Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01009263.1 Hibiscus syriacus cultivar Beakdansim tig00112914_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: 63957
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32


Found at i:40811 original size:2 final size:2

Alignment explanation


    Indices: 40804--40832  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

      40794 TAAAATTTTA

                                                       
      40804 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 A

      40833 AGAGATAAGG


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:63278 original size:21 final size:20

Alignment explanation


    Indices: 63254--63316  Score: 57
    Period size: 21  Copynumber: 3.4  Consensus size: 20

      63244 CAACTTTGAA

                                 
      63254 AAATAGTTTTCAAAGTTTGGT
          1 AAAT-GTTTTCAAAGTTTGGT

                               *
      63275 AAATG-TTTC----TTT-GA
          1 AAATGTTTTCAAAGTTTGGT

                                 
      63289 AAATGGTTTTCAAAGTTTGGT
          1 AAAT-GTTTTCAAAGTTTGGT

                   
      63310 AAATGTT
          1 AAATGTT

      63317 CTTTGAAAAA


Statistics
Matches: 33,  Mismatches: 2, Indels: 15
        0.66            0.04        0.30

Matches are distributed among these distances:
  14    5  0.15
  15    4  0.12
  16    4  0.12
  19    4  0.12
  20    7  0.21
  21    9  0.27

ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44


Consensus pattern (20 bp):   
AAATGTTTTCAAAGTTTGGT

Found at i:63290 original size:36 final size:35

Alignment explanation


    Indices: 63247--63363  Score: 166
    Period size: 36  Copynumber: 3.3  Consensus size: 35

      63237 TAGTAACCAA

                                                
      63247 CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
          1 CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATG-TT

                       *                       
      63283 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTT
          1 CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTT

                                          *      
      63317 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGCTT
          1 CTTTGAAAAATAG-TTTTCAAAGTTTGGTAAATG-TT

             *         
      63354 -GTTGAAAAAT
          1 CTTTGAAAAAT

      63364 GATAATGGGA


Statistics
Matches: 74,  Mismatches: 4, Indels: 6
        0.88            0.05        0.07

Matches are distributed among these distances:
  34    7  0.09
  35   32  0.43
  36   33  0.45
  37    2  0.03

ACGTcount: A:0.32, C:0.06, G:0.19, T:0.43


Consensus pattern (35 bp):   
CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTT

Found at i:63759 original size:16 final size:17

Alignment explanation


    Indices: 63738--63769  Score: 57
    Period size: 16  Copynumber: 1.9  Consensus size: 17

      63728 TTACTATTAA

                             
      63738 CGTGAATAGT-AAATTT
          1 CGTGAATAGTGAAATTT

                            
      63754 CGTGAATAGTGAAATT
          1 CGTGAATAGTGAAATT

      63770 CAGTCGGCGA


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  16   10  0.67
  17    5  0.33

ACGTcount: A:0.38, C:0.06, G:0.22, T:0.34


Consensus pattern (17 bp):   
CGTGAATAGTGAAATTT
Done.