Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01005867.1 Hibiscus syriacus cultivar Beakdansim tig00013792_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: 53970
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30


Found at i:2132 original size:31 final size:33

Alignment explanation


    Indices: 2096--2158  Score: 85
    Period size: 33  Copynumber: 2.0  Consensus size: 33

       2086 AATTATAAAA

                                     *       
       2096 TATAAAA-GAAT-AAAAATAATAGACAAATATG
          1 TATAAAATGAATAAAAAATAATAGAAAAATATG

                      *           *         
       2127 TATAAAATGATTAAAAAATAATTGAAAAATAT
          1 TATAAAATGAATAAAAAATAATAGAAAAATAT

       2159 ATTTGTAATA


Statistics
Matches: 27,  Mismatches: 3, Indels: 2
        0.84            0.09        0.06

Matches are distributed among these distances:
  31    7  0.26
  32    3  0.11
  33   17  0.63

ACGTcount: A:0.63, C:0.02, G:0.08, T:0.27


Consensus pattern (33 bp):   
TATAAAATGAATAAAAAATAATAGAAAAATATG

Found at i:22358 original size:21 final size:21

Alignment explanation


    Indices: 22310--22358  Score: 71
    Period size: 21  Copynumber: 2.3  Consensus size: 21

      22300 GTCTGAGTTA

                     *           
      22310 CCCGCGACGGCCGCAATAGCG
          1 CCCGCGACGACCGCAATAGCG

            * *                  
      22331 TCTGCGACGACCGCAATAGCG
          1 CCCGCGACGACCGCAATAGCG

                   
      22352 CCCGCGA
          1 CCCGCGA

      22359 AGATCGTAAT


Statistics
Matches: 23,  Mismatches: 5, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  21   23  1.00

ACGTcount: A:0.20, C:0.41, G:0.31, T:0.08


Consensus pattern (21 bp):   
CCCGCGACGACCGCAATAGCG

Found at i:48062 original size:66 final size:66

Alignment explanation


    Indices: 47946--48070  Score: 187
    Period size: 66  Copynumber: 1.9  Consensus size: 66

      47936 GTCCCTTTTT

                  *                             *                            
      47946 TTCTTCTGGTTGGTGGGTGCAACTTCTCTCCCACGTTCCTCAGTAACAGTCGACTCGTTAGTGCT
          1 TTCTTCAGGTTGGTGGGTGCAACTTCTCTCCCACGTCCCTCAGTAACAGTCGACTCGTTAGTGCT

             
      48011 C
         66 C

                                 **    *             *   *             
      48012 TTCTTCAGGTTGGTGGGTGCAGTTTCTTTCCCACGTCCCTCGGTAGCAGTCGACTCGTT
          1 TTCTTCAGGTTGGTGGGTGCAACTTCTCTCCCACGTCCCTCAGTAACAGTCGACTCGTT

      48071 CGAGTTCCCG


Statistics
Matches: 52,  Mismatches: 7, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  66   52  1.00

ACGTcount: A:0.12, C:0.28, G:0.25, T:0.35


Consensus pattern (66 bp):   
TTCTTCAGGTTGGTGGGTGCAACTTCTCTCCCACGTCCCTCAGTAACAGTCGACTCGTTAGTGCT
C

Found at i:53471 original size:24 final size:24

Alignment explanation


    Indices: 53402--53473  Score: 117
    Period size: 24  Copynumber: 3.0  Consensus size: 24

      53392 TTGATGACCT

                  *              *  
      53402 GAGTTTAAGCACCATAGATATAAG
          1 GAGTTTGAGCACCATAGATATCAG

                                    
      53426 GAGTTTGAGCACCATAGATATCAG
          1 GAGTTTGAGCACCATAGATATCAG

             *                      
      53450 GTGTTTGAGCACCATAGATATCAG
          1 GAGTTTGAGCACCATAGATATCAG

      53474 AGGCGTGAGC


Statistics
Matches: 45,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  24   45  1.00

ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26


Consensus pattern (24 bp):   
GAGTTTGAGCACCATAGATATCAG

Found at i:53482 original size:24 final size:24

Alignment explanation


    Indices: 53409--53483  Score: 75
    Period size: 24  Copynumber: 3.1  Consensus size: 24

      53399 CCTGAGTTTA

                                      
      53409 AGCACCATAGATAT-A-AGGAGTTTG
          1 AGCACCATAGATATCAGAGGAG--TG

                                 **  
      53433 AGCACCATAGATATCAG-GTGTTTG
          1 AGCACCATAGATATCAGAG-GAGTG

                                *   
      53457 AGCACCATAGATATCAGAGGCGTG
          1 AGCACCATAGATATCAGAGGAGTG

               
      53481 AGC
          1 AGC

      53484 GTTAATATCA


Statistics
Matches: 43,  Mismatches: 4, Indels: 8
        0.78            0.07        0.15

Matches are distributed among these distances:
  24   39  0.91
  25    3  0.07
  26    1  0.02

ACGTcount: A:0.33, C:0.17, G:0.27, T:0.23


Consensus pattern (24 bp):   
AGCACCATAGATATCAGAGGAGTG
Done.