Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01004636.1 Hibiscus syriacus cultivar Beakdansim tig00010378_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: 36952
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:98 original size:13 final size:13

Alignment explanation


    Indices: 80--117  Score: 51
    Period size: 12  Copynumber: 3.0  Consensus size: 13

         70 GCTCATGAAC

                         
         80 TCATAAATGTGCG
          1 TCATAAATGTGCG

                       **
         93 TCATAAAT-TGTT
          1 TCATAAATGTGCG

                         
        105 TCATAAATGTGCG
          1 TCATAAATGTGCG

        118 CTAGATTTAT


Statistics
Matches: 20,  Mismatches: 4, Indels: 2
        0.77            0.15        0.08

Matches are distributed among these distances:
  12   10  0.50
  13   10  0.50

ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37


Consensus pattern (13 bp):   
TCATAAATGTGCG

Found at i:26173 original size:13 final size:14

Alignment explanation


    Indices: 26155--26185  Score: 55
    Period size: 13  Copynumber: 2.3  Consensus size: 14

      26145 TTTTCTCATG

                          
      26155 TTTTCTTTT-TTTA
          1 TTTTCTTTTATTTA

                          
      26168 TTTTCTTTTATTTA
          1 TTTTCTTTTATTTA

                
      26182 TTTT
          1 TTTT

      26186 TGTATGCATT


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13    9  0.53
  14    8  0.47

ACGTcount: A:0.10, C:0.06, G:0.00, T:0.84


Consensus pattern (14 bp):   
TTTTCTTTTATTTA

Found at i:27818 original size:2 final size:2

Alignment explanation


    Indices: 27811--27878  Score: 136
    Period size: 2  Copynumber: 34.0  Consensus size: 2

      27801 TTAAGGCTTT

                                                                          
      27811 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA

                                                  
      27853 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

      27879 ATTGCCCACT


Statistics
Matches: 66,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   66  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:36148 original size:3 final size:3

Alignment explanation


    Indices: 36140--36175  Score: 56
    Period size: 3  Copynumber: 12.3  Consensus size: 3

      36130 GTTATATATG

                         *                                   
      36140 TTA TTA TTA TCA -TA TTA TTA TTA TTA TTA TTA TTA T
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T

      36176 CTTTCATATT


Statistics
Matches: 30,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
   2    1  0.03
   3   29  0.97

ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64


Consensus pattern (3 bp):   
TTA

Done.