Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01009104.1 Hibiscus syriacus cultivar Beakdansim tig00112569_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: 33476
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33


Found at i:3950 original size:22 final size:20

Alignment explanation


    Indices: 3925--3964  Score: 53
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       3915 ATGTTTGTTT

                                  
       3925 ATGGTAATGGGAGCTAAGTATG
          1 ATGGTAAT--GAGCTAAGTATG

                 *            
       3947 ATGGTCATGAGCTAAGTA
          1 ATGGTAATGAGCTAAGTA

       3965 CATCATCTCC


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  20   10  0.59
  22    7  0.41

ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28


Consensus pattern (20 bp):   
ATGGTAATGAGCTAAGTATG

Found at i:8218 original size:22 final size:20

Alignment explanation


    Indices: 8193--8232  Score: 53
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       8183 ATGTTTGTTT

                                  
       8193 ATGGTAATGGGAGCTAAGTATG
          1 ATGGTAAT--GAGCTAAGTATG

                 *            
       8215 ATGGTCATGAGCTAAGTA
          1 ATGGTAATGAGCTAAGTA

       8233 CATCATCTCC


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  20   10  0.59
  22    7  0.41

ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28


Consensus pattern (20 bp):   
ATGGTAATGAGCTAAGTATG

Found at i:12486 original size:22 final size:20

Alignment explanation


    Indices: 12461--12500  Score: 53
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      12451 ATGTTTGTTT

                                  
      12461 ATGGTAATGGGAGCTAAGTATG
          1 ATGGTAAT--GAGCTAAGTATG

                 *            
      12483 ATGGTCATGAGCTAAGTA
          1 ATGGTAATGAGCTAAGTA

      12501 CATCATCTCC


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  20   10  0.59
  22    7  0.41

ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28


Consensus pattern (20 bp):   
ATGGTAATGAGCTAAGTATG

Found at i:16748 original size:22 final size:20

Alignment explanation


    Indices: 16723--16762  Score: 53
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      16713 ATGTTTGTTT

                                  
      16723 ATGGTAATGGGAGCTAAGTATG
          1 ATGGTAAT--GAGCTAAGTATG

                 *            
      16745 ATGGTCATGAGCTAAGTA
          1 ATGGTAATGAGCTAAGTA

      16763 CATCATCTCC


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  20   10  0.59
  22    7  0.41

ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28


Consensus pattern (20 bp):   
ATGGTAATGAGCTAAGTATG

Found at i:16997 original size:15 final size:15

Alignment explanation


    Indices: 16974--17009  Score: 54
    Period size: 15  Copynumber: 2.4  Consensus size: 15

      16964 ACTAATATTC

                *    *     
      16974 TTATCATAATATATA
          1 TTATAATAACATATA

                           
      16989 TTATAATAACATATA
          1 TTATAATAACATATA

                  
      17004 TTATAA
          1 TTATAA

      17010 AGCTAATAAT


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  15   19  1.00

ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44


Consensus pattern (15 bp):   
TTATAATAACATATA

Found at i:22662 original size:24 final size:25

Alignment explanation


    Indices: 22642--22692  Score: 68
    Period size: 25  Copynumber: 2.1  Consensus size: 25

      22632 ATCAGAAAAC

                 *                   
      22642 AAAATGAAACACTCAAAAGAAAGAA
          1 AAAATCAAACACTCAAAAGAAAGAA

                  * *                
      22667 AAAATCCAGCACTCAAAAG-AAGAA
          1 AAAATCAAACACTCAAAAGAAAGAA

              
      22691 AA
          1 AA

      22693 GCTGATGTAA


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  24    7  0.30
  25   16  0.70

ACGTcount: A:0.65, C:0.16, G:0.12, T:0.08


Consensus pattern (25 bp):   
AAAATCAAACACTCAAAAGAAAGAA

Found at i:31628 original size:33 final size:33

Alignment explanation


    Indices: 31584--31651  Score: 84
    Period size: 33  Copynumber: 2.1  Consensus size: 33

      31574 CATCACCATA

                              *               
      31584 TTCCATCACCATATCA-CGCCAATAACATCATCC
          1 TTCCATCACCATATCATCACCAATAA-ATCATCC

                  *     *         *          
      31617 TTCCATTACCATTTCATCACCATTAAATCATCC
          1 TTCCATCACCATATCATCACCAATAAATCATCC

              
      31650 TT
          1 TT

      31652 TATTCATCAC


Statistics
Matches: 30,  Mismatches: 4, Indels: 2
        0.83            0.11        0.06

Matches are distributed among these distances:
  33   23  0.77
  34    7  0.23

ACGTcount: A:0.31, C:0.35, G:0.01, T:0.32


Consensus pattern (33 bp):   
TTCCATCACCATATCATCACCAATAAATCATCC

Found at i:32068 original size:13 final size:13

Alignment explanation


    Indices: 32052--32076  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

      32042 TTTGGAGTGC

                         
      32052 AAAAGAAGAAAAG
          1 AAAAGAAGAAAAG

                        
      32065 AAAAGAAGAAAA
          1 AAAAGAAGAAAA

      32077 ATTCAAAGCA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

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


Consensus pattern (13 bp):   
AAAAGAAGAAAAG
Done.