Reference genome / locus
Amplicons
| Assay | Target group | Forward primer | Reverse primer | Size (bp) | Genomes | Reference |
|---|---|---|---|---|---|---|
| COI | ||||||
| folmer_COI | metazoa | LCO1490: GGTCAACAAATCATAAAGATATTGG | HCO2198: TAAACTTCAGGGTGACCAAAAAATCA | 658 | Folmer et al. 1994 β | |
| geller_COI | metazoa | jgLCO1490: TITCIACIAAYCAYAARGAYATTGG | jgHCO2198: TAIACYTCIGGRTGICCRAARAAYCA | β | Geller et al. 2013 β | |
| leray_COI | metazoa | mlCOIintF: GGWACWGGWTGAACWGTWTAYCCYCC | jgHCO2198: TAIACYTCIGGRTGICCRAARAAYCA | 313 | Leray et al. 2013 β | |
| Leray-XT | metazoa | mlCOIintF-XT: GGWACWRGWTGRACWITITAYCCYCC | jgHCO2198: TAIACYTCIGGRTGICCRAARAAYCA | 313 | Wangensteen et al. 2018 β | |
| lobo_COI | metazoa | LoboF1: KBTCHACAAAYCAYAARGAYATHGG | LoboR1: TAAACYTCWGGRTGWCCRAARAAYCA | β | Lobo et al. 2013 β | |
| fwh1 | invertebrates | fwhF1: YTCHACWAAYCAYAARGAYATYGG | fwhR1: ARTCARTTWCCRAAHCCHCC | 178 | Vamos et al. 2017 β | |
| fwh2 | invertebrates | fwhF2: GGDACWGGWTGAACWGTWTAYCCHCC | fwhR2: GTRATWGCHCCDGCAARWACWGG | 205 | Vamos et al. 2017 β | |
| wilderlab_CI | invertebrates | wilderlab_fwhF2: DACWGGWTGAACWGTWTAYCCHCC | wilderlab_coi_reverse: GTTGTAATAAAATTAAYDGCYCCTARAATDGA | 76 | Wilkinson et al. 2024 β | |
| wilderlab_EA | freshwater mussels | wilderlab_EA_F: TATATAATGTTATTGTAACRGCGC | wilderlab_EA_R: CCCARCATCAAAGGAATCAAYCA | β | Wilkinson et al. 2024 β | |
| wilderlab_XG | bullies | wilderlab_XG_F: GCAATYTCCCAGTATCARACACC | wilderlab_XG_R: GCAGCAAGMACGGGGAG | β | Wilkinson et al. 2024 β | |
| 12S rRNA | ||||||
| MiFish-U | fish | MiFish-U-F: GTCGGTAAAACTCGTGCCAGC | MiFish-U-R: CATAGTGGGGTATCTAATCCCAGTTTG | 163β185 | Miya et al. 2015 β | |
| MiFish-E | elasmobranchs | MiFish-E-F: GTTGGTAAATCTCGTGCCAGC | MiFish-E-R: CATAGTGGGGTATCTAATCCTAGTTTG | 163β185 | Miya et al. 2015 β | |
| MiFish-U/E | fish | MiFish-U/E-F: GTYGGTAAAWCTCGTGCCAGC | MiFish-U/E-R: CATAGTGGGGTATCTAATCCYAGTTTG | 163β185 | Miya et al. 2015 β | |
| batra | amphibians | L3541: ACACCGCCCGTCACCCT | H3596: GTAYACTTACCATGTTACGACTT | β | Valentini et al. 2016 β | |
| teleo | fish | L1848: ACACCGCCCGTCACTCT | H1913: CTTCCGGTACACTTACCATG | 63 | Valentini et al. 2016 β | |
| MiMammal-U | mammals | MiMammal-U-F: GGGTTGGTAAATTTCGTGCCAGC | MiMammal-U-R: CATAGTGGGGTATCTAATCCCAGTTTG | β | Ushio et al. 2017 β | |
| MiMammal-E | elephants | MiMammal-E-F: GGACTGGTCAATTTCGTGCCAGC | MiMammal-E-R: CATAGTGAGGTATCTAATCTCAGTTTG | β | Ushio et al. 2017 β | |
