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Sequence Manipulation Suite:

Primer Map

Primer Map accepts a DNA sequence and returns a textual map showing the annealing positions of PCR primers. Restriction endonuclease cut sites, and the protein translations of the DNA sequence can also be shown. Use this program to produce a useful reference figure, particularly when you have designed a large number of primers for a particular template. Primer Map supports the entire IUPAC alphabet and several genetic codes.

Paste a raw sequence or one or more FASTA sequences into the text area below. Input limit is 200,000,000 characters.

Below are Microsynth's standard primers that are available free of charge for Sanger sequencing. The round brackets surround the name of the primer, and the sequence is written in the 5' to 3' direction.

(1492r) GGTTACCTTGTTACGACTT,
(27f) AGAGTTTGATCMTGGCTCAG,
(3-AOX1) GCAAATGGCATTCTGACATCC,
(518r) GTATTACCGCGGCTGCTGG,
(5-AOX1) GACTGGTTCCAATTGACAAGC,
(785f) GGATTAGATACCCTGGTA,
(-96gLLL) CCTCATAGTTAGCGTAAC,
(AmpStart) AAAACAGGAAGGCAAAATGC,
(AmpStop) TCAGGCAACTATGGATGAAC,
(BGH-rev) TAGAAGGCACAGTCGAGG,
(C-CMV-24) TAGGACAAGGCTGGTGGGCAC,
(CEP4-for) AGCTCGTTTAGTGAACCG,
(CMV-for) CGCAAATGGGCGGTAGGCGTG,
(CMV-rev) AGTAGGAAAGTCCCGTAAGG,
(EBV-rev) GTGGTTTGTCCAAACTCATC,
(EF1alpha) TCAAGCCTCAGACAGTGGTTC,
(EGFP-C1-anti) GGTTCAGGGGGAGGTGTG,
(EGFP-C-F-31) CAAAGACCCCAACGAGAAG,
(EGFP-C-for) GTCCTGCTGGAGTTCGTG,
(EGFP-C-Rev) AGCTGCAATAAACAAGTT,
(EGFP-for) CAACGAGAAGCGCGATC,
(EGFP-N-for) CAACGGGACTTTCCAAAATG,
(EGFP-N-R+33) CGGACACGCTGAACTTGTG,
(EGFP-N-rev) GCTTGCCGTAGGTGGCATC,
(FastBac-for) TACTGTTTTCGTAACAGTTTTG,
(FastBac-rev) CATTTTATGTTTCAGGTTCAGG,
(GAL4-AD) TACCACTACAATGGATG,
(GAL4-BD) TCATCGGAAGAGAGTAG,
(GEX3-rev) GCTTACAGACAAGCTGTGAC,
(GEX3-rev-25) GAGCTGCATGTGTCAGAGG,
(GEX5-for) CCAGCAAGTATATAGCATGG,
(GL2) CTTTATGTTTTTGGCGTCTTCC,
(GL3) CCGGGCCTTTCTTTATGTTTTTG,
(HCO-2198) TAAACTTCAGGGTGACCAAAAAATCA,
(hU6-f) GAGGGCCTATTTCCCATGATT,
(IRES-for) TAGGCGTGTACGGTGGG,
(IRES-R-359) ACCCCAACAGCTGGCCCTCG,
(IRES-rev) TATAGACAAACGCACACCG,
(ITS1) TCCGTAGGTGAACCTGCGG,
(ITS4) TCCTCCGCTTATTGATATGC,
(LacOp-for) CGGATAACAATTTCACACAG,
(LCO-1490) GGTCAACAAATCATAAAGATATTGG,
(M13) TGTAAAACGACGGCCAG,
(M13-40) GTTTTCCCAGTCACGAC,
(M13r) CAGGAAACAGCTATGAC,
(malE) GGTCGTCAGACTGTCGATG,
(pBABE-5-fwd) CTTTATCCAGCCCTCAC,
(pBAD-F+50) TTATCGCAACTCTCTACTGT,
(pBAD-for) ATGCCATAGCATTTTTATCC,
(pBAD-rev) GATTTAATCTGTATCAGG,
(pCIneo-for) CCACTCCCAGTTCAATTACAG,
(pCI-rev) GCAATAGCATCACAAATTTCAC,
(pDONR-3) GCAATGTAACATCAGAGAT,
(pDONR-5) TAACGCTAGCATGGATCTC,
(PEN1-737R) TCCAGCTCGACCAGGAT,
(pENTattL1-for) TCGCGTTAACGCTAGCATGG,
(pENTattL2-rev) ACATCAGAGATTTTGAGACACG,
(pET-down) GATTATGCGGCCGTGTAC,
(pETG-for) CTGGCAAGCCACGTTTGG,
(pET-T7side) GGGAATTGTGAGCGGATAAC,
(pET-up) ATGCGTCCGGCGTAG,
(pGMP-rev) GATATAGTTCCTCCTTTCAGC,
(pHEN-rev) AGATCCTCTTCTGAGATG,
(pJET1.2-for) CGACTCACTATAGGGAG,
(pJET1.2-rev) ATCGATTTTCCATGGCAG,
(pJET1-for) CTGAACACCATATCCATCC,
(pJET1-rev) GCAGCTGAGAATATTGTAG,
(pKK223-3-for) GGCGTTTCACTTCTGAGTTC,
(pKK223-3-rev) CGGTTCTGGCAAATATTCTG,
(PolyT-A) TTTTTTTTTTTTTTTTTTTTA,
(pTRE-for) TAAGCAGAGCTCGTTTAGTG,
(pUCM13-52) GCTGCAAGGCGATTAAGTTG,
(pUCM13-rev-157) TGCTTCCGGCTCGTATGTTG,
(Puro-rev) TGTACTCGGTCATGGTAAGC,
(Qe30-for) CTTTCGTCTTCACCTCGAG,
(Qe30-rev) CCAAGCTAGCTTGGATTCTC,
(QE-for) GTATCACGAGGCCCTTTCG,
(QE-rev) GTTCTGAGGTCATTACTGG,
(RV3) CTAGCAAAATAGGCTGTCC,
(RV4) GACGATAGTCATGCCCCGC,
(Short-T7) TAATACGACTCACTATAGG,
(SK) CTAGAACTAGTGGATCC,
(SP6) ATTTAGGTGACACTATAG,
(SUMO-5) CCTTAAGATTCTTGTACGACG,
(SV40-for) GCCCCTAACTCCGCCCATCC,
(SV40-pA-rev) CCTCTACAAATGTGGTATGG,
(T3) TTAACCCTCACTAAAGG,
(T7) TAATACGACTCACTATAGGG,
(T7probis) TCCCGCGAAATTAATACG,
(T7terbis) AACCCCTCAAGACCCG,
(T7term) TGCTAGTTATTGCTCAGCGG,
(TET-CMV-for) CCTCCATAGAAGACACC,
(U6) GGGCAGGAAGAGGGCCTAT,
(WHV-5R) AGCAGCGTATCCACATAGCG,
(XL39-rev) TAGGACAAGGCTGGTGG

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Sun 14 Jun 00:36:59 2020