Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01003606.1 Hibiscus syriacus cultivar Beakdansim tig00007625_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: 51047
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33


Found at i:4759 original size:5 final size:5

Alignment explanation


    Indices: 4749--4774  Score: 52
    Period size: 5  Copynumber: 5.2  Consensus size: 5

       4739 TATTATTATT

                                           
       4749 TCGGG TCGGG TCGGG TCGGG TCGGG T
          1 TCGGG TCGGG TCGGG TCGGG TCGGG T

       4775 TTCTAAGTCA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   21  1.00

ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23


Consensus pattern (5 bp):   
TCGGG

Found at i:13192 original size:18 final size:18

Alignment explanation


    Indices: 13169--13203  Score: 61
    Period size: 18  Copynumber: 1.9  Consensus size: 18

      13159 AATAAGGAGC

                      *       
      13169 AGAAGGAATTGGTTAAAT
          1 AGAAGGAATTAGTTAAAT

                             
      13187 AGAAGGAATTAGTTAAA
          1 AGAAGGAATTAGTTAAA

      13204 ATCAAACGCT


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

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.49, C:0.00, G:0.26, T:0.26


Consensus pattern (18 bp):   
AGAAGGAATTAGTTAAAT

Found at i:32793 original size:31 final size:31

Alignment explanation


    Indices: 32755--32825  Score: 124
    Period size: 31  Copynumber: 2.3  Consensus size: 31

      32745 GTAATACATA

                      *                    
      32755 TGTATATATGTTAATCAAACTTGGTTGCTGG
          1 TGTATATATGCTAATCAAACTTGGTTGCTGG

                                           
      32786 TGTATATATGCTAATCAAACTTGGTTGCTGG
          1 TGTATATATGCTAATCAAACTTGGTTGCTGG

                     
      32817 TGTGATATA
          1 TGT-ATATA

      32826 GGGATATGTA


Statistics
Matches: 38,  Mismatches: 1, Indels: 1
        0.95            0.03        0.03

Matches are distributed among these distances:
  31   33  0.87
  32    5  0.13

ACGTcount: A:0.27, C:0.10, G:0.23, T:0.41


Consensus pattern (31 bp):   
TGTATATATGCTAATCAAACTTGGTTGCTGG

Found at i:42304 original size:37 final size:36

Alignment explanation


    Indices: 42260--42378  Score: 170
    Period size: 35  Copynumber: 3.3  Consensus size: 36

      42250 TGGCAACCAA

                                                 
      42260 CTTTGAAAAATTAGTTTTCAAAGTTTGGTAAATGTTT
          1 CTTTGAAAAA-TAGTTTTCAAAGTTTGGTAAATGTTT

                       *              *         
      42297 CTTTG-AAAATGGTTTTCAAAGTTTGATAAATGTTT
          1 CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT

                                          *      
      42332 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
          1 CTTTGAAAAATAG-TTTTCAAAGTTTGGTAAATGTTT

             *         
      42369 -GTTGAAAAAT
          1 CTTTGAAAAAT

      42379 GATAATGGGA


Statistics
Matches: 74,  Mismatches: 6, Indels: 5
        0.87            0.07        0.06

Matches are distributed among these distances:
  35   29  0.39
  36   19  0.26
  37   26  0.35

ACGTcount: A:0.33, C:0.05, G:0.18, T:0.45


Consensus pattern (36 bp):   
CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT

Done.