Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01005880.1 Hibiscus syriacus cultivar Beakdansim tig00013812_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: 65502
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33


Found at i:4321 original size:19 final size:18

Alignment explanation


    Indices: 4286--4320  Score: 61
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       4276 AGAATGTCCA

                 *            
       4286 GGGGGTATCGATTCCCCG
          1 GGGGGAATCGATTCCCCG

                             
       4304 GGGGGAATCGATTCCCC
          1 GGGGGAATCGATTCCCC

       4321 CCTAAAGGAA


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

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.14, C:0.29, G:0.37, T:0.20


Consensus pattern (18 bp):   
GGGGGAATCGATTCCCCG

Found at i:4658 original size:15 final size:16

Alignment explanation


    Indices: 4620--4662  Score: 54
    Period size: 15  Copynumber: 2.8  Consensus size: 16

       4610 CTTATATGTA

                       *     
       4620 CATGAATACATGATATG
          1 CATGAA-ACATAATATG

                            
       4637 CAT-AAACATAATA-G
          1 CATGAAACATAATATG

                        
       4651 CATGAAACATAA
          1 CATGAAACATAA

       4663 GATATGATAT


Statistics
Matches: 24,  Mismatches: 1, Indels: 4
        0.83            0.03        0.14

Matches are distributed among these distances:
  14    4  0.17
  15   15  0.62
  16    2  0.08
  17    3  0.12

ACGTcount: A:0.51, C:0.14, G:0.12, T:0.23


Consensus pattern (16 bp):   
CATGAAACATAATATG

Found at i:20271 original size:2 final size:2

Alignment explanation


    Indices: 20266--20291  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

      20256 ATGAGAGATG

                                                  
      20266 TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA

      20292 CACAGAGAGA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:21346 original size:2 final size:2

Alignment explanation


    Indices: 21339--21373  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

      21329 ACGTTATTAA

                                                                
      21339 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      21374 AGTCTCAAAC


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:34945 original size:31 final size:31

Alignment explanation


    Indices: 34887--34955  Score: 86
    Period size: 31  Copynumber: 2.2  Consensus size: 31

      34877 GAGTATTGCT

                 *                *        
      34887 GAGCTTGACTCGACTCGAAAATTCTGAAATG
          1 GAGCTCGACTCGACTCGAAAATCCTGAAATG

                                         *  
      34918 GAGCTCGACTCGAACTCG-AAATCCTGAACTG
          1 GAGCTCGACTCG-ACTCGAAAATCCTGAAATG

            *      
      34949 AAGCTCG
          1 GAGCTCG

      34956 TAAGCAGCTC


Statistics
Matches: 33,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
  31   28  0.85
  32    5  0.15

ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22


Consensus pattern (31 bp):   
GAGCTCGACTCGACTCGAAAATCCTGAAATG

Found at i:48971 original size:21 final size:21

Alignment explanation


    Indices: 48929--48972  Score: 52
    Period size: 21  Copynumber: 2.1  Consensus size: 21

      48919 TGAAATAAAA

                            **   
      48929 TAAAAATAAAATGTATGTATT
          1 TAAAAATAAAATGTATACATT

                        * *      
      48950 TAAAAATAAAATTTTTACATT
          1 TAAAAATAAAATGTATACATT

              
      48971 TA
          1 TA

      48973 GTTAATATTA


Statistics
Matches: 19,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41


Consensus pattern (21 bp):   
TAAAAATAAAATGTATACATT

Found at i:58250 original size:17 final size:18

Alignment explanation


    Indices: 58217--58252  Score: 56
    Period size: 17  Copynumber: 2.1  Consensus size: 18

      58207 TTTTATAATT

                              
      58217 TTATAACTATTACAATGA
          1 TTATAACTATTACAATGA

                        *     
      58235 TTATAA-TATTATAATGA
          1 TTATAACTATTACAATGA

             
      58252 T
          1 T

      58253 CATTTTGTAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  17   11  0.65
  18    6  0.35

ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44


Consensus pattern (18 bp):   
TTATAACTATTACAATGA
Done.