Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01007273.1 Hibiscus syriacus cultivar Beakdansim tig00019283_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: 60374
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33


Found at i:23970 original size:17 final size:17

Alignment explanation


    Indices: 23919--23971  Score: 58
    Period size: 17  Copynumber: 3.3  Consensus size: 17

      23909 TAAGAAAAAA

                             
      23919 TTATTATTTAATTAGAC
          1 TTATTATTTAATTAGAC

             *   *          *
      23936 TAATTTTTTAATT---T
          1 TTATTATTTAATTAGAC

                             
      23950 TTATTATTTAATTAGAC
          1 TTATTATTTAATTAGAC

                 
      23967 TTATT
          1 TTATT

      23972 TCTCAATAAC


Statistics
Matches: 27,  Mismatches: 6, Indels: 6
        0.69            0.15        0.15

Matches are distributed among these distances:
  14   11  0.41
  17   16  0.59

ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60


Consensus pattern (17 bp):   
TTATTATTTAATTAGAC

Found at i:36596 original size:18 final size:20

Alignment explanation


    Indices: 36551--36596  Score: 53
    Period size: 18  Copynumber: 2.5  Consensus size: 20

      36541 CCTTCTCTTA

                  *           * 
      36551 AAGAAGCAATACATGTAATC
          1 AAGAAGTAATACATGTAAGC

                                
      36571 AA-AAGTAAT-CA-GTAAGC
          1 AAGAAGTAATACATGTAAGC

                     
      36588 AAGAAGTAA
          1 AAGAAGTAA

      36597 CAGATTATGA


Statistics
Matches: 23,  Mismatches: 2, Indels: 4
        0.79            0.07        0.14

Matches are distributed among these distances:
  17    7  0.30
  18    8  0.35
  19    6  0.26
  20    2  0.09

ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17


Consensus pattern (20 bp):   
AAGAAGTAATACATGTAAGC

Found at i:38107 original size:2 final size:2

Alignment explanation


    Indices: 38100--38127  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

      38090 CACAAATTTA

                                                     
      38100 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

      38128 GTCTGACTAG


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:38611 original size:11 final size:10

Alignment explanation


    Indices: 38595--38621  Score: 54
    Period size: 10  Copynumber: 2.7  Consensus size: 10

      38585 TATTCTTAAT

                      
      38595 AAAAAAAGAA
          1 AAAAAAAGAA

                      
      38605 AAAAAAAGAA
          1 AAAAAAAGAA

                   
      38615 AAAAAAA
          1 AAAAAAA

      38622 TGACGATCAA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   17  1.00

ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00


Consensus pattern (10 bp):   
AAAAAAAGAA

Found at i:54865 original size:2 final size:2

Alignment explanation


    Indices: 54854--54882  Score: 51
    Period size: 2  Copynumber: 15.0  Consensus size: 2

      54844 GGTAATGAAG

                                                        
      54854 AT AT -T 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

      54883 TCAGATTGCA


Statistics
Matches: 26,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   1    1  0.04
   2   25  0.96

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
AT

Done.