| MiMammal-B | bears | MiMammal-B-F: GGGTTGGTTAATTTCGTGCCAGC | MiMammal-B-R: CATAGTGGGGTATCTAATCCCAGTTTG | β | Ushio et al. 2017 β | |
| MarVer1 | vertebrates | MarVer1F: CGTGCCAGCCACCGCG | MarVer1R: GGGTATCTAATCCYAGTTTG | 205 | Valsecchi et al. 2020 β | |
| wilderlab_RV | vertebrates | 12S-V5-F: TTAGATACCCCACTATGC | 12S-V5-R: TAGAACAGGCTCCTCTAG | 100 | Riaz et al. 2011 β | |
| wilderlab_LG | fish | wilderlab_LG_F: CGGCGTAAAGWGTGGTTAGG | MiFish-U-R: CATAGTGGGGTATCTAATCCCAGTTTG | 113 | Ling et al. 2023 β | |
| wilderlab_LX | fish and sharks | wilderlab_LX_F: GGTAAAWCTCGTGCCAGC | MiFish-U/E-R: CATAGTGGGGTATCTAATCCYAGTTTG | β | Miya et al. 2015 β | |
| wilderlab_LV | vertebrates | wilderlab_LV_F: TCGTGCCAGCCRCCGC | wilderlab_LV_R: CATAGTGGGGTATCTAATCCCAGTTTG | 133 | Orchard and Wilkinson 2023 β | |
| wilderlab_LM | vertebrates | MarVer1F: CGTGCCAGCCACCGCG | MarVer1R: GGGTATCTAATCCYAGTTTG | 202 | Valsecchi et al. 2020 β | |
| 16S rRNA | ||||||
| Vert-16S-eDNA | vertebrates | Vert-16S-eDNA-F1: AGACGAGAAGACCCTDTGGAGCTT | Vert-16S-eDNA-R1: GATCCAACATCGAGGTCGTAA | 250 | Vences et al. 2016 β | |
| MarVer3 | vertebrates | MarVer3F: AGACGAGAAGACCCTRTG | MarVer3R: GGATTGCGCTGTTATCCC | 245 | Valsecchi et al. 2020 β | |
| 16S_FishSyn_Short | fish | 16S_FishSyn_Short_F: GACGAGAAGACCCTGTGGAGC | 16S_FishSyn_Short_R: CCGYGGTCGCCCCAAC | 80 | Nester et al. 2020 β | |
| 16S_FishSyn_Long | fish | 16S_FishSyn_Long_F: GACGAGAAGACCCTDTGGAG | 16S_FishSyn_Long_R: GRATTGCGNTGTTATCCCT | 200 | Nester et al. 2020 β | |
| wilderlab_WV | vertebrates | wilderlab_WV_F: GACGAGAAGACCCTWTGGAGC | wilderlab_WV_R: CCRYGGTCGCCCCAAC | 80 | Wilkinson et al. 2024 β | |
| MiDeca | decapods | MiDeca-F: GGACGATAAGACCCTATAAA | MiDeca-R: ACGCTGTTATCCCTAAAGT | 168 | Komai et al. 2019 β | |
| prie_veneroida | venerid clams | prie_veneroida_F: CSCTGTTATCCCYRCGGTA | prie_veneroida_R: TTDTAAAAGCCGAGAAGACCC | β | PriΓ© et al. 2020 β | |
| wilderlab_HD | decapods | MiDeca-F: GGACGATAAGACCCTATAAA | MiDeca-R: ACGCTGTTATCCCTAAAGT | 168 | Wilkinson et al. 2024 β | |
| wilderlab_WG | venerid clams | wilderlab_WG_F: CSCTGTTATCCCYRCGGTA | wilderlab_WG_R: TTDTAAAAGMCGAGAAGACCC | 130 | Wilkinson et al. 2024 β | |
| wilderlab_ZP | zooplankton | wilderlab_ZP_F: GGACGATAAGACCCTATAAADCTT | wilderlab_ZP_R: CGCTGTTATCCCTAAAGTAAYTT | 120β170 | Wilkinson et al. 2024 β | |
| wilderlab_ZC | decapods | wilderlab_ZC_F: GGACGATAAGACCCTATAAADCTT | wilderlab_ZC_R: CGCTGTTATCCCTAAAGTAAYTT | 115 | Wilkinson et al. 2024 β | |
| wilderlab_DG | decapods | wilderlab_DG_F: TCTTCGGTTGGGGCGAC | wilderlab_DG_R: GGATTGCGCTGTTATCCCT | 95 | Wilkinson et al. 2024 β | |
