Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01006618.1 Hibiscus syriacus cultivar Beakdansim tig00016248_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: 67190
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36


Found at i:51777 original size:20 final size:20

Alignment explanation


    Indices: 51752--51803  Score: 70
    Period size: 20  Copynumber: 2.6  Consensus size: 20

      51742 TCTGTGATTA

                            *    
      51752 ATGGTATCGATAC-CATCCTC
          1 ATGGTATCGATACTC-CCCTC

                                
      51772 ATGGTATCGATACTCCCCTC
          1 ATGGTATCGATACTCCCCTC

            *           
      51792 TTGGTATCGATA
          1 ATGGTATCGATA

      51804 GCACTTGAAT


Statistics
Matches: 29,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  20   28  0.97
  21    1  0.03

ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33


Consensus pattern (20 bp):   
ATGGTATCGATACTCCCCTC

Found at i:56275 original size:80 final size:81

Alignment explanation


    Indices: 55852--56463  Score: 684
    Period size: 80  Copynumber: 7.6  Consensus size: 81

      55842 CATTTAAGAT

                       *    *               *         *  *    *              
      55852 TTCATCTAACTTGCATGA-TGACA-CTTTCCTGCCAAATGCATAGTTAGGACATTTATCTTTTTA
          1 TTCATCTAACTGGCATAATTGACACCTTT-CTACCAAATGCACAGCTAGGCCATTTATC-TTTTA

                           *  
      55915 CTCAACGGTCTTTAATCG
         64 CTCAACGGTCTTTAACCG

                                            *   *                           *
      55933 TTCATCTAACTGGCATAATTGACACCTTTTCTGCCATATGCACAGCTAGGCCATTTATCTTTTAT
          1 TTCATCTAACTGGCATAATTGACACC-TTTCTACCAAATGCACAGCTAGGCCATTTATCTTTTAC

                   *         
      55998 TCAACGGCCTTTAACCG
         65 TCAACGGTCTTTAACCG

            *                   * *  *   * *                                 
      56015 CTCATCTAACTGGCATAATTTAAACATTTTTTCCAAATG--CAGCTAGGCCATTTATCTTTTACT
          1 TTCATCTAACTGGCATAATTGACACCTTTCTACCAAATGCACAGCTAGGCCATTTATCTTTTACT

               *** *        
      56078 CAATAATTTTTAACCG
         66 CAACGGTCTTTAACCG

                                *          *               *                 
      56094 TTCATCTAACTGGCATAATTTACACCTTTCTGCCAAATGCACAGCTATGCCATTTATCTTTTACT
          1 TTCATCTAACTGGCATAATTGACACCTTTCTACCAAATGCACAGCTAGGCCATTTATCTTTTACT

            *      *      * 
      56159 GAACGGTATTTAACTG
         66 CAACGGTCTTTAACCG

                 *     *                     *    * **     *                 
      56175 TTCATATAACTAGCATAATTGACACCTTTCTACGAAATACGTAGCTACGCCATTTAT-TTTTACT
          1 TTCATCTAACTGGCATAATTGACACCTTTCTACCAAATGCACAGCTAGGCCATTTATCTTTTACT

                 *       *  
      56239 CAACGATCTTTAATCG
         66 CAACGGTCTTTAACCG

                       * *                             *                     
      56255 TTCATCTAACTAGTATAATTGACACCTTTCTACCAAATGCACAACTAGGCCATTTATC-TTTACT
          1 TTCATCTAACTGGCATAATTGACACCTTTCTACCAAATGCACAGCTAGGCCATTTATCTTTTACT

               *           *
      56319 CAATGGTCTTTAACCA
         66 CAACGGTCTTTAACCG

                 **     *            *                       *               
      56335 TTCATAGAACTGACATAATTGACACATTTCTACCAAATGCACAG-TAGGTCATTTATCTTTTACT
          1 TTCATCTAACTGGCATAATTGACACCTTTCTACCAAATGCACAGCTAGGCCATTTATCTTTTACT

               * *          
      56399 CAATGTTC-TT-ACCG
         66 CAACGGTCTTTAACCG

                                           *            *      
      56413 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGTTAGGCC
          1 TTCATCTAACTGGCATAATTGACACCTTTCTACCAAATGCACAGCTAGGCC

      56464 TGAAAGGCAC


Statistics
Matches: 447,  Mismatches: 76, Indels: 18
        0.83            0.14        0.03

Matches are distributed among these distances:
  78   42  0.09
  79   87  0.19
  80  135  0.30
  81  107  0.24
  82   47  0.11
  83   26  0.06
  84    3  0.01

ACGTcount: A:0.29, C:0.24, G:0.12, T:0.36


Consensus pattern (81 bp):   
TTCATCTAACTGGCATAATTGACACCTTTCTACCAAATGCACAGCTAGGCCATTTATCTTTTACT
CAACGGTCTTTAACCG

Found at i:56858 original size:55 final size:55

Alignment explanation


    Indices: 56735--56892  Score: 234
    Period size: 55  Copynumber: 2.9  Consensus size: 55

      56725 TCATATATTT

                                                              *    
      56735 CCCATACAGAAATTCATACACTTAGTATAGATTTCTTAG-TTTGCACATATAGTG
          1 CCCATACAGAAATTCATACACTTAGTATAGATTTCTTAGTTTTGCACATAAAGTG

                                                                      
      56789 CCCATAC-GAAAATTCATACACTTAGTAT-GAATTTCTTAGTTTTGCAC-TCAAAGTG
          1 CCCATACAG-AAATTCATACACTTAGTATAG-ATTTCTTAGTTTTGCACAT-AAAGTG

                                                        *    
      56844 CCCATACAGAAATTCATACACTTAGTATAGATTTCTTAAGTTTTTCACA
          1 CCCATACAGAAATTCATACACTTAGTATAGATTTCTT-AGTTTTGCACA

      56893 ATTAGTGCCA


Statistics
Matches: 94,  Mismatches: 2, Indels: 13
        0.86            0.02        0.12

Matches are distributed among these distances:
  53    2  0.02
  54   36  0.38
  55   45  0.48
  56   11  0.12

ACGTcount: A:0.34, C:0.20, G:0.11, T:0.35


Consensus pattern (55 bp):   
CCCATACAGAAATTCATACACTTAGTATAGATTTCTTAGTTTTGCACATAAAGTG

Found at i:65392 original size:28 final size:28

Alignment explanation


    Indices: 65360--65422  Score: 108
    Period size: 28  Copynumber: 2.2  Consensus size: 28

      65350 TCTTGTTTTG

                             *        * 
      65360 CAAGAACTTAGTGGATTGTTTCTCCAGC
          1 CAAGAACTTAGTGGATTATTTCTCCAAC

                                        
      65388 CAAGAACTTAGTGGATTATTTCTCCAAC
          1 CAAGAACTTAGTGGATTATTTCTCCAAC

                   
      65416 CAAGAAC
          1 CAAGAAC

      65423 AAGATGACGG


Statistics
Matches: 33,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  28   33  1.00

ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29


Consensus pattern (28 bp):   
CAAGAACTTAGTGGATTATTTCTCCAAC
Done.