Multiple primer analyzer

Instruments

Consumables

For analyzing and comparing multiple primer sequences simultaneously.

Write or paste your primer sequences to the input field (upper window). The analyzer accepts text and table format (can be copied from an Excel file, for example). Note: This analyzer requires at least 2 primer sequences in the input field. For single primers (determination of primer Tm) you can choose the Tm calculator for PCR.

A name is required for each primer (eg. Seq1 agtcagtcagtcagtcagtc).

The name and sequence string can be separated with either space or tab, as long as the style is the same for all the primers

Degenerate primer sequences are also accepted

NOTE: If the PCR primer contains desired mismatches, e.g. for creating a mutation or a restriction site, make sure to calculate the Tm only for the correctly matched sequence.

The results will appear instantly in the output fields (lower windows), and update automatically if you make changes to the sequences. The analyzer will give the following results:

Tm (°C)*

CG content (%)

Length of the primers (nt)

Number of individual bases (A, T, C and G)

Extinction coefficient (l/(mol·cm))

Molecular weight (g/mol)

Amount / OD unit (nmol/OD₂₆₀)

Mass (µg/OD₂₆₀)

Primer-dimer estimation**

The results can be copied and pasted to other programs (Word, Excel, etc.). The analyzer uses point as a decimal separator (not a comma). This is significant when copying results to Excel.

Tm calculator for single primers Thermo Scientific DNA polymerases and cloning Important instructions on annealing temperature What do you think about this calculator?

This application requires
Java Virtual Machine
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*	The calculated Tm for a given primer can vary significantly between different calculation methods. This Tm calculator uses a modified nearest-neighbor method based on the method described by Breslauer et al., Proc.Natl.Acad.Sci 83, 3746-50 (1986). Finnzymes uses this method for optimizing PCR protocols.
**	The analyzer reports possible primer-dimers based on the detection parameters given below the sequence input window. The dimer information is intended to be used as a preliminary guide when selecting suitable primer combinations. It is not conclusive data. In the actual amplification reaction the primer-dimer formation can vary depending on the PCR conditions.