PRIMER Input Form
A string to identify your output.
E.g. 50,2 requires primers to surround the 2 bases at positions 50 and 51. Or mark the source sequence with [ and ]: e.g. ...ATCT[CCCC]TCAT.. means that primers must flank the central CCCC.
E.g. 401,7 68,3 forbids selection of primers in the 7 bases starting at 401 and the 3 bases at 68. Or mark the source sequence with < and >: e.g. ...ATCT<CCCC>TCAT.. forbids primers in the central CCCC.
General Primer Picking Conditions
Other Per-Sequence Inputs
Objective Function Penalty Weights for Primers
Objective Function Penalty Weights for Primer
|Hyb Oligo Excluded Region:|
|Hyb Oligo Size:||Min||Opt||Max|
|Hyb Oligo Tm:||Min||Opt||Max|
|Hyb Oligo GC%||Min:||Opt:||Max:|
|Hyb Oligo Self Complementarity:||Hyb Oligo Max 3' Self Complementarity:|
|Max #Ns:||Hyb Oligo Max Poly-X:|
|Hyb Oligo Mishyb Library:||Hyb Oligo Max Mishyb:|
|Hyb Oligo Min Sequence Quality:|
|Hyb Oligo Salt Concentration:||Hyb Oligo DNA Concentration:|
Objective Function Penalty Weights for Hyb Oligos (Internal Oligos)
Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
Redistributions must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. Redistributions of source code must also reproduce this information in the source code itself.
If the program is modified, redistributions must include a notice (in the same places as above) indicating that the redistributed program is not identical to the version distributed by Whitehead Institute.
All advertising materials mentioning features or use of this software must display the following acknowledgment:
This product includes software developed by the Whitehead Institute for Biomedical Research.
The name of the Whitehead Institute may not be used to endorse or promote products derived from this software without specific prior written permission.
Steve Rozen, Helen J. Skaletsky (1998) Primer3. Code available at http://www-genome.wi.mit.edu/genome_software/other/primer3.html.
We gratefully acknowledge the support of Digital Equipment Corporation, which provided the Alphas which were used for much of the development of Primer3, and of Centerline Software, Inc., whose TestCenter memory-error, -leak, and test-coverage checker we use regularly to discover and correct otherwise latent errors in Primer3.