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 : 179
Length : 21
Sequence : 5�-AAAGCTTTGAGAGCACTGTGG-3�
3�-GGTGTCACGAGAGTTTCGAAA-5�

Tm (basic) : 62,0 �C
Tm (salt) : 59,4 �C
Tm (NN) : 61,9 �C

GC % : 47,6 %
3�-tail GC % : 57,1 %
dG : -38,8 kcal/mol
3�-tail dG : -11,3 kCal/mol

Lower primer
5'-position : 778
Length : 21
Sequence : 5�-CACGATATGCAGCAGGCTCTA-3�
3�-ATCTCGGACGACGTATAGCAC-5�

Tm (basic) : 64,0 �C
Tm (salt) : 61,3 �C
Tm (NN) : 63,7 �C

GC % : 52,4 %
3�-tail GC % : 57,1 %
dG : -39,7 kcal/mol
3�-tail dG : -12,0 kCal/mol

Primer pair properties

Length difference : 0
Tm (basic) difference: 2,0 �C
Tm (salt) difference : 2,0 �C
Tm (NN) difference : 1,8 �C
GC % difference : 4,8 %

PCR product
Position : 179 - 778
Length : 600 bp
GC% : 51,3 %

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

Upper primer self annealing:

5'-AAAGCTTTGAGAGCACTGTGG-3'
||||||||
3'-GGTGTCACGAGAGTTTCGAAA-5'
 dG: -10,90 kcal/mol

5'-AAAGCTTTGAGAGCACTGTGG-3'
: ||| : : ::: :
3'-GGTGTCACGAGAGTTTCGAAA-5'
dG: -1,53 kcal/mol

5'-AAAGCTTTGAGAGCACTGTGG-3'
||| :::
3'-GGTGTCACGAGAGTTTCGAAA-5'
dG: -0,08 kcal/mol

Upper primer loops:

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

Lower primer self annealing:

5'-CACGATATGCAGCAGGCTCTA-3'
: |||| :
3'-ATCTCGGACGACGTATAGCAC-5'
dG: -3,84 kcal/mol

5'-CACGATATGCAGCAGGCTCTA-3'
: ::: ||| :
3'-ATCTCGGACGACGTATAGCAC-5'
dG: -1,88 kcal/mol

5'-CACGATATGCAGCAGGCTCTA-3'
: ::: ||| :
3'-ATCTCGGACGACGTATAGCAC-5'
dG: -1,53 kcal/mol

5'-CACGATATGCAGCAGGCTCTA-3'
: |||| :
3'-ATCTCGGACGACGTATAGCAC-5'
dG: -0,70 kcal/mol

Lower primer loops:

None!

Upper primer - Lower primer annealing:

5'-AAAGCTTTGAGAGCACTGTGG-3'
||||| ::
3'-ATCTCGGACGACGTATAGCAC-5'
dG: -4,71 kcal/mol

5'-AAAGCTTTGAGAGCACTGTGG-3'
:: ||| :
3'-ATCTCGGACGACGTATAGCAC-5'
dG: -1,88 kcal/mol

5'-AAAGCTTTGAGAGCACTGTGG-3'
|||
3'-ATCTCGGACGACGTATAGCAC-5'
dG: -1,53 kcal/mol

5'-AAAGCTTTGAGAGCACTGTGG-3'
 : ||| : : : :::
3'-ATCTCGGACGACGTATAGCAC-5'
dG: -1,53 kcal/mol

5'-AAAGCTTTGAGAGCACTGTGG-3'
||| :
3'-ATCTCGGACGACGTATAGCAC-5'
dG: -0,34 kcal/mol

5'-AAAGCTTTGAGAGCACTGTGG-3'
: ::: |||
3'-ATCTCGGACGACGTATAGCAC-5'
dG: -0,34 kcal/mol