| Sponge16S | porifera | Sponge16S_377For: NGAGTACTGTRAAGGAAAGYTG | Sponge16S_583Rev: AGATCACTTGGYTTCGGG | β | Alexander et al. 2019 β | |
| wilderlab_UM | bacteria | F785e: GGATTAGATACCCTGGTA | 907R: CCGTCAATTCMTTTRAGTTT | 102 | Wilkinson et al. 2024 β | |
| ND5 | ||||||
| MiFish-tuna | tunas (Thunnus) | MiFish-tuna-F: ATGTCCTTCCTCCTTATCGGCTG | MiFish-tuna-R: TTGCCAGTGGCAGCTACGATC | 180 | Miya et al. 2015 β | |
| Cyt b | ||||||
| wilderlab_YG | vertebrates | wilderlab_YG_F: CBGAYATCTCYACCGCYTTYTC | wilderlab_YG_R: AAAGAAAGATGCGCCRTTRGCATG | β | Wilkinson et al. 2024 β | |
| 18S rRNA | ||||||
| amaral_zettler_18S | protists | 1389F: TTGTACACACCGCCC | 1510R: CCTTCYGCAGGTTCACCTAC | β | Amaral-Zettler et al. 2009 β | |
| wilderlab_BE | eukaryotes | 1380F: CCCTGCCHTTTGTACACAC | 1510R: CCTTCYGCAGGTTCACCTAC | 125 | Wilkinson et al. 2024 β | |
| wilderlab_BU | protists | 1389F: TTGTACACACCGCCC | 1510R: CCTTCYGCAGGTTCACCTAC | 120 | Wilkinson et al. 2024 β | |
| wilderlab_BX | eukaryotes | 18S_1F: GCCAGTAGTCATATGCTTGTCT | 18S_400R: GCCTGCTGCCTTCCTT | 400 | Pochon et al. 2013 β | |
| ITS1 | ||||||
| wilderlab_GV | vascular plants | wilderlab_GV_F: GTGAACCTGCGGAAGGATC | wilderlab_GV_R: GATATCCGTTGCCGAGAGTC | 250 | Wilkinson et al. 2024 β | |
| wilderlab_GF | fungi | Fung02_F: GGAAGTAAAAGTCGTAACAAGG | Fung02_R: CAAGAGATCCGTTGYTGAAAGTK | 124 | Epp et al. 2012 β | |
| ITS2 | ||||||
| CoralTTS2 | scleractinia | SCLER5.8SFor: GARTCTTTGAACGCAAATGGC | SCLER28SRev: GCTTATTAATATGCTTAAATTCAGCG | β | Alexander et al. 2019 β | |
| CoralTTS2_acro | acropora | SCLER5.8SFor: GARTCTTTGAACGCAAATGGC | Coralacro_874Rev: TCGCCGTTACTGAGGGAATC | β | Alexander et al. 2019 β | |
| wilderlab_GD | Scleractinia | SCLER5.8SFor: GARTCTTTGAACGCAAATGGC | SCLER28SRev: GCTTATTAATATGCTTAAATTCAGCG | 375 | Wilkinson et al. 2024 β | |
| trnL | ||||||
| wilderlab_TP | vascular plants | A49425: GGGCAATCCTGAGCCAA | B49466: CCATTGAGTCTCTGCACCTATC | 53 | Taberlet et al. 2007 β | |
| rbcL | ||||||
| wilderlab_MZ | vascular plants | wilderlab_rbclZ1: GTCACCACAAACAGAGACTAAAGCAAGT | rbcL19b: CTTCTTCAGGTGGAACTCCAG | 155 | Wilkinson et al. 2024 β | |
| tufA | ||||||
| wilderlab_TC | Caulerpa | wilderlab_TC_F: CAACTCGACCAGTTGCTACCG | wilderlab_TC_R: ACTGTGGATAATGCAATACCTTTACCTC | 66 | DiBattista et al. 2024 β | |
| 28S rRNA | ||||||
| wilderlab_MC | marine sponges | 28S POR 100 FDG: TTCCCTCAGTAACGGCGAGY | LSU 300RV: CAACTTTCCCTCACGGTACTT | 318 | Martineau et al. 2024 β Redmond et al. 2011 β | |
