Primers analysis and compatibility

Paste or type the primer or primers sequence(s) at any TAB Editors, the program will immediately show primer characteristics:
length in bases, melting temperature, CG% content, molecular weight, the extinction coefficient (e260), nmol per 1 OD, the mass - µg per 1 OD, linguistic complexity (%) and primer quality (%);
minimal and maximal optimal annealing temperature for unknown PCR products. Tm calculation based on chosen the formula from “Primers Design Options”.

If the primer is self-complementary, the program will show a picture of where this self-complementarity happens. All primers analysed for self-dimers formation and by your wishes primers can analysed with each other for detection cross dimers formation. A self-priming ability will also be detected and shown by the program. When the two primers are forming such a dimer, the program will also show it.

Web Java version for on-line primer test with Tm calculation for normal and degenerated nucleotide combinations based on the nearest neighbour thermodynamic parameters and comprehensive dilution protocol available at WebTols.
Comprehensive analysis of the list of primers with prediction of the oligonucleotides properties, self and cross dimers detection and temperature of annealing calculation is available at jPCR Web Tools.


Primers list or PCR sets analyses

Tables format description for PCR sets analysis

You can directly import the table from text file or from the clipboard via copy and paste operations from Microsoft Word or Excel sheet, or primer’s list from FastPCR's", or the table with TAB or whitespace separators.
The program reads columns, where the first column is for the name of the primer and the second column is its sequence, as well as for PCR sets of more than one primer, all sequences from subsequent columns will receive the same name:

"Within primer pair (set)" - for cross-dimer detection of associated oligos from a single group (assays with multiple oligos). This is the situation where a group of assays in one raw can be analyzed separately from the other groups (raw). The number of oligos in a raw can be any and does not depend on the other groups located in the other raw.

"Cross-dimer detection", the analysis is performed for all oligos in the list. Except if "Within primer pair (set)" is selected, as the task has priority here.

"All PCR sets against all other" is for analyzing all sets (all raws) against each other. The software identifies the individual sets (with an individual number of oligos) and analyses them for "Cross-dimer detection" against each other.

For detection of only the most likely 3'-end dimers, it is better to use check - "Detection only 3'-end dimers". But other likely and dangerous dimers do not belong in this category, like equal length DNA duplexes. In this case, "Detection only strong dimers" must be selected.

The oligos must be in the same format. If you are using TAB format (or splitting oligos via empty space) as a table in Excel, or in FASTA format. If oligos are TAB-formatted as a table in Excel, in this case the number of columns can be any number, and there can be a different number of columns for each group (raw) of assays with multiple oligos.

"All primers against selected": you can select one or more oligos from the list to analyse them with all others.


Single or list of primers is evaluate by FastPCR for calculation Tm (default or other formula) for normal and degenerated nucleotide combinations, CG content, the extinction coefficient, nmol per OD, the mass - µg per OD, the molecular weight, linguistic complexity (%) and primer quality (%).
All primers analysed for self-dimers formation and by your wishes primers can analysed with each other for detection cross dimers formation.