Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01003185.1 Hibiscus syriacus cultivar Beakdansim tig00006701_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: 49270
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32


Found at i:3763 original size:34 final size:38

Alignment explanation


    Indices: 3699--3792  Score: 101
    Period size: 34  Copynumber: 2.6  Consensus size: 38

       3689 CCTCCTCCTC

                    *             *   *           
       3699 CTTCAAGAGCTTAAACTCATA-ATTGGTTC-T-TT-TT
          1 CTTCAAGAACTTAAACTCATAGCTTGATTCTTCTTCTT

                            *                     
       3733 CTTCAAGAACTTAAACCCATAGCTT-ATTCTTCTTCTT
          1 CTTCAAGAACTTAAACTCATAGCTTGATTCTTCTTCTT

                                    
       3770 CTTC-AGAAGCTTAAACTCATAGC
          1 CTTCAAGAA-CTTAAACTCATAGC

       3793 AATTAAAAAA


Statistics
Matches: 50,  Mismatches: 5, Indels: 7
        0.81            0.08        0.11

Matches are distributed among these distances:
  34   22  0.44
  35    3  0.06
  36    6  0.12
  37   19  0.38

ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38


Consensus pattern (38 bp):   
CTTCAAGAACTTAAACTCATAGCTTGATTCTTCTTCTT

Found at i:21322 original size:60 final size:60

Alignment explanation


    Indices: 21209--21323  Score: 140
    Period size: 60  Copynumber: 1.9  Consensus size: 60

      21199 AATGACCATT

                              *  *       *   *       *      *           
      21209 TTGTAACTTTTAATAGTCGATGGACTCAATAAATAAACACCCTATAATTAGATGATAAGG
          1 TTGTAACTTTTAATAGTCAATAGACTCAACAAAGAAACACCATATAATCAGATGATAAGG

                          *                   *        *  *        
      21269 TTGTAACTTTTAATTGTCAATAGACTCAACAAAGCAACACCATGTAGTCAGATGA
          1 TTGTAACTTTTAATAGTCAATAGACTCAACAAAGAAACACCATATAATCAGATGA

      21324 CCATTTGTGT


Statistics
Matches: 45,  Mismatches: 10, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  60   45  1.00

ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30


Consensus pattern (60 bp):   
TTGTAACTTTTAATAGTCAATAGACTCAACAAAGAAACACCATATAATCAGATGATAAGG

Found at i:43272 original size:34 final size:33

Alignment explanation


    Indices: 43229--43319  Score: 137
    Period size: 34  Copynumber: 2.7  Consensus size: 33

      43219 ATAGCGCTGC

                                              
      43229 CATTGAACCATAGCCAAGCCGTACTCGTAAAGTT
          1 CATTGAACCATA-CCAAGCCGTACTCGTAAAGTT

                                     *        
      43263 CATTGAACCATCACCAAGCCGTACTTGTAAAGTT
          1 CATTGAACCAT-ACCAAGCCGTACTCGTAAAGTT

                   *               
      43297 CATTGAATCATTACCAAGCCGTA
          1 CATTGAACCA-TACCAAGCCGTA

      43320 TTGGTGAAGT


Statistics
Matches: 53,  Mismatches: 2, Indels: 4
        0.90            0.03        0.07

Matches are distributed among these distances:
  34   51  0.96
  35    2  0.04

ACGTcount: A:0.33, C:0.26, G:0.15, T:0.25


Consensus pattern (33 bp):   
CATTGAACCATACCAAGCCGTACTCGTAAAGTT

Found at i:45231 original size:60 final size:60

Alignment explanation


    Indices: 45138--45253  Score: 205
    Period size: 60  Copynumber: 1.9  Consensus size: 60

      45128 AAAACAACAA

                   *                               *                    
      45138 AGAATGAGATAAGGAAAATGCAACTTATGCGTCCACAACTAGCAGGAAGATACATATGAG
          1 AGAATGAAATAAGGAAAATGCAACTTATGCGTCCACAACAAGCAGGAAGATACATATGAG

                       *                                            
      45198 AGAATGAAATAGGGAAAATGCAACTTATGCGTCCACAACAAGCAGGAAGATACATA
          1 AGAATGAAATAAGGAAAATGCAACTTATGCGTCCACAACAAGCAGGAAGATACATA

      45254 CTTGCAAAGC


Statistics
Matches: 53,  Mismatches: 3, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  60   53  1.00

ACGTcount: A:0.45, C:0.16, G:0.22, T:0.17


Consensus pattern (60 bp):   
AGAATGAAATAAGGAAAATGCAACTTATGCGTCCACAACAAGCAGGAAGATACATATGAG
Done.