Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01003428.1 Hibiscus syriacus cultivar Beakdansim tig00007225_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: 184769
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33


File 2 of 2

Found at i:169957 original size:60 final size:59

Alignment explanation


    Indices: 169893--170019  Score: 139
    Period size: 59  Copynumber: 2.1  Consensus size: 59

     169883 ATAGTCGGAT

                     *        *   *                  *            *    * 
     169893 GACCATTTCGTAACTTTTCATAGTCA-AAGGACTCAACAAAGTAACATCATATAGTCGAGG
          1 GACCATTTCATAACTTTTAATAATCAGAA-GACTCAA-AAAATAACATCATATAATCGAAG

                    *    *          *                             *    
     169953 GACCATTTTATAATTTTTAATAATGAGAAGACTCAAAAAATAACATCATATAATTGAAG
          1 GACCATTTCATAACTTTTAATAATCAGAAGACTCAAAAAATAACATCATATAATCGAAG

                    
     170012 GACCATTT
          1 GACCATTT

     170020 GTGTGCTTTA


Statistics
Matches: 56,  Mismatches: 10, Indels: 3
        0.81            0.14        0.04

Matches are distributed among these distances:
  59   27  0.48
  60   27  0.48
  61    2  0.04

ACGTcount: A:0.41, C:0.16, G:0.13, T:0.30


Consensus pattern (59 bp):   
GACCATTTCATAACTTTTAATAATCAGAAGACTCAAAAAATAACATCATATAATCGAAG

Found at i:171589 original size:37 final size:37

Alignment explanation


    Indices: 171517--171589  Score: 94
    Period size: 37  Copynumber: 2.0  Consensus size: 37

     171507 TATATTTTAA

                                          *      
     171517 ATTTTGTAAAAAAAATTATATAAATATTATGAATTTT
          1 ATTTTGTAAAAAAAATTATATAAATATTATCAATTTT

                 *    *                 *        
     171554 ATTTTTTAAAGAAAA-TATATAAATATTTTACAATTT
          1 ATTTTGTAAAAAAAATTATATAAATATTAT-CAATTT

     171590 GTAATATTAT


Statistics
Matches: 31,  Mismatches: 4, Indels: 2
        0.84            0.11        0.05

Matches are distributed among these distances:
  36   13  0.42
  37   18  0.58

ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47


Consensus pattern (37 bp):   
ATTTTGTAAAAAAAATTATATAAATATTATCAATTTT

Found at i:171771 original size:20 final size:20

Alignment explanation


    Indices: 171735--171772  Score: 58
    Period size: 20  Copynumber: 1.9  Consensus size: 20

     171725 ATCATATTTC

                       **       
     171735 CTGGTAATCTTTTATTCTCA
          1 CTGGTAATCTTAAATTCTCA

                              
     171755 CTGGTAATCTTAAATTCT
          1 CTGGTAATCTTAAATTCT

     171773 GTGAACTAAA


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   16  1.00

ACGTcount: A:0.24, C:0.18, G:0.11, T:0.47


Consensus pattern (20 bp):   
CTGGTAATCTTAAATTCTCA

Found at i:172423 original size:20 final size:21

Alignment explanation


    Indices: 172400--172439  Score: 55
    Period size: 21  Copynumber: 2.0  Consensus size: 21

     172390 TTTTTTTTAA

                                 
     172400 AAAATACT-TTTTTGAAAAAT
          1 AAAATACTATTTTTGAAAAAT

                  *       *     
     172420 AAAATATTATTTTTTAAAAA
          1 AAAATACTATTTTTGAAAAA

     172440 AGTTAACAAA


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  20    7  0.41
  21   10  0.59

ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42


Consensus pattern (21 bp):   
AAAATACTATTTTTGAAAAAT

Done.