Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01007890.1 Hibiscus syriacus cultivar Beakdansim tig00110272_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: 286089
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


File 2 of 2

Found at i:265945 original size:136 final size:134

Alignment explanation


    Indices: 265687--265949  Score: 350
    Period size: 136  Copynumber: 1.9  Consensus size: 134

     265677 AGCAAGAGGT

                 *                         *    *   *                 *      
     265687 GGATCGACATTTCCAGTAGAGAGTTCATAATGAGAATAACTCATCCGATGAGGGAGAATAAGTTC
          1 GGATCAACATTTCCAGTAGAGAGTTCATAATAAGAAAAACCCATCCGATGAGGGAGAAGAAGTTC

                                *               *    *                       
     265752 ATAATGAGAACTTATTCAACTTTAGCTTGATTCATCTCATATGGAGTTGAATCAACAACACCTCA
         66 ATAATGAGAACTTATTCAACCTTAGCTTGATTCATCACATAAGGAGTTG-A-CAACAACACCTCA

                  
     265817 TTTGAG
        129 TTTGAG

                             *                                               
     265823 GGATCAACATTTCCAGTGGAGAGTTCATAATAAGAAAAACCCATCCGATGAGGGAGAAGAAGTTC
          1 GGATCAACATTTCCAGTAGAGAGTTCATAATAAGAAAAACCCATCCGATGAGGGAGAAGAAGTTC

                            *               *                     *         
     265888 ATAATGAGAAGAACTTGTTCAACCTTAGC-TGTTTACATCACATAAGGAGTTG-GAACAACACC
         66 ATAAT--G-AGAACTTATTCAACCTTAGCTTGATT-CATCACATAAGGAGTTGACAACAACACC

     265950 GACCTTTGCT


Statistics
Matches: 111,  Mismatches: 12, Indels: 8
        0.85            0.09        0.06

Matches are distributed among these distances:
 136   73  0.66
 138    5  0.05
 139   33  0.30

ACGTcount: A:0.36, C:0.17, G:0.20, T:0.26


Consensus pattern (134 bp):   
GGATCAACATTTCCAGTAGAGAGTTCATAATAAGAAAAACCCATCCGATGAGGGAGAAGAAGTTC
ATAATGAGAACTTATTCAACCTTAGCTTGATTCATCACATAAGGAGTTGACAACAACACCTCATT
TGAG

Found at i:266301 original size:23 final size:23

Alignment explanation


    Indices: 266252--266302  Score: 57
    Period size: 23  Copynumber: 2.2  Consensus size: 23

     266242 CCATTTACAG

                *   *          *   
     266252 AACCCGGGTCCAAACTAAACCCA
          1 AACCTGGGCCCAAACTAAAACCA

                          *       *
     266275 AACCTGGGCCCAAATTAAAACCT
          1 AACCTGGGCCCAAACTAAAACCA

                 
     266298 AACCT
          1 AACCT

     266303 AAACCTAACT


Statistics
Matches: 23,  Mismatches: 5, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  23   23  1.00

ACGTcount: A:0.39, C:0.35, G:0.12, T:0.14


Consensus pattern (23 bp):   
AACCTGGGCCCAAACTAAAACCA

Found at i:274318 original size:15 final size:16

Alignment explanation


    Indices: 274300--274331  Score: 57
    Period size: 15  Copynumber: 2.1  Consensus size: 16

     274290 AATACTTAGA

                            
     274300 ATAAATAT-TGATAAT
          1 ATAAATATATGATAAT

                            
     274315 ATAAATATATGATAAT
          1 ATAAATATATGATAAT

             
     274331 A
          1 A

     274332 AAAACATGTT


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  15    8  0.50
  16    8  0.50

ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38


Consensus pattern (16 bp):   
ATAAATATATGATAAT

Found at i:282604 original size:6 final size:6

Alignment explanation


    Indices: 282590--282629  Score: 71
    Period size: 6  Copynumber: 6.7  Consensus size: 6

     282580 TTCAATCATG

                *                                         
     282590 TTTAAT TTTATT TTTATT TTTATT TTTATT TTTATT TTTA
          1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTA

     282630 CAGGAACCGA


Statistics
Matches: 33,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
   6   33  1.00

ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80


Consensus pattern (6 bp):   
TTTATT

Found at i:285504 original size:14 final size:14

Alignment explanation


    Indices: 285482--285514  Score: 57
    Period size: 14  Copynumber: 2.4  Consensus size: 14

     285472 CGGTATACAA

                *         
     285482 GATAAAGTCATGGG
          1 GATAGAGTCATGGG

                          
     285496 GATAGAGTCATGGG
          1 GATAGAGTCATGGG

                 
     285510 GATAG
          1 GATAG

     285515 TCCTTGTAGG


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  14   18  1.00

ACGTcount: A:0.33, C:0.06, G:0.39, T:0.21


Consensus pattern (14 bp):   
GATAGAGTCATGGG

Done.