Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01001766.1 Hibiscus syriacus cultivar Beakdansim tig00003564_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: 42617
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:178 original size:26 final size:27

Alignment explanation


    Indices: 143--197  Score: 76
    Period size: 26  Copynumber: 2.1  Consensus size: 27

        133 AGGACTATAA

                                 *     
        143 AAACAACAAACCATGAA-CATTACATT
          1 AAACAACAAACCATGAATCATGACATT

                       *  *            
        169 AAACAACAAACTATTAATCATGACATT
          1 AAACAACAAACCATGAATCATGACATT

              
        196 AA
          1 AA

        198 GAATACCAAA


Statistics
Matches: 25,  Mismatches: 3, Indels: 1
        0.86            0.10        0.03

Matches are distributed among these distances:
  26   15  0.60
  27   10  0.40

ACGTcount: A:0.55, C:0.20, G:0.04, T:0.22


Consensus pattern (27 bp):   
AAACAACAAACCATGAATCATGACATT

Found at i:4455 original size:26 final size:27

Alignment explanation


    Indices: 4404--4461  Score: 91
    Period size: 27  Copynumber: 2.2  Consensus size: 27

       4394 TTTGACAATC

                *       *              
       4404 TTAATTTCATGATTTTTTTAATTCAAA
          1 TTAAATTCATGAATTTTTTAATTCAAA

                                       
       4431 TTAAATTCATGAATTTTTTAA-TCAAA
          1 TTAAATTCATGAATTTTTTAATTCAAA

                 
       4457 TTAAA
          1 TTAAA

       4462 CTCAACTTGG


Statistics
Matches: 29,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  26   10  0.34
  27   19  0.66

ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50


Consensus pattern (27 bp):   
TTAAATTCATGAATTTTTTAATTCAAA

Found at i:4752 original size:16 final size:15

Alignment explanation


    Indices: 4719--4757  Score: 51
    Period size: 16  Copynumber: 2.5  Consensus size: 15

       4709 ATATGATCAA

                         * 
       4719 ATTTTAATTTTTATT
          1 ATTTTAATTTTTACT

                         *  
       4734 ATTTTAAGTTTTTCCT
          1 ATTTTAA-TTTTTACT

                    
       4750 ATTTTAAT
          1 ATTTTAAT

       4758 CAACGTAAAT


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  15    8  0.38
  16   13  0.62

ACGTcount: A:0.26, C:0.05, G:0.03, T:0.67


Consensus pattern (15 bp):   
ATTTTAATTTTTACT

Found at i:20705 original size:2 final size:2

Alignment explanation


    Indices: 20698--20728  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

      20688 AATCTGGTAC

                                                          
      20698 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      20729 AACTATTGTT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:28322 original size:25 final size:25

Alignment explanation


    Indices: 28294--28346  Score: 70
    Period size: 25  Copynumber: 2.1  Consensus size: 25

      28284 ATTTAAGGAT

                 *                   
      28294 TTTAATTTTTTTAGAAATTATAAAA
          1 TTTAAATTTTTTAGAAATTATAAAA

                         * *   *     
      28319 TTTAAATTTTTTATACATTTTAAAA
          1 TTTAAATTTTTTAGAAATTATAAAA

               
      28344 TTT
          1 TTT

      28347 TGTGTTTGTC


Statistics
Matches: 24,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  25   24  1.00

ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57


Consensus pattern (25 bp):   
TTTAAATTTTTTAGAAATTATAAAA

Found at i:30590 original size:3 final size:3

Alignment explanation


    Indices: 30582--30607  Score: 52
    Period size: 3  Copynumber: 8.7  Consensus size: 3

      30572 CGATCTTTGA

                                              
      30582 TCT TCT TCT TCT TCT TCT TCT TCT TC
          1 TCT TCT TCT TCT TCT TCT TCT TCT TC

      30608 AACTTGTTCG


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   23  1.00

ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65


Consensus pattern (3 bp):   
TCT

Found at i:37163 original size:19 final size:19

Alignment explanation


    Indices: 37136--37182  Score: 85
    Period size: 19  Copynumber: 2.5  Consensus size: 19

      37126 TGTCGAGTTC

                *              
      37136 GATGAAGCAGAATATTGGA
          1 GATGGAGCAGAATATTGGA

                               
      37155 GATGGAGCAGAATATTGGA
          1 GATGGAGCAGAATATTGGA

                     
      37174 GATGGAGCA
          1 GATGGAGCA

      37183 AAGAGGAAAA


Statistics
Matches: 27,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  19   27  1.00

ACGTcount: A:0.38, C:0.06, G:0.36, T:0.19


Consensus pattern (19 bp):   
GATGGAGCAGAATATTGGA

Found at i:39716 original size:21 final size:21

Alignment explanation


    Indices: 39675--39715  Score: 57
    Period size: 20  Copynumber: 2.0  Consensus size: 21

      39665 AAACATATTT

                    *            
      39675 TGAAAAATGATTTTCTTAAAA
          1 TGAAAAATCATTTTCTTAAAA

                          *      
      39696 TGAAAAA-CATTTTTTTAAAA
          1 TGAAAAATCATTTTCTTAAAA

      39716 AAATATTTGG


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  20   11  0.61
  21    7  0.39

ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39


Consensus pattern (21 bp):   
TGAAAAATCATTTTCTTAAAA
Done.