Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01005249.1 Hibiscus syriacus cultivar Beakdansim tig00011873_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: 335851
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33


File 2 of 2

Found at i:329849 original size:20 final size:20

Alignment explanation


    Indices: 329826--329979  Score: 245
    Period size: 20  Copynumber: 7.7  Consensus size: 20

     329816 CGATAGTCAG

                *               
     329826 ATTCACGTTGCGATTTACGT
          1 ATTCGCGTTGCGATTTACGT

                                
     329846 ATTCGCGTTGCGATTTACGT
          1 ATTCGCGTTGCGATTTACGT

                                
     329866 ATTCGCGTTGCGATTTACGT
          1 ATTCGCGTTGCGATTTACGT

                                
     329886 ATTCGCGTTGCGATTTACGT
          1 ATTCGCGTTGCGATTTACGT

                                
     329906 ATTCGCGTTGCGATTTACGT
          1 ATTCGCGTTGCGATTTACGT

             *               * **
     329926 AATCGCGTTGCGATTTTCCAA
          1 ATTCGCGTTGCGA-TTTACGT

                                
     329947 ATTCGCGTTGCGATTTACGT
          1 ATTCGCGTTGCGATTTACGT

                  *      
     329967 ATTCGCATTGCGA
          1 ATTCGCGTTGCGA

     329980 ATTAGGAAAA


Statistics
Matches: 123,  Mismatches: 10, Indels: 2
        0.91            0.07        0.01

Matches are distributed among these distances:
  20  107  0.87
  21   16  0.13

ACGTcount: A:0.18, C:0.21, G:0.23, T:0.38


Consensus pattern (20 bp):   
ATTCGCGTTGCGATTTACGT

Found at i:329877 original size:60 final size:58

Alignment explanation


    Indices: 329806--329979  Score: 231
    Period size: 60  Copynumber: 2.9  Consensus size: 58

     329796 CAATAGTCAG

                *                   *                                   
     329806 AATCTCGTTGCGATAGTCAGATTCACGTTGCGATTTACGTATTCGCGTTGCGATTTACGT
          1 AATCGCGTTGCGAT--TCAGATTCGCGTTGCGATTTACGTATTCGCGTTGCGATTTACGT

             *             *                                            
     329866 ATTCGCGTTGCGATTTACGTATTCGCGTTGCGATTTACGTATTCGCGTTGCGATTTACGT
          1 AATCGCGTTGCGATTCA-G-ATTCGCGTTGCGATTTACGTATTCGCGTTGCGATTTACGT

                                *                          *      
     329926 AATCGCGTTGCGATTTTCCAAATTCGCGTTGCGATTTACGTATTCGCATTGCGA
          1 AATCGCGTTGCGA--TT-CAGATTCGCGTTGCGATTTACGTATTCGCGTTGCGA

     329980 ATTAGGAAAA


Statistics
Matches: 101,  Mismatches: 8, Indels: 9
        0.86            0.07        0.08

Matches are distributed among these distances:
  58    2  0.02
  59    1  0.01
  60   63  0.62
  61   32  0.32
  62    2  0.02
  63    1  0.01

ACGTcount: A:0.18, C:0.21, G:0.24, T:0.37


Consensus pattern (58 bp):   
AATCGCGTTGCGATTCAGATTCGCGTTGCGATTTACGTATTCGCGTTGCGATTTACGT

Found at i:330000 original size:21 final size:21

Alignment explanation


    Indices: 329976--330021  Score: 74
    Period size: 21  Copynumber: 2.2  Consensus size: 21

     329966 TATTCGCATT

                                 
     329976 GCGAATTAGGAAAATCGCAAC
          1 GCGAATTAGGAAAATCGCAAC

                   *            *
     329997 GCGAATTTGGAAAATCGCAAT
          1 GCGAATTAGGAAAATCGCAAC

                
     330018 GCGA
          1 GCGA

     330022 TAGTCAGAAT


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  21   23  1.00

ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17


Consensus pattern (21 bp):   
GCGAATTAGGAAAATCGCAAC

Done.