Primer3web  version 4.1.0  -   Pick primers from a DNA sequence. disclaimer code
cautions
Basic Primer Design Settings

Select the Task for primer selection

Paste source sequence below (5'->3', string of ACGTNacgtn -- other letters treated as N -- numbers and blanks ignored). FASTA format ok. Please N-out undesirable sequence (vector, ALUs, LINEs, etc.) or use a Mispriming Library (repeat library)

Pick left primer, or use left primer below Pick hybridization probe (internal oligo), or use oligo below Pick right primer, or use right primer below (5' to 3' on opposite strand)
Sequence Id A string to identify your output.
Targets 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.
Overlap Junction List E.g. 27 requires one primer to overlap the junction between positions 27 and 28. Or mark the source sequence with -: e.g. ...ATCTAC-TGTCAT.. means that primers must overlap the junction between the C and T.
Excluded Regions 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.
Pair OK Region List See manual for help.
Included Region E.g. 20,400: only pick primers in the 400 base region starting at position 20. Or use { and } in the source sequence to mark the beginning and end of the included region: e.g. in ATC{TTC...TCT}AT the included region is TTC...TCT.
Start Codon Position
Internal Oligo Excluded Region
Force Left Primer Start Force Right Primer Start
Force Left Primer End Force Right Primer End

Sequence Quality

Min Sequence Quality Min End Sequence Quality Sequence Quality Range Min Sequence Quality Range Max

Copyright Notice and Disclaimer

Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006,2007,2008,2009,2010,2011,2012,2013,2017
Whitehead Institute for Biomedical Research, Steve Rozen, Andreas Untergasser, Maido Remm, Triinu Koressaar and Helen Skaletsky.
All rights reserved.

    This file is part of the primer3web suite.

    The primer3 suite and libraries are free software;
    you can redistribute them and/or modify them under the terms
    of the GNU General Public License as published by the Free
    Software Foundation; either version 2 of the License, or (at
    your option) any later version.

    This software is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with this software (file gpl-2.0.txt in the source
    distribution); if not, write to the Free Software
    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
OWNERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Citing Primer3

We request but do not require that use of this software be cited in publications as

* Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M and Rozen SG.
Primer3--new capabilities and interfaces.
Nucleic Acids Res. 2012 Aug 1;40(15):e115.

* Koressaar T and Remm M.
Enhancements and modifications of primer design program Primer3.
Bioinformatics 23(10):1289-1291.

* Koressaar T, Lepamets M, Kaplinski L, Raime K, Andreson R and Remm M.
Primer3_masker: integrating masking of template sequence with primer design software.
Bioinformatics 2018;34(11):1937-1938.

The papers are available at:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3424584/
https://www.ncbi.nlm.nih.gov/pubmed/17379693
https://www.ncbi.nlm.nih.gov/pubmed/29360956

Source code available at https://github.com/primer3-org.

Acknowledgments

Initial development of Primer3 was funded by Howard Hughes Medical Institute and by the National Institutes of Health, National Human Genome Research Institute under grants R01-HG00257 (to David C. Page) and P50-HG00098 (to Eric S. Lander). Ongoing development is partly funded by institutional grant IUT34-11 from the Estonian Ministry of Education and Research and by Centre of Excellence in Genomics and Translational Medicine at University of Tartu (funding from EU ERDF).

Primer3 was a complete re-implementation of an earlier program: Primer 0.5 (Steve Lincoln, Mark Daly, and Eric S. Lander).


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