OligoCalculator

OligoCalculator supports both single-sequence analysis and Batch FASTA analysis.

Features

• Molecular weight calculation
• Extinction coefficient calculation
• GC content calculation
• Tm calculation with concentration correction
• Reverse and complement sequence output
• Support for modified oligo syntax

Usage

Single

• Enter one sequence in the 5' -> 3' direction
• Insert 5' / internal / 3' modifications with the existing controls
• The page calculates complement, reverse, MW, GC, Tm, and extinction

Batch FASTA

• Each record must start with >
• Multiple FASTA records can be pasted in one input box
• Multi-line sequences are merged automatically
• The same modification syntax from Single mode is supported

Example:

>seq_1
ATCGATCGATCG
>seq_2
/5bio/ATCG*/rA//3bhq1/

Batch mode validates each record and then calculates results record by record. An invalid record will not block valid records in the same batch.

Tm Options

Tm Options controls the shared calculation conditions.

• Oligo Conc.: oligo concentration
• Na+ Conc.: monovalent ion concentration
• Mg2+ Conc.: divalent ion concentration
• dNTPs Conc.: dNTP concentration
• I don't know these concentrations: use the simplified estimation mode

Recommended usage:

• If your buffer conditions are known, fill in the concentrations for a more realistic Tm
• If the conditions are unknown, the simplified option is useful for a quick estimate