Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01002416.1 Hibiscus syriacus cultivar Beakdansim tig00004938_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: 66030
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:2234 original size:17 final size:17

Alignment explanation


    Indices: 2203--2240  Score: 51
    Period size: 16  Copynumber: 2.2  Consensus size: 17

       2193 TGTTATTTAA

                 *           
       2203 AAAATTATTTTTTA-TT
          1 AAAATAATTTTTTATTT

                              
       2219 AAAATAATTTTGTTATTT
          1 AAAATAATTTT-TTATTT

                
       2237 AAAA
          1 AAAA

       2241 GTAAAAAAAT


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  16   10  0.53
  17    3  0.16
  18    6  0.32

ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53


Consensus pattern (17 bp):   
AAAATAATTTTTTATTT

Found at i:2238 original size:18 final size:18

Alignment explanation


    Indices: 2193--2240  Score: 55
    Period size: 18  Copynumber: 2.7  Consensus size: 18

       2183 TATAATAAAA

                              
       2193 TGTTATTTAAAAAATTAT
          1 TGTTATTTAAAAAATTAT

                *               
       2211 T-TTTTATTAAAATAATT-T
          1 TGTTAT-TTAAAA-AATTAT

                        
       2229 TGTTATTTAAAA
          1 TGTTATTTAAAA

       2241 GTAAAAAAAT


Statistics
Matches: 25,  Mismatches: 2, Indels: 6
        0.76            0.06        0.18

Matches are distributed among these distances:
  17    3  0.12
  18   15  0.60
  19    7  0.28

ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54


Consensus pattern (18 bp):   
TGTTATTTAAAAAATTAT

Found at i:2278 original size:42 final size:45

Alignment explanation


    Indices: 2250--2338  Score: 121
    Period size: 45  Copynumber: 2.0  Consensus size: 45

       2240 AGTAAAAAAA

                      *                                  
       2250 TTTAAATAACGTTTAATATTAATATATTTAATAAAAAAATAATAT
          1 TTTAAATAACATTTAATATTAATATATTTAATAAAAAAATAATAT

                 *                                 *      
       2295 TTTAAGTAACATTTAATATTAAT-T-TTCTAAT-AAAAATTAATAT
          1 TTTAAATAACATTTAATATTAATATATT-TAATAAAAAAATAATAT

             
       2338 T
          1 T

       2339 AAATAGTATT


Statistics
Matches: 40,  Mismatches: 3, Indels: 4
        0.85            0.06        0.09

Matches are distributed among these distances:
  43   14  0.35
  44    5  0.12
  45   21  0.52

ACGTcount: A:0.49, C:0.03, G:0.02, T:0.45


Consensus pattern (45 bp):   
TTTAAATAACATTTAATATTAATATATTTAATAAAAAAATAATAT

Found at i:2768 original size:15 final size:15

Alignment explanation


    Indices: 2748--2795  Score: 69
    Period size: 15  Copynumber: 3.2  Consensus size: 15

       2738 TTTCCTTATT

                           
       2748 CTTCTCATTCCCCTC
          1 CTTCTCATTCCCCTC

                  * *      
       2763 CTTCTCCTCCCCCTC
          1 CTTCTCATTCCCCTC

                      *    
       2778 CTTCTCATTCTCCTC
          1 CTTCTCATTCCCCTC

               
       2793 CTT
          1 CTT

       2796 TTTCTTCTTT


Statistics
Matches: 28,  Mismatches: 5, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  15   28  1.00

ACGTcount: A:0.04, C:0.54, G:0.00, T:0.42


Consensus pattern (15 bp):   
CTTCTCATTCCCCTC

Found at i:16727 original size:17 final size:16

Alignment explanation


    Indices: 16707--16739  Score: 57
    Period size: 17  Copynumber: 2.0  Consensus size: 16

      16697 TATTTTTATC

                             
      16707 AATAATAAATTTTAAAT
          1 AATAATAAA-TTTAAAT

                            
      16724 AATAATAAATTTAAAT
          1 AATAATAAATTTAAAT

      16740 TGATGGAAAA


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

Matches are distributed among these distances:
  16    7  0.44
  17    9  0.56

ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39


Consensus pattern (16 bp):   
AATAATAAATTTAAAT

Found at i:37967 original size:29 final size:30

Alignment explanation


    Indices: 37935--38002  Score: 122
    Period size: 29  Copynumber: 2.3  Consensus size: 30

      37925 ATGCAATCCA

                                          
      37935 GGCGACCTATA-AGGACGCCGGGCGTGCAT
          1 GGCGACCTATATAGGACGCCGGGCGTGCAT

                                          
      37964 GGCGACCT-TATAGGACGCCGGGCGTGCAT
          1 GGCGACCTATATAGGACGCCGGGCGTGCAT

                      
      37993 GGCGACCTAT
          1 GGCGACCTAT

      38003 GTTGTCACTG


Statistics
Matches: 37,  Mismatches: 0, Indels: 3
        0.93            0.00        0.08

Matches are distributed among these distances:
  28    2  0.05
  29   34  0.92
  30    1  0.03

ACGTcount: A:0.19, C:0.28, G:0.37, T:0.16


Consensus pattern (30 bp):   
GGCGACCTATATAGGACGCCGGGCGTGCAT

Found at i:49333 original size:21 final size:21

Alignment explanation


    Indices: 49308--49360  Score: 56
    Period size: 21  Copynumber: 2.5  Consensus size: 21

      49298 TTTACGTTCT

                                 
      49308 ATTTTTATTTAATTTTATT-C
          1 ATTTTTATTTAATTTTATTGC

                  *      *         
      49328 ACTTTTAATTCT-TTTTTATTGC
          1 A-TTTTTATT-TAATTTTATTGC

                       
      49350 ATTTTTATTTA
          1 ATTTTTATTTA

      49361 TTTAAAAAGG


Statistics
Matches: 26,  Mismatches: 3, Indels: 7
        0.72            0.08        0.19

Matches are distributed among these distances:
  20    2  0.08
  21   21  0.81
  22    3  0.12

ACGTcount: A:0.23, C:0.08, G:0.02, T:0.68


Consensus pattern (21 bp):   
ATTTTTATTTAATTTTATTGC
Done.