Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01001341.1 Hibiscus syriacus cultivar Beakdansim tig00002618_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: 75459
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:7079 original size:21 final size:19

Alignment explanation


    Indices: 7041--7086  Score: 58
    Period size: 20  Copynumber: 2.3  Consensus size: 19

       7031 AATTAATCTT

                                
       7041 ACTAAGTATTAAAGCTAAGA
          1 ACTAA-TATTAAAGCTAAGA

                                 
       7061 ACTAATATTAAGGAGCTAAGA
          1 ACTAATATTAA--AGCTAAGA

                  
       7082 A-TAAT
          1 ACTAAT

       7087 GATTCAATGA


Statistics
Matches: 24,  Mismatches: 0, Indels: 4
        0.86            0.00        0.14

Matches are distributed among these distances:
  19    6  0.25
  20    9  0.38
  21    9  0.38

ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26


Consensus pattern (19 bp):   
ACTAATATTAAAGCTAAGA

Found at i:17392 original size:21 final size:19

Alignment explanation


    Indices: 17354--17399  Score: 58
    Period size: 20  Copynumber: 2.3  Consensus size: 19

      17344 AATTAATCTT

                                
      17354 ACTAAGTATTAAAGCTAAGA
          1 ACTAA-TATTAAAGCTAAGA

                                 
      17374 ACTAATATTAAGGAGCTAAGA
          1 ACTAATATTAA--AGCTAAGA

                  
      17395 A-TAAT
          1 ACTAAT

      17400 GATTCAATGA


Statistics
Matches: 24,  Mismatches: 0, Indels: 4
        0.86            0.00        0.14

Matches are distributed among these distances:
  19    6  0.25
  20    9  0.38
  21    9  0.38

ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26


Consensus pattern (19 bp):   
ACTAATATTAAAGCTAAGA

Found at i:18948 original size:35 final size:35

Alignment explanation


    Indices: 18903--18971  Score: 120
    Period size: 35  Copynumber: 2.0  Consensus size: 35

      18893 GCAAAAGAAT

                           *                   
      18903 ATATCACGGTAACTCGGACGGTATTTCTGAAGCAA
          1 ATATCACGGTAACTCAGACGGTATTTCTGAAGCAA

                 *                            
      18938 ATATCGCGGTAACTCAGACGGTATTTCTGAAGCA
          1 ATATCACGGTAACTCAGACGGTATTTCTGAAGCA

      18972 GAAAAGGCAA


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

Matches are distributed among these distances:
  35   32  1.00

ACGTcount: A:0.30, C:0.20, G:0.23, T:0.26


Consensus pattern (35 bp):   
ATATCACGGTAACTCAGACGGTATTTCTGAAGCAA

Found at i:27586 original size:37 final size:37

Alignment explanation


    Indices: 27545--27621  Score: 145
    Period size: 37  Copynumber: 2.1  Consensus size: 37

      27535 TTTAATTTTG

                                   *             
      27545 GTCACCTACCGTTAAAAAATTAATGGTATGTTGACAT
          1 GTCACCTACCGTTAAAAAATTAACGGTATGTTGACAT

                                                 
      27582 GTCACCTACCGTTAAAAAATTAACGGTATGTTGACAT
          1 GTCACCTACCGTTAAAAAATTAACGGTATGTTGACAT

               
      27619 GTC
          1 GTC

      27622 GCCATAGGAT


Statistics
Matches: 39,  Mismatches: 1, Indels: 0
        0.98            0.03        0.00

Matches are distributed among these distances:
  37   39  1.00

ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31


Consensus pattern (37 bp):   
GTCACCTACCGTTAAAAAATTAACGGTATGTTGACAT

Found at i:27720 original size:30 final size:31

Alignment explanation


    Indices: 27686--27755  Score: 92
    Period size: 30  Copynumber: 2.3  Consensus size: 31

      27676 TTAATTGTTT

                            *     *        
      27686 AAAGAAAAAACGTAATGTTG-TTTGATCTTG
          1 AAAGAAAAAACGTAATATTGATATGATCTTG

                                            
      27716 AAAG--AAAACGTAATATTGAATATGATCTTG
          1 AAAGAAAAAACGTAATATTG-ATATGATCTTG

                      
      27746 AAAGAAAAAA
          1 AAAGAAAAAA

      27756 ATAATTGAGT


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

Matches are distributed among these distances:
  28   13  0.38
  30   17  0.50
  32    4  0.12

ACGTcount: A:0.50, C:0.06, G:0.17, T:0.27


Consensus pattern (31 bp):   
AAAGAAAAAACGTAATATTGATATGATCTTG

Found at i:68927 original size:24 final size:24

Alignment explanation


    Indices: 68908--68984  Score: 154
    Period size: 24  Copynumber: 3.2  Consensus size: 24

      68898 TTTTCAGTTT

                                    
      68908 GGTTTTCTAGTTACTGTTCAGTGG
          1 GGTTTTCTAGTTACTGTTCAGTGG

                                    
      68932 GGTTTTCTAGTTACTGTTCAGTGG
          1 GGTTTTCTAGTTACTGTTCAGTGG

                                    
      68956 GGTTTTCTAGTTACTGTTCAGTGG
          1 GGTTTTCTAGTTACTGTTCAGTGG

                 
      68980 GGTTT
          1 GGTTT

      68985 GTTGATTGTT


Statistics
Matches: 53,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   53  1.00

ACGTcount: A:0.12, C:0.12, G:0.30, T:0.47


Consensus pattern (24 bp):   
GGTTTTCTAGTTACTGTTCAGTGG
Done.