Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01001721.1 Hibiscus syriacus cultivar Beakdansim tig00003481_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: 50918
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.32


Found at i:11552 original size:16 final size:17

Alignment explanation


    Indices: 11527--11559  Score: 50
    Period size: 16  Copynumber: 2.0  Consensus size: 17

      11517 GGGTCTGCTG

                 *           
      11527 GTGGACTGATG-TGTTT
          1 GTGGAATGATGATGTTT

                             
      11543 GTGGAATGATGATGTTT
          1 GTGGAATGATGATGTTT

      11560 TTGAGGTAAA


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  16   10  0.67
  17    5  0.33

ACGTcount: A:0.18, C:0.03, G:0.36, T:0.42


Consensus pattern (17 bp):   
GTGGAATGATGATGTTT

Found at i:22993 original size:11 final size:11

Alignment explanation


    Indices: 22977--23003  Score: 54
    Period size: 11  Copynumber: 2.5  Consensus size: 11

      22967 TTAAAAAAAC

                       
      22977 CCCGACCCGAA
          1 CCCGACCCGAA

                       
      22988 CCCGACCCGAA
          1 CCCGACCCGAA

                 
      22999 CCCGA
          1 CCCGA

      23004 ATTTTTTTTA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   16  1.00

ACGTcount: A:0.26, C:0.56, G:0.19, T:0.00


Consensus pattern (11 bp):   
CCCGACCCGAA

Found at i:26810 original size:15 final size:15

Alignment explanation


    Indices: 26774--26829  Score: 60
    Period size: 15  Copynumber: 3.7  Consensus size: 15

      26764 CACAGATCAA

                  *         
      26774 GATGATCATGAGA-TT
          1 GATGATGATGA-ATTT

                           
      26789 GATGATGATGAATTT
          1 GATGATGATGAATTT

                    * *   *
      26804 GATGATGAAGTATTG
          1 GATGATGATGAATTT

                       
      26819 GATGATGATGA
          1 GATGATGATGA

      26830 TGAGGGTGGA


Statistics
Matches: 34,  Mismatches: 6, Indels: 2
        0.81            0.14        0.05

Matches are distributed among these distances:
  14    1  0.03
  15   33  0.97

ACGTcount: A:0.34, C:0.02, G:0.30, T:0.34


Consensus pattern (15 bp):   
GATGATGATGAATTT

Found at i:40472 original size:32 final size:33

Alignment explanation


    Indices: 40431--40494  Score: 121
    Period size: 33  Copynumber: 2.0  Consensus size: 33

      40421 AGTTGACAAG

                                             
      40431 TTGGAAATTTCATC-TGGTTGGTGGCCAACTTA
          1 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA

                                            
      40463 TTGGAAATTTCATCTTGGTTGGTGGCCAACTT
          1 TTGGAAATTTCATCTTGGTTGGTGGCCAACTT

      40495 TGAACATGTG


Statistics
Matches: 31,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  32   14  0.45
  33   17  0.55

ACGTcount: A:0.20, C:0.16, G:0.25, T:0.39


Consensus pattern (33 bp):   
TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA

Found at i:41480 original size:30 final size:30

Alignment explanation


    Indices: 41444--41505  Score: 115
    Period size: 30  Copynumber: 2.1  Consensus size: 30

      41434 AAAGAGTAAG

                                          
      41444 TAGTTTTTTAGTAGAATTTCTTTGACTATA
          1 TAGTTTTTTAGTAGAATTTCTTTGACTATA

                         *                
      41474 TAGTTTTTTAGTATAATTTCTTTGACTATA
          1 TAGTTTTTTAGTAGAATTTCTTTGACTATA

              
      41504 TA
          1 TA

      41506 TATAGGGCTA


Statistics
Matches: 31,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  30   31  1.00

ACGTcount: A:0.27, C:0.06, G:0.11, T:0.55


Consensus pattern (30 bp):   
TAGTTTTTTAGTAGAATTTCTTTGACTATA

Found at i:41503 original size:15 final size:15

Alignment explanation


    Indices: 41458--41503  Score: 51
    Period size: 15  Copynumber: 3.1  Consensus size: 15

      41448 TTTTTAGTAG

                           
      41458 AATTTCTTTGACTAT
          1 AATTTCTTTGACTAT

                         *   
      41473 ATAGTTT-TTT-AGTAT
          1 A-A-TTTCTTTGACTAT

                           
      41488 AATTTCTTTGACTAT
          1 AATTTCTTTGACTAT

             
      41503 A
          1 A

      41504 TATATAGGGC


Statistics
Matches: 25,  Mismatches: 2, Indels: 8
        0.71            0.06        0.23

Matches are distributed among these distances:
  13    3  0.12
  14    4  0.16
  15   11  0.44
  16    4  0.16
  17    3  0.12

ACGTcount: A:0.28, C:0.09, G:0.09, T:0.54


Consensus pattern (15 bp):   
AATTTCTTTGACTAT
Done.