Oligo Explorer - 1.1.

2 11/04/2013

Sequence

Filename : Consenso110413.txt
Length : 843 bp
Unresolved : 0 bp
GC % : 50,9 %

Upper primer
5'-position : 178
Length : 22
Sequence : 5�-AAAAGCTTTGAGAGCACTGTGG-3�
3�-GGTGTCACGAGAGTTTCGAAAA-5�

Tm (basic) : 64,0 �C
Tm (salt) : 60,3 �C
Tm (NN) : 63,1 �C

GC % : 45,5 %
3�-tail GC % : 57,1 %
dG : -40,8 kcal/mol
3�-tail dG : -11,3 kCal/mol

Lower primer
5'-position : 767
Length : 19
Sequence : 5�-GCAGGCTCTACATTTCGGG-3�
3�-GGGCTTTACATCTCGGACG-5�

Tm (basic) : 60,0 �C
Tm (salt) : 59,5 �C
Tm (NN) : 63,0 �C

GC % : 57,9 %
3�-tail GC % : 57,1 %
dG : -38,7 kcal/mol
3�-tail dG : -15,2 kCal/mol

Primer pair properties

Length difference : 3
Tm (basic) difference: 4,0 �C
Tm (salt) difference : 0,8 �C
Tm (NN) difference : 0,0 �C
GC % difference : 12,4 %

PCR product
Position : 178 - 767
Length : 590 bp
GC% : 51,4 %

Tm(product) : 79,8 �C
Tm(annealing) : 59,9 �C

Upper primer self annealing:

5'-AAAAGCTTTGAGAGCACTGTGG-3'
||||||||
3'-GGTGTCACGAGAGTTTCGAAAA-5'
 dG: -10,90 kcal/mol

5'-AAAAGCTTTGAGAGCACTGTGG-3'
: ||| : : ::: :
3'-GGTGTCACGAGAGTTTCGAAAA-5'
dG: -1,53 kcal/mol

5'-AAAAGCTTTGAGAGCACTGTGG-3'
||| :::
3'-GGTGTCACGAGAGTTTCGAAAA-5'
dG: -0,68 kcal/mol

5'-AAAAGCTTTGAGAGCACTGTGG-3'
||| :::
3'-GGTGTCACGAGAGTTTCGAAAA-5'
dG: -0,08 kcal/mol

Upper primer loops:

5'-AAAAGCTTT
: ||| G
3'-GGTGTCACGAGA
dG: -1,41 kcal/mol

Lower primer self annealing:

None!

Lower primer loops:

None!

Upper primer - Lower primer annealing:

5'-AAAAGCTTTGAGAGCACTGTGG-3'
: |||||
3'-GGGCTTTACATCTCGGACG-5'
dG: -4,71 kcal/mol

5'-AAAAGCTTTGAGAGCACTGTGG-3'
: ||| :
3'-GGGCTTTACATCTCGGACG-5'
dG: -1,53 kcal/mol

5'-AAAAGCTTTGAGAGCACTGTGG-3'
||| :
3'-GGGCTTTACATCTCGGACG-5'
dG: -0,68 kcal/mol

5'-AAAAGCTTTGAGAGCACTGTGG-3'
||| : : ::
3'-GGGCTTTACATCTCGGACG-5'
dG: -0,68 kcal/mol

5'-AAAAGCTTTGAGAGCACTGTGG-3'
: :: |||
3'-GGGCTTTACATCTCGGACG-5'
dG: -0,34 kcal/mol

5'-AAAAGCTTTGAGAGCACTGTGG-3'
: : ||| :
3'-GGGCTTTACATCTCGGACG-5'
dG: -0,08 kcal/mol
 5'-AAAAGCTTTGAGAGCACTGTGG-3'
:: : ||| :
3'-GGGCTTTACATCTCGGACG-5'
dG: 0,04 kcal/mol