Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01008255.1 Hibiscus syriacus cultivar Beakdansim tig00110908_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: 300600
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33


File 3 of 3

Found at i:300449 original size:3 final size:3

Alignment explanation


    Indices: 300428--300578  Score: 166
    Period size: 3  Copynumber: 49.7  Consensus size: 3

     300418 TTATTTATTA

                                                 *                      
     300428 AAT AAT AAAT ATAT AAAT AAT ATAT AAT ATT AAT AAT AAT AAT AAAT
          1 AAT AAT -AAT A-AT -AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT

                                                                      * 
     300475 AAT AAT -AT AAT AAT AAT ATAT AAT AAT AAT AAT AAT AAT -AT ACT
          1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT

                                *        *           *               *     
     300519 AAT AAT AAT AAT -AT TAT AAT ATT AAT AAT -GT AAT AAT AAT ATT AAT
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT

                              
     300565 AAT AAT AAT AAT AA
          1 AAT AAT AAT AAT AA

     300579 AATGGAAAAA


Statistics
Matches: 127,  Mismatches: 11, Indels: 20
        0.80            0.07        0.13

Matches are distributed among these distances:
   2    7  0.06
   3  103  0.81
   4   16  0.13
   5    1  0.01

ACGTcount: A:0.62, C:0.01, G:0.01, T:0.37


Consensus pattern (3 bp):   
AAT

Found at i:300491 original size:43 final size:42

Alignment explanation


    Indices: 300426--300577  Score: 186
    Period size: 43  Copynumber: 3.5  Consensus size: 42

     300416 AATTATTTAT

                                                        
     300426 TAAATAATAAATATATAAATAATATATAATATTAATAATAATAA
          1 TAAATAATAAATA-AT-AATAATATATAATATTAATAATAATAA

                                          *            
     300470 TAAATAATAATATAATAATAATATATAATAATAATAATAATAA
          1 TAAATAATAA-ATAATAATAATATATAATATTAATAATAATAA

                  *                                      
     300513 T--ATACT-AATAATAATAATATTATAATATTAATAATGTAATAA
          1 TAAATAATAAATAATAATAATA-TATAATATTAATAA--TAATAA

                                    
     300555 TAATATTAAT-AATAATAATAATA
          1 TAA-A-TAATAAATAATAATAATA

     300578 AAATGGAAAA


Statistics
Matches: 96,  Mismatches: 4, Indels: 14
        0.84            0.04        0.12

Matches are distributed among these distances:
  39   12  0.12
  40   14  0.15
  41    4  0.04
  42    7  0.07
  43   27  0.28
  44   12  0.12
  45    4  0.04
  46   16  0.17

ACGTcount: A:0.61, C:0.01, G:0.01, T:0.38


Consensus pattern (42 bp):   
TAAATAATAAATAATAATAATATATAATATTAATAATAATAA

Done.