Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01003957.1 Hibiscus syriacus cultivar Beakdansim tig00008557_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: 57879
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:20469 original size:55 final size:51

Alignment explanation


    Indices: 20371--20476  Score: 124
    Period size: 55  Copynumber: 2.0  Consensus size: 51

      20361 GAGTTTTAAT

                                                  *       *    
      20371 TATAGATATAATATATGTTTATTATTATTATTATTATTTAATTTAATTATA
          1 TATAGATATAATATATGTTTATTATTATTATTATTATTAAATTTAAATATA

                *                  *                                
      20422 TATATATATATATATATGTTTTGGTTATTAATTATTAATTA-TAAATTTAAATATA
          1 TATAGATATA-ATATATG-TTT-ATTATT-ATTATT-ATTATTAAATTTAAATATA

      20477 ATTATAATTA


Statistics
Matches: 46,  Mismatches: 4, Indels: 6
        0.82            0.07        0.11

Matches are distributed among these distances:
  51    9  0.20
  52    7  0.15
  53    3  0.07
  54    5  0.11
  55   18  0.39
  56    4  0.09

ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55


Consensus pattern (51 bp):   
TATAGATATAATATATGTTTATTATTATTATTATTATTAAATTTAAATATA

Found at i:20551 original size:2 final size:2

Alignment explanation


    Indices: 20544--20571  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

      20534 ATACTTTTAC

                                                     
      20544 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      20572 GGTCTAATAT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:27228 original size:18 final size:19

Alignment explanation


    Indices: 27205--27282  Score: 76
    Period size: 18  Copynumber: 4.4  Consensus size: 19

      27195 GTTTCTGAGG

                            *  
      27205 GGAATTGA-AATCTGTGAA
          1 GGAATTGAGAATCTGTTAA

                               
      27223 GGAATT-AGAATCTGTTAA
          1 GGAATTGAGAATCTGTTAA

            *      *      *    
      27241 TGAATT-TGAATCTATTAA
          1 GGAATTGAGAATCTGTTAA

                             * 
      27259 GGAATT-AGAATCTG-TCA
          1 GGAATTGAGAATCTGTTAA

                   
      27276 GGAATTG
          1 GGAATTG

      27283 GTTTTGACTG


Statistics
Matches: 50,  Mismatches: 8, Indels: 4
        0.81            0.13        0.06

Matches are distributed among these distances:
  17    9  0.18
  18   41  0.82

ACGTcount: A:0.37, C:0.06, G:0.23, T:0.33


Consensus pattern (19 bp):   
GGAATTGAGAATCTGTTAA

Found at i:32676 original size:23 final size:23

Alignment explanation


    Indices: 32626--32676  Score: 77
    Period size: 23  Copynumber: 2.3  Consensus size: 23

      32616 GATTCCCTCC

                            *      
      32626 AGGGGGAATCGGTTCCTATTCAA
          1 AGGGGGAATCGGTTCCCATTCAA

                             *     
      32649 AGGGGGAATCGGTTCCCCTT-AA
          1 AGGGGGAATCGGTTCCCATTCAA

                  
      32671 AGGGGG
          1 AGGGGG

      32677 TGTCGATTCC


Statistics
Matches: 26,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
  22    8  0.31
  23   18  0.69

ACGTcount: A:0.24, C:0.18, G:0.37, T:0.22


Consensus pattern (23 bp):   
AGGGGGAATCGGTTCCCATTCAA

Found at i:48890 original size:29 final size:30

Alignment explanation


    Indices: 48858--48937  Score: 74
    Period size: 29  Copynumber: 2.7  Consensus size: 30

      48848 CCAATTATAT

                                      *   
      48858 AACTTTTAAAAATTACATTTTTATC-CCTA
          1 AACTTTTAAAAATTACATTTTTATCTACTA

                    *   *   *  *           
      48887 AACTTTTCTAAAGTT-TATATTTATCTACTA
          1 AACTTTT-AAAAATTACATTTTTATCTACTA

                  *    *         
      48917 AACTTTCAAAATTTACATTTT
          1 AACTTTTAAAAATTACATTTT

      48938 GGTCACTAGT


Statistics
Matches: 38,  Mismatches: 10, Indels: 5
        0.72            0.19        0.09

Matches are distributed among these distances:
  29   20  0.53
  30   18  0.47

ACGTcount: A:0.36, C:0.15, G:0.01, T:0.47


Consensus pattern (30 bp):   
AACTTTTAAAAATTACATTTTTATCTACTA

Found at i:53349 original size:24 final size:24

Alignment explanation


    Indices: 53317--53365  Score: 80
    Period size: 24  Copynumber: 2.0  Consensus size: 24

      53307 GTATTAAATC

                                    
      53317 TTCAAGTAACCATCAATAGACTTA
          1 TTCAAGTAACCATCAATAGACTTA

                       * *          
      53341 TTCAAGTAACCGTGAATAGACTTA
          1 TTCAAGTAACCATCAATAGACTTA

             
      53365 T
          1 T

      53366 AGGTCAGAGA


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  24   23  1.00

ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31


Consensus pattern (24 bp):   
TTCAAGTAACCATCAATAGACTTA
Done.