Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01002411.1 Hibiscus syriacus cultivar Beakdansim tig00004930_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: 64129
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.34


Found at i:2455 original size:36 final size:36

Alignment explanation


    Indices: 2414--2516  Score: 170
    Period size: 36  Copynumber: 2.9  Consensus size: 36

       2404 AGTTGAGTAT

                                                
       2414 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
          1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA

                  *                   *        *
       2450 TATCAGTTTTGGTACATTCGTGTATCGATGTTATCC
          1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA

                          *                
       2486 TATCAGCTTTGGTATATTCGTGTATCAATGT
          1 TATCAGCTTTGGTACATTCGTGTATCAATGT

       2517 CCAGCACCGT


Statistics
Matches: 61,  Mismatches: 6, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  36   61  1.00

ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44


Consensus pattern (36 bp):   
TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA

Found at i:10505 original size:36 final size:36

Alignment explanation


    Indices: 10464--10566  Score: 188
    Period size: 36  Copynumber: 2.9  Consensus size: 36

      10454 AGTTGAGTAT

                  *                             
      10464 TATCAGTTTTGGTACATTCGTGTATCAATGTTATCA
          1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA

                                               *
      10500 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCC
          1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA

                                           
      10536 TATCAGCTTTGGTACATTCGTGTATCAATGT
          1 TATCAGCTTTGGTACATTCGTGTATCAATGT

      10567 CCAGCACCGT


Statistics
Matches: 65,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  36   65  1.00

ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43


Consensus pattern (36 bp):   
TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA

Found at i:20683 original size:2 final size:2

Alignment explanation


    Indices: 20676--20725  Score: 100
    Period size: 2  Copynumber: 25.0  Consensus size: 2

      20666 TAAAAATCAG

                                                                          
      20676 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                       
      20718 AT AT AT AT
          1 AT AT AT AT

      20726 TTAATTTTTA


Statistics
Matches: 48,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   48  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:22382 original size:48 final size:48

Alignment explanation


    Indices: 22310--22413  Score: 154
    Period size: 48  Copynumber: 2.2  Consensus size: 48

      22300 TTTTAGTTGT

                      *     *  *       *         *          
      22310 TTTTCATGTCGAATTGGCACTATGTAATTGTAGGCATTATTAGGGCCC
          1 TTTTCATGTCAAATTGACAATATGTAAATGTAGGCATCATTAGGGCCC

                                                         *  
      22358 TTTTCATGTCAAATTGACAATATGTAAATGTAGGCATCATTAGGGGCC
          1 TTTTCATGTCAAATTGACAATATGTAAATGTAGGCATCATTAGGGCCC

                    
      22406 TTTTCATG
          1 TTTTCATG

      22414 ACGGGCGTTT


Statistics
Matches: 50,  Mismatches: 6, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  48   50  1.00

ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38


Consensus pattern (48 bp):   
TTTTCATGTCAAATTGACAATATGTAAATGTAGGCATCATTAGGGCCC

Found at i:26550 original size:14 final size:14

Alignment explanation


    Indices: 26531--26569  Score: 51
    Period size: 14  Copynumber: 2.8  Consensus size: 14

      26521 TAATGGGGAG

                          
      26531 TAATCCCTGCAAAA
          1 TAATCCCTGCAAAA

                      *   
      26545 TAATCCCTGCGAAA
          1 TAATCCCTGCAAAA

            *    *     
      26559 GAATCTCTGCA
          1 TAATCCCTGCA

      26570 TATAGACAGA


Statistics
Matches: 21,  Mismatches: 4, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  14   21  1.00

ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23


Consensus pattern (14 bp):   
TAATCCCTGCAAAA

Found at i:56893 original size:31 final size:29

Alignment explanation


    Indices: 56853--56921  Score: 84
    Period size: 31  Copynumber: 2.3  Consensus size: 29

      56843 TTATAATATA

                *        *                 
      56853 TAATGATTATTTTGTAAAAACTTAATAAATT
          1 TAATAATTATTTTATAAAAAC-TAA-AAATT

                               *      *  
      56884 TAATAATTATTTTATAAAATCTAAAATTT
          1 TAATAATTATTTTATAAAAACTAAAAATT

                     
      56913 TAATAATTA
          1 TAATAATTA

      56922 AAAAAATTAT


Statistics
Matches: 34,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
  29   13  0.38
  30    3  0.09
  31   18  0.53

ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46


Consensus pattern (29 bp):   
TAATAATTATTTTATAAAAACTAAAAATT
Done.