Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01005423.1 Hibiscus syriacus cultivar Beakdansim tig00012439_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: 38670
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33


Found at i:4295 original size:24 final size:23

Alignment explanation


    Indices: 4250--4300  Score: 66
    Period size: 24  Copynumber: 2.2  Consensus size: 23

       4240 GTTGGAAGCT

                            *      
       4250 ATAAAATACTTTATAATTTATTC
          1 ATAAAATACTTTATAAATTATTC

                     *   *          
       4273 ATAAACATATTTTTTAAATTATTC
          1 ATAAA-ATACTTTATAAATTATTC

                
       4297 ATAA
          1 ATAA

       4301 TTTATAATAT


Statistics
Matches: 24,  Mismatches: 3, Indels: 1
        0.86            0.11        0.04

Matches are distributed among these distances:
  23    5  0.21
  24   19  0.79

ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47


Consensus pattern (23 bp):   
ATAAAATACTTTATAAATTATTC

Found at i:4314 original size:2 final size:2

Alignment explanation


    Indices: 4303--4339  Score: 60
    Period size: 2  Copynumber: 19.5  Consensus size: 2

       4293 ATTCATAATT

                                                                      
       4303 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       4340 TTTTACAAAG


Statistics
Matches: 33,  Mismatches: 0, Indels: 4
        0.89            0.00        0.11

Matches are distributed among these distances:
   1    2  0.06
   2   31  0.94

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:20386 original size:15 final size:15

Alignment explanation


    Indices: 20357--20397  Score: 66
    Period size: 15  Copynumber: 2.8  Consensus size: 15

      20347 TTCATATCAA

                  *        
      20357 TAAAATGTC-AAAAT
          1 TAAAATATCTAAAAT

                           
      20371 TAAAATATCTAAAAT
          1 TAAAATATCTAAAAT

                        
      20386 TAAAATATCTAA
          1 TAAAATATCTAA

      20398 TCACGTTAAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  14    8  0.32
  15   17  0.68

ACGTcount: A:0.59, C:0.07, G:0.02, T:0.32


Consensus pattern (15 bp):   
TAAAATATCTAAAAT

Found at i:22153 original size:18 final size:18

Alignment explanation


    Indices: 22130--22166  Score: 65
    Period size: 18  Copynumber: 2.1  Consensus size: 18

      22120 ATTACAAGAT

                        *     
      22130 GATATATGTTCATAACTA
          1 GATATATGTTCACAACTA

                              
      22148 GATATATGTTCACAACTA
          1 GATATATGTTCACAACTA

             
      22166 G
          1 G

      22167 CGGTGCTTAT


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35


Consensus pattern (18 bp):   
GATATATGTTCACAACTA

Found at i:22274 original size:16 final size:16

Alignment explanation


    Indices: 22249--22301  Score: 54
    Period size: 16  Copynumber: 3.3  Consensus size: 16

      22239 ACTCGACTCA

                 *          
      22249 TTGCTCGTTAAGCTCG
          1 TTGCTTGTTAAGCTCG

                        *   
      22265 TTGCTTGTTAAGTTCG
          1 TTGCTTGTTAAGCTCG

                   *      *  
      22281 TTG-TTCATTAAGCGCG
          1 TTGCTT-GTTAAGCTCG

                 
      22297 TTGCT
          1 TTGCT

      22302 AGTCTTGTTG


Statistics
Matches: 30,  Mismatches: 5, Indels: 3
        0.79            0.13        0.08

Matches are distributed among these distances:
  15    2  0.07
  16   27  0.90
  17    1  0.03

ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43


Consensus pattern (16 bp):   
TTGCTTGTTAAGCTCG
Done.