Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01006687.1 Hibiscus syriacus cultivar Beakdansim tig00016614_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: 66836
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33


Found at i:3645 original size:31 final size:31

Alignment explanation


    Indices: 3610--3669  Score: 93
    Period size: 31  Copynumber: 1.9  Consensus size: 31

       3600 AATGATTAAA

                  * *                      
       3610 TTAAAATTTAAGAATTAAATTAATATTATAT
          1 TTAAAACTCAAGAATTAAATTAATATTATAT

                        *                
       3641 TTAAAACTCAAGGATTAAATTAATATTAT
          1 TTAAAACTCAAGAATTAAATTAATATTAT

       3670 CTAAATTTTA


Statistics
Matches: 26,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  31   26  1.00

ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42


Consensus pattern (31 bp):   
TTAAAACTCAAGAATTAAATTAATATTATAT

Found at i:3773 original size:11 final size:11

Alignment explanation


    Indices: 3759--3791  Score: 57
    Period size: 11  Copynumber: 3.0  Consensus size: 11

       3749 CATTATTATT

                       
       3759 TAGTGATTAAA
          1 TAGTGATTAAA

                       
       3770 TAGTGATTAAA
          1 TAGTGATTAAA

                  *    
       3781 TAGTGAATAAA
          1 TAGTGATTAAA

       3792 AATGAAACGA


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  11   21  1.00

ACGTcount: A:0.48, C:0.00, G:0.18, T:0.33


Consensus pattern (11 bp):   
TAGTGATTAAA

Found at i:11320 original size:23 final size:23

Alignment explanation


    Indices: 11286--11343  Score: 64
    Period size: 23  Copynumber: 2.5  Consensus size: 23

      11276 TAATTTTATA

                  *     *        * 
      11286 TTAAAAGATAAATTTAT-AAATT
          1 TTAAAAAATAAACTTATAAAACT

                                    
      11308 TTAAAAAATTAAACTTATAAAACT
          1 TTAAAAAA-TAAACTTATAAAACT

                  *     
      11332 TTAAAAGATAAA
          1 TTAAAAAATAAA

      11344 AATAAATTAT


Statistics
Matches: 30,  Mismatches: 4, Indels: 3
        0.81            0.11        0.08

Matches are distributed among these distances:
  22    7  0.23
  23   12  0.40
  24   11  0.37

ACGTcount: A:0.59, C:0.03, G:0.03, T:0.34


Consensus pattern (23 bp):   
TTAAAAAATAAACTTATAAAACT

Found at i:21841 original size:2 final size:2

Alignment explanation


    Indices: 21834--21875  Score: 84
    Period size: 2  Copynumber: 21.0  Consensus size: 2

      21824 AAGATTATGA

                                                                          
      21834 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      21876 TCACTATAAA


Statistics
Matches: 40,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   40  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:34854 original size:2 final size:2

Alignment explanation


    Indices: 34847--34886  Score: 80
    Period size: 2  Copynumber: 20.0  Consensus size: 2

      34837 ACCATGAAAG

                                                                       
      34847 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      34887 TTGTAAAACA


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   38  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:38983 original size:13 final size:13

Alignment explanation


    Indices: 38965--38989  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

      38955 CCGTCAAACT

                         
      38965 ATAAATAAAAAAA
          1 ATAAATAAAAAAA

                        
      38978 ATAAATAAAAAA
          1 ATAAATAAAAAA

      38990 TAAATTATAA


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:0.84, C:0.00, G:0.00, T:0.16


Consensus pattern (13 bp):   
ATAAATAAAAAAA

Found at i:59568 original size:33 final size:33

Alignment explanation


    Indices: 59529--59594  Score: 132
    Period size: 33  Copynumber: 2.0  Consensus size: 33

      59519 CCGATAAAAT

                                             
      59529 TATATTTAAATTATACGAGAATTGAAATTTTTA
          1 TATATTTAAATTATACGAGAATTGAAATTTTTA

                                             
      59562 TATATTTAAATTATACGAGAATTGAAATTTTTA
          1 TATATTTAAATTATACGAGAATTGAAATTTTTA

      59595 AAGGATGCAG


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  33   33  1.00

ACGTcount: A:0.42, C:0.03, G:0.09, T:0.45


Consensus pattern (33 bp):   
TATATTTAAATTATACGAGAATTGAAATTTTTA

Found at i:64387 original size:17 final size:17

Alignment explanation


    Indices: 64365--64399  Score: 61
    Period size: 17  Copynumber: 2.1  Consensus size: 17

      64355 GTTTAAAAAG

                  *          
      64365 AAATTATCTGATTGAAT
          1 AAATTAGCTGATTGAAT

                             
      64382 AAATTAGCTGATTGAAT
          1 AAATTAGCTGATTGAAT

             
      64399 A
          1 A

      64400 TTGATTTCAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37


Consensus pattern (17 bp):   
AAATTAGCTGATTGAAT
Done.