Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01008184.1 Hibiscus syriacus cultivar Beakdansim tig00110785_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: 1549336
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


File 8 of 8

Found at i:1548214 original size:19 final size:19

Alignment explanation


    Indices: 1548192--1548310  Score: 123
    Period size: 19  Copynumber: 6.8  Consensus size: 19

    1548182 GAAACCAAAA

                *              
    1548192 TCGCATTGCGATTTTCATT
          1 TCGCGTTGCGATTTTCATT

                               
    1548211 TCGCGTTGCGA--TTC-TT
          1 TCGCGTTGCGATTTTCATT

                               
    1548227 T--CGTTGCGATTTTCATT
          1 TCGCGTTGCGATTTTCATT

                *             *
    1548244 TCGCATTGCGA--TTC-TG
          1 TCGCGTTGCGATTTTCATT

                               
    1548260 T--CGTTGCGATTTTCATT
          1 TCGCGTTGCGATTTTCATT

                           **  
    1548277 TCGCGTTGCGATTTTGGTT
          1 TCGCGTTGCGATTTTCATT

                           
    1548296 TCGCGTTGCGATTTT
          1 TCGCGTTGCGATTTT

    1548311 AGTTTCGTGT


Statistics
Matches: 83,  Mismatches: 7, Indels: 20
        0.75            0.06        0.18

Matches are distributed among these distances:
  14   15  0.18
  16   11  0.13
  17   11  0.13
  19   46  0.55

ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47


Consensus pattern (19 bp):   
TCGCGTTGCGATTTTCATT

Found at i:1548233 original size:14 final size:14

Alignment explanation


    Indices: 1548214--1548270  Score: 60
    Period size: 14  Copynumber: 3.7  Consensus size: 14

    1548204 TTTCATTTCG

                          
    1548214 CGTTGCGATTCTTT
          1 CGTTGCGATTCTTT

                             
    1548228 CGTTGCGATTTTCATTT
          1 CGTTGCGA--TTC-TTT

                          * 
    1548245 CGCATTGCGATTCTGT
          1 CG--TTGCGATTCTTT

                      
    1548261 CGTTGCGATT
          1 CGTTGCGATT

    1548271 TTCATTTCGC


Statistics
Matches: 37,  Mismatches: 1, Indels: 10
        0.77            0.02        0.21

Matches are distributed among these distances:
  14   16  0.43
  16    7  0.19
  17    8  0.22
  19    6  0.16

ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46


Consensus pattern (14 bp):   
CGTTGCGATTCTTT

Found at i:1548239 original size:33 final size:33

Alignment explanation


    Indices: 1548197--1548289  Score: 168
    Period size: 33  Copynumber: 2.8  Consensus size: 33

    1548187 CAAAATCGCA

                                         *   
    1548197 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
          1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG

                              *              
    1548230 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
          1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG

                                       
    1548263 TTGCGATTTTCATTTCGCGTTGCGATT
          1 TTGCGATTTTCATTTCGCGTTGCGATT

    1548290 TTGGTTTCGC


Statistics
Matches: 57,  Mismatches: 3, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  33   57  1.00

ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47


Consensus pattern (33 bp):   
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG

Found at i:1548315 original size:19 final size:19

Alignment explanation


    Indices: 1548261--1548317  Score: 89
    Period size: 19  Copynumber: 3.0  Consensus size: 19

    1548251 GCGATTCTGT

                                
    1548261 CGTTGCGATTTTCA-TTTCG
          1 CGTTGCGATTTT-AGTTTCG

                        *      
    1548280 CGTTGCGATTTTGGTTTCG
          1 CGTTGCGATTTTAGTTTCG

                               
    1548299 CGTTGCGATTTTAGTTTCG
          1 CGTTGCGATTTTAGTTTCG

    1548318 TGTGCGAAAG


Statistics
Matches: 35,  Mismatches: 2, Indels: 2
        0.90            0.05        0.05

Matches are distributed among these distances:
  19   35  1.00

ACGTcount: A:0.09, C:0.18, G:0.26, T:0.47


Consensus pattern (19 bp):   
CGTTGCGATTTTAGTTTCG

Done.