alignment explanation


    Indices: 153214--153407  Score: 253
    Period size: 60  Copynumber: 3.2  Consensus size: 60

     153204 CTTTAAATAT

                                                     **                  
     153214 CGCGTTGCGATTTACGGATACGCATTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
          1 CGCGTTGCGATTTACGGATACGCATTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA

                       *                      ***  *                    
     153275 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
          1 CGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACGGATA

             *                     *             *               * **  *
     153335 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
          1 CGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACGGATA

                         
     153395 CGCGTTGCGATTT
          1 CGCGTTGCGATTT

     153408 TCCAAAATCG


Statistics
Matches: 113,  Mismatches: 20, Indels: 1
        0.84            0.15        0.01

Matches are distributed among these distances:
  60   84  0.74
  61   29  0.26

ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36


Consensus pattern (60 bp):   
CGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACGGATA

Found at i:172733 original size:51 final size:51

Alignment explanation


    Indices: 172657--172763  Score: 135
    Period size: 51  Copynumber: 2.1  Consensus size: 51

     172647 TTTTACAGTG

                 *          *  *                                
     172657 TTATTGGAACTCGTCATGTTGAGATGACGAATTCCAATAAAAAA-ATATTTT
          1 TTATTCGAACTCGTCACGTCGAGATGACGAATTCCAATAAAAAATA-ATTTT

                                       *  *   *       *        
     172708 TTATTCGAACTCGTCACGTCGAGATGATGAGTTCGAATAAAATATAATTTT
          1 TTATTCGAACTCGTCACGTCGAGATGACGAATTCCAATAAAAAATAATTTT

                 
     172759 TTATT
          1 TTATT

     172764 AAAATCTATC


Statistics
Matches: 48,  Mismatches: 7, Indels: 2
        0.84            0.12        0.04

Matches are distributed among these distances:
  51   47  0.98
  52    1  0.02

ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37


Consensus pattern (51 bp):   
TTATTCGAACTCGTCACGTCGAGATGACGAATTCCAATAAAAAATAATTTT

Done.