Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01005230.1 Hibiscus syriacus cultivar Beakdansim tig00011840_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: 33475
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:2814 original size:16 final size:16

Alignment explanation


    Indices: 2789--2821  Score: 57
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       2779 AACAATATGA

                 *          
       2789 TGTATGCGAATCTTAC
          1 TGTATACGAATCTTAC

                            
       2805 TGTATACGAATCTTAC
          1 TGTATACGAATCTTAC

             
       2821 T
          1 T

       2822 TGTTGGGAAA


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

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.27, C:0.18, G:0.15, T:0.39


Consensus pattern (16 bp):   
TGTATACGAATCTTAC

Found at i:3467 original size:17 final size:17

Alignment explanation


    Indices: 3445--3489  Score: 58
    Period size: 17  Copynumber: 2.7  Consensus size: 17

       3435 AAAGTATTTG

                           *  
       3445 TTTCTCGAACA-AGAGTT
          1 TTTCTCGAA-AGAGAATT

                             
       3462 TTTCTCGAAAGAGAATT
          1 TTTCTCGAAAGAGAATT

                        
       3479 TTTCTC-AAAGA
          1 TTTCTCGAAAGA

       3490 AAGGGAATGG


Statistics
Matches: 26,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  16    6  0.23
  17   20  0.77

ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36


Consensus pattern (17 bp):   
TTTCTCGAAAGAGAATT

Found at i:15290 original size:12 final size:12

Alignment explanation


    Indices: 15275--15300  Score: 52
    Period size: 12  Copynumber: 2.2  Consensus size: 12

      15265 TAACTCCAAT

                        
      15275 GAATTAGTATTG
          1 GAATTAGTATTG

                        
      15287 GAATTAGTATTG
          1 GAATTAGTATTG

              
      15299 GA
          1 GA

      15301 GGAATAAGCA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   14  1.00

ACGTcount: A:0.35, C:0.00, G:0.27, T:0.38


Consensus pattern (12 bp):   
GAATTAGTATTG

Found at i:29825 original size:5 final size:5

Alignment explanation


    Indices: 29815--29869  Score: 67
    Period size: 5  Copynumber: 10.8  Consensus size: 5

      29805 AAACACTATG

                                       *           *                     
      29815 AAAAT AAAAT AATAAT AAAAAT AGAAT -AAAT AGAAT AAAAT AAAAT AAAAT
          1 AAAAT AAAAT AA-AAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT

                
      29866 AAAA
          1 AAAA

      29870 ATATAAAGAT


Statistics
Matches: 43,  Mismatches: 4, Indels: 6
        0.81            0.08        0.11

Matches are distributed among these distances:
   4    3  0.07
   5   32  0.74
   6    6  0.14
   7    2  0.05

ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20


Consensus pattern (5 bp):   
AAAAT

Found at i:31555 original size:31 final size:31

Alignment explanation


    Indices: 31511--31575  Score: 112
    Period size: 31  Copynumber: 2.1  Consensus size: 31

      31501 TGTAATATAA

                    *                      
      31511 TCCCCCAATATTTAGTCCGTTTGCAATATGG
          1 TCCCCCAACATTTAGTCCGTTTGCAATATGG

                *                          
      31542 TCCCTCAACATTTAGTCCGTTTGCAATATGG
          1 TCCCCCAACATTTAGTCCGTTTGCAATATGG

               
      31573 TCC
          1 TCC

      31576 TCGATGTAAC


Statistics
Matches: 32,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  31   32  1.00

ACGTcount: A:0.22, C:0.28, G:0.15, T:0.35


Consensus pattern (31 bp):   
TCCCCCAACATTTAGTCCGTTTGCAATATGG

Found at i:31671 original size:29 final size:29

Alignment explanation


    Indices: 31612--31671  Score: 68
    Period size: 29  Copynumber: 2.1  Consensus size: 29

      31602 GCGAACGGAC

                *              *  *   *  
      31612 TAAATGTTGGGGGACTCTATTGCAAGTTT
          1 TAAAAGTTGGGGGACTCTAATGAAAGCTT

                                          
      31641 TAAAAGTTGGGGGAC-CTAAATGAAAGCTT
          1 TAAAAGTTGGGGGACTCT-AATGAAAGCTT

              
      31670 TA
          1 TA

      31672 GAAAAGTTCA


Statistics
Matches: 26,  Mismatches: 4, Indels: 2
        0.81            0.12        0.06

Matches are distributed among these distances:
  28    2  0.08
  29   24  0.92

ACGTcount: A:0.32, C:0.10, G:0.27, T:0.32


Consensus pattern (29 bp):   
TAAAAGTTGGGGGACTCTAATGAAAGCTT
Done.