Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01001297.1 Hibiscus syriacus cultivar Beakdansim tig00002536_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: 51633
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33


Found at i:25755 original size:39 final size:39

Alignment explanation


    Indices: 25687--25782  Score: 102
    Period size: 39  Copynumber: 2.5  Consensus size: 39

      25677 AATATAAGGA

                  *    * *                     *   
      25687 CCTGCGGTAAGATTTTAGCATGTGAACAAAGAAAATGTG
          1 CCTGCGATAAGGTCTTAGCATGTGAACAAAGAAAAGGTG

             *                 *    *        *     
      25726 CTTGCGATAAGGTCTTAGCCTGTGTACAAAGAAGAGGTG
          1 CCTGCGATAAGGTCTTAGCATGTGAACAAAGAAAAGGTG

                * *           
      25765 CCTGTGGTAAGGTCTTAG
          1 CCTGCGATAAGGTCTTAG

      25783 TAGTCATAGA


Statistics
Matches: 46,  Mismatches: 11, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  39   46  1.00

ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27


Consensus pattern (39 bp):   
CCTGCGATAAGGTCTTAGCATGTGAACAAAGAAAAGGTG

Found at i:28076 original size:49 final size:49

Alignment explanation


    Indices: 28004--28229  Score: 259
    Period size: 49  Copynumber: 4.7  Consensus size: 49

      27994 CCAAAATAAA

                                      *   *       *          
      28004 TGCATAACGGTGCATTTTGGCATAAAGGGTTCCACTAAAGAAAGTTAAG
          1 TGCATAACGGTGCATTTTGGCATAAAAGGTGCCACTAATGAAAGTTAAG

                                            *          *    *
      28053 TGCATAACGGTGCATTTTGGCATAAAAGGTGCAACTAATGAAAATTAAA
          1 TGCATAACGGTGCATTTTGGCATAAAAGGTGCCACTAATGAAAGTTAAG

                     *       **                              
      28102 TGCATAACGATGCATTTCAGCATAAAAGGTGCCACTAATGAAAGTTAAG
          1 TGCATAACGGTGCATTTTGGCATAAAAGGTGCCACTAATGAAAGTTAAG

                                              *  *   *      *
      28151 TGCATAACGGTG-----T--CATAAAAGGTGCCATTAGTGATAGTTAAA
          1 TGCATAACGGTGCATTTTGGCATAAAAGGTGCCACTAATGAAAGTTAAG

                              *            *     
      28193 TGCATAACGGTGCATTATCGGCATAAAAGGTCCCACT
          1 TGCATAACGGTGCATT-TTGGCATAAAAGGTGCCACT

      28230 CATGGTATTC


Statistics
Matches: 148,  Mismatches: 21, Indels: 15
        0.80            0.11        0.08

Matches are distributed among these distances:
  42   37  0.25
  49   97  0.66
  50   14  0.09

ACGTcount: A:0.36, C:0.15, G:0.22, T:0.26


Consensus pattern (49 bp):   
TGCATAACGGTGCATTTTGGCATAAAAGGTGCCACTAATGAAAGTTAAG

Found at i:28169 original size:42 final size:42

Alignment explanation


    Indices: 28122--28204  Score: 130
    Period size: 42  Copynumber: 2.0  Consensus size: 42

      28112 TGCATTTCAG

                                        *             
      28122 CATAAAAGGTGCCACTAATGAAAGTTAAGTGCATAACGGTGT
          1 CATAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGT

                          *  *   *                   
      28164 CATAAAAGGTGCCATTAGTGATAGTTAAATGCATAACGGTG
          1 CATAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTG

      28205 CATTATCGGC


Statistics
Matches: 37,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  42   37  1.00

ACGTcount: A:0.37, C:0.13, G:0.24, T:0.25


Consensus pattern (42 bp):   
CATAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGT

Found at i:35136 original size:28 final size:26

Alignment explanation


    Indices: 35105--35162  Score: 71
    Period size: 28  Copynumber: 2.2  Consensus size: 26

      35095 TTCTACTTTA

                    *       *           
      35105 TTTATTTTCTTATAATTTTTCATTTATT
          1 TTTATTTTATTATAA-CTTTCA-TTATT

                         *            
      35133 TTTATTTTATTATTACTTTCATTATT
          1 TTTATTTTATTATAACTTTCATTATT

                
      35159 TTTA
          1 TTTA

      35163 ACCCCCCATT


Statistics
Matches: 27,  Mismatches: 3, Indels: 2
        0.84            0.09        0.06

Matches are distributed among these distances:
  26    9  0.33
  27    5  0.19
  28   13  0.48

ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71


Consensus pattern (26 bp):   
TTTATTTTATTATAACTTTCATTATT

Found at i:44152 original size:21 final size:20

Alignment explanation


    Indices: 44128--44179  Score: 50
    Period size: 20  Copynumber: 2.5  Consensus size: 20

      44118 AAAATACCTC

                                 
      44128 GTATCGATACTGACCCTCTAA
          1 GTATCGATACTGACCC-CTAA

                *    *  **    * 
      44149 GTATTGATATTGGTCCCTGA
          1 GTATCGATACTGACCCCTAA

                       
      44169 GTATCGATACT
          1 GTATCGATACT

      44180 CCTTGAAGGG


Statistics
Matches: 24,  Mismatches: 7, Indels: 1
        0.75            0.22        0.03

Matches are distributed among these distances:
  20   12  0.50
  21   12  0.50

ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35


Consensus pattern (20 bp):   
GTATCGATACTGACCCCTAA

Found at i:47383 original size:45 final size:45

Alignment explanation


    Indices: 47293--47411  Score: 138
    Period size: 45  Copynumber: 2.7  Consensus size: 45

      47283 GGTAATCATG

                      * *                                
      47293 AAAATAAGCTCATGAGCTTAT-AGAATAATGGCAAGTATATTGGT
          1 AAAATAAGCTAACGAGCTTATGAGAATAATGGCAAGTATATTGGT

                                             *      *     
      47337 AAAATAAGCTAACGAGCTTATGA-AATAAATGGTAAGTATTTTGGT
          1 AAAATAAGCTAACGAGCTTATGAGAAT-AATGGCAAGTATATTGGT

                          *          *      
      47382 AAAATAAGC-ATACAAGCTTATG-GGATAATG
          1 AAAATAAGCTA-ACGAGCTTATGAGAATAATG

      47412 TTAAGTGATT


Statistics
Matches: 65,  Mismatches: 6, Indels: 8
        0.82            0.08        0.10

Matches are distributed among these distances:
  44   27  0.42
  45   38  0.58

ACGTcount: A:0.43, C:0.08, G:0.20, T:0.29


Consensus pattern (45 bp):   
AAAATAAGCTAACGAGCTTATGAGAATAATGGCAAGTATATTGGT

Done.