| wilderlab_MA | Antipatharia and Octocorallia | Anth-28S-eDNA-F: CGTGAAACCGYTRRAAGGG | Anth-28S-eDNA-R: TTGGTCCGTGTTTCAAGACG | 300β500 | McCartin et al. 2024 β | |
| Scler-28S-eDNA | Scleractinia | Scler-28S-eDNA-F: AKGGAAACGAATGGRCTMAG | Scler-28S-eDNA-R: TCCTTGGTCCGTGTTTCAAG | 350β450 | McCartin et al. 2024 β | |
This tool visualises the binding positions of eDNA metabarcoding primer sets on reference mitochondrial, chloroplast, and nuclear rDNA sequences using in-silico PCR. To report issues or suggest primers to add, reach out to @PieterPrvst.
In-silico PCR is performed using fuzzy string matching with a tolerance of up to 4 substitutions per primer, allowing for degenerate bases and minor mismatches. IUPAC ambiguity codes in primer sequences are expanded to character classes before matching. Primer pairs producing an amplicon larger than 3Γ the published insert size are excluded as likely false positives. Amplicon sizes shown are insert sizes (excluding primers), consistent with published values.
Sequences are fetched from NCBI GenBank. Gene annotations are parsed from GenBank feature tables; tRNA features are included for chloroplast genomes only.
| Accession | Species | Common name | Group |
|---|---|---|---|
| NC_001960 | Salmo salar | Atlantic salmon | mito |
| NC_012059 | Tursiops truncatus | Bottlenose dolphin | mito |
| NC_014398 | Carcinus maenas | Green crab | mito |
| NC_006161 | Mytilus edulis | Blue mussel | mito |
| NC_057111.1 | Anodonta nuttalliana | Freshwater mussel | mito |
| NC_009626 | Penaeus vannamei | Pacific shrimp | mito |
| NC_006894 | Axinella corrugata | Sponge | mito |
| NC_022819 | Scyliorhinus canicula | Catshark | mito |
| PV069720.1 | Thunnus orientalis | Pacific bluefin tuna | mito |
| PV383170.1 | Meretrix lamarckii | Venerid clam | mito |
| NC_002081 | Gadus morhua | Atlantic cod | mito |
| NC_001276 | Crassostrea gigas | Pacific oyster | mito |
| NC_020752 | Orcinus orca | Killer whale | mito |
| NC_035345 | Zostera marina | Eelgrass (cp) | plastid |
| NC_039377.1 | Caulerpa lentillifera | Caulerpa (cp) | plastid |
| JF906995.1 | Alexandrium tamarense | Alexandrium (rDNA) | nuclear |
| MT937135.1 | Zostera marina | Eelgrass (rDNA) | nuclear |
| LC544104.1 | Rhizophagus sp. | Rhizophagus (rDNA) | nuclear |
| NW_028146387.1 | Pavona decussata | Pavona (rDNA) | nuclear |
| AB511881.1 | Halichondria okadai | Halichondria (rDNA) | nuclear |
| U00096_rrnB | Escherichia coli | E. coli (rrnB) | bacteria |