Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01007183.1 Hibiscus syriacus cultivar Beakdansim tig00018896_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: 35028
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31


Found at i:10889 original size:2 final size:2

Alignment explanation


    Indices: 10884--10937  Score: 108
    Period size: 2  Copynumber: 27.0  Consensus size: 2

      10874 AATTAGTTGA

                                                                          
      10884 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

                             
      10926 AT AT AT AT AT AT
          1 AT AT AT AT AT AT

      10938 CCAGAGGATA


Statistics
Matches: 52,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   52  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:11823 original size:45 final size:42

Alignment explanation


    Indices: 11772--11855  Score: 123
    Period size: 45  Copynumber: 1.9  Consensus size: 42

      11762 ATGTATATCA

                            *                            
      11772 TTTACCAACACTTTAGTAACTTCTGTGACAAAGAAAAAGAGTGTC
          1 TTTACCAACACTTTAGGAAC-T-TGTGAC-AAGAAAAAGAGTGTC

                     *                             
      11817 TTTACCAACTCTTTAGGAACTTGTGACAAGAAAAAGAGT
          1 TTTACCAACACTTTAGGAACTTGTGACAAGAAAAAGAGT

      11856 CTTTATTCTT


Statistics
Matches: 37,  Mismatches: 2, Indels: 3
        0.88            0.05        0.07

Matches are distributed among these distances:
  42   12  0.32
  43    6  0.16
  44    1  0.03
  45   18  0.49

ACGTcount: A:0.38, C:0.17, G:0.17, T:0.29


Consensus pattern (42 bp):   
TTTACCAACACTTTAGGAACTTGTGACAAGAAAAAGAGTGTC

Found at i:25232 original size:3 final size:3

Alignment explanation


    Indices: 25224--25278  Score: 110
    Period size: 3  Copynumber: 18.3  Consensus size: 3

      25214 GTATGGTCAT

                                                                           
      25224 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA

                     
      25272 TTA TTA T
          1 TTA TTA T

      25279 GAACATGTAT


Statistics
Matches: 52,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   52  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (3 bp):   
TTA

Found at i:30587 original size:18 final size:15

Alignment explanation


    Indices: 30549--30585  Score: 65
    Period size: 15  Copynumber: 2.4  Consensus size: 15

      30539 TCATGCGAAC

                           
      30549 AAATATTATTTTTGA
          1 AAATATTATTTTTGA

                           
      30564 AAATATTATTTTTGA
          1 AAATATTATTTTTGA

                   
      30579 ATAATAT
          1 A-AATAT

      30586 ATGTATATTA


Statistics
Matches: 21,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  15   16  0.76
  16    5  0.24

ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51


Consensus pattern (15 bp):   
AAATATTATTTTTGA

Found at i:32091 original size:186 final size:185

Alignment explanation


    Indices: 31771--32131  Score: 598
    Period size: 186  Copynumber: 1.9  Consensus size: 185

      31761 TTTTATAATT

                  *           *                              *         *     
      31771 AAAAAATAGTTTATAATTGATTTAAATAATATATAATAATAAAATAAAATTTTATATAATTTTCT
          1 AAAAAACAGTTTATAATTAATTTAAATAATATATAATAATAAAATAAAAATTTATATAAATTTCT

                                                                          *  
      31836 AATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAATTGGGTTTTAGAT
         66 AATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAATTGGGTTTTAAAT

                           *            *           *              
      31901 GGTTTGGGCTGAGCCTATATGTTATATATAATATATTTAATATTTTTTAATTCAG
        131 GGTTTGGGCTGAGCCCATATGTTATATAAAATATATTTAAAATTTTTTAATTCAG

                                                 *                           
      31956 AAAAAACAGTTTATAATTAATTTAAATAATATATAATTATAAAATAAAAAATTTATATAAAATTT
          1 AAAAAACAGTTTATAATTAATTTAAATAATATATAATAATAAAAT-AAAAATTTATAT-AAATTT

                                           *                                 
      32021 -TAATTAATTAATATTGATTTAGGTTTAAAATTTATTGGATCTTAAATTATTAATTGGGTTTTAA
         64 CTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAATTGGGTTTTAA

                      *                                    
      32085 ATGGTTTGGGTTGAGCCCATATGTTATATAAAATATATTTAAAATTT
        129 ATGGTTTGGGCTGAGCCCATATGTTATATAAAATATATTTAAAATTT

      32132 AAAATTTTAT


Statistics
Matches: 163,  Mismatches: 11, Indels: 3
        0.92            0.06        0.02

Matches are distributed among these distances:
 185   42  0.26
 186  116  0.71
 187    5  0.03

ACGTcount: A:0.42, C:0.03, G:0.11, T:0.45


Consensus pattern (185 bp):   
AAAAAACAGTTTATAATTAATTTAAATAATATATAATAATAAAATAAAAATTTATATAAATTTCT
AATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAATTGGGTTTTAAAT
GGTTTGGGCTGAGCCCATATGTTATATAAAATATATTTAAAATTTTTTAATTCAG
Done.