CRISPOR (
citation
) is a program that helps design, evaluate and clone guide sequences for the CRISPR/Cas9 system.
CRISPOR Manual
June 2020: saCas9 primer fixes, Snapgene/Geneious improvements, better export for Cpf1
Full list of changes
Step 1
Planning a lentiviral gene knockout screen? Use
CRISPOR Batch
Sequence name (optional):
Enter a single genomic sequence, < 2000 bp, typically an exon
Clear Box
-
Reset to default
cttcctttgtccccaatctgggcgcgcgccggcgccccctggcggcctaaggactcggcgcgccggaagtggccagggcgggggcgacctcggctcacagcgcgcccggctattctcgcagctcaccatgGATGATGATATCGCCGCGCTCGTCGTCGACAACGGCTCCGGCATGTGCAAGGCCGGCTTCGCGGGCGACGATGCCCCCCGGGCCGTCTTCCCCTCCATCGTGGGGCGCC
Text case is preserved, e.g. you can mark ATGs with lowercase.
Instead of a sequence, you can paste a chromosome range, e.g. chr1:11,130,540-11,130,751
Step 2
Select a genome
-- No Genome: no specificity, only cleavage efficiency scores (max. len 25kbp)
Acanthamoeba castellanii str. Neff - Acanthamoeba castellanii Neff strain - NCBI GCF_000313135.1 (Acastellanii.strNEFF v1)
Actinobacillus pleuropneumoniae KL16 - porcine pleuropneumonia KL16 - Genbank CP022715
Actinobacillus pleuropneumoniae serovar 5b str. L20 - Actinobacillus pleuropneumoniae L20 - NCBI GCA_000015885.1 (ASM1588v1)
Acyrthosiphon pisum - Acyrthosiphon pisum - EnsemblMetazoa 76 (GCA_000142985.2)
Adineta vaga - Bdelloid Rotifers - Genoscope V2.0
Advenella kashmirensis W13003 - Advenella kashmirensis W13003 - NCBI GCF_000506985.1 (Advkasv1.0)
Aedes aegypti - Yellow fever mosquito - EnsemblMetazoa 76 (AaegL3)
Aedes aegypti - yellow fever mosquito - NCBI GCF_002204515.2 (AaegL5.0)
Aedes albopictus - forest day mosquito - NCBI GCF_001876365.2 (canu_80X_arrow2.2)
Agrobacterium sp. ATCC 31749 - Agrobacterium sp. ATCC 31749 - NCBI GCF_000214615.1 (Agro31749_1.0)
Amphimedon queenslandica - Amphimedon queenslandica - EnsemblMetazoa 76 (Aqu1)
Anaplasma phagocytophilum str. HGE1 - Anaplasma phagocytophilum str. HGE1 - NCBI GCA_000478425.1 (ASM47842v1)
Anas platyrhynchos - Mallard - Ensembl 76 (BGI_duck_1.0)
Anopheles arabiensis - A. arabiensis - VectorBase D1
Anopheles darlingi - Anopheles darlingi - EnsemblMetazoa 76 (AdarC3)
Anopheles gambiae - African malaria mosquito - EnsemblMetazoa 76 (AgamP4)
Apis mellifera - Apis mellifera - EnsemblMetazoa 76 (GCA_000002195.1)
Aquilegia caerulea - Aquilegia caerulea - Phytozome V9, Dec 2012
Arabidopsis lyrata - Arabidopsis lyrata - Phytozome V9, Dec 2012
Arabidopsis thaliana - Arabidopsis thaliana - Phytozome V9, Dec 2012
Arabidopsis thaliana - Thale-cress - EnsemblPlants 76 (TAIR10)
Artemisia annua - sweet Annie - NCBI GCA_003112345.1 (ASM311234v1)
Aspergillus carbonarius ITEM 5010 - Aspergillus carbonarius ITEM 5010 - NCBI GCA_001990825.1 (Aspca3)
Aspergillus niger - A. niger - Phytozome 12, ATCC1015, V4.0
Astyanax mexicanus - Blind cave fish - Ensembl 76 (AstMex102)
Atta cephalotes - Atta cephalotes - EnsemblMetazoa 76 (GCA_000143395.2)
Bacillus RZ2MS9 - Bacillus sp. B14905 - Genbank NZ_AAXV01000001.1
Bacillus amyloliquefaciens DSM 7 - Bacillus amyloliquefaciens ATCC 23350 - NCBI GCF_000196735.1 (ASM19673v1)
Bacillus cereus NC7401 - Bacillus cereus NC7401 - NCBI GCF_000283675.1 (ASM28367v1)
Bacillus phage PfNC7401 - Bacillus phage PfNC7401 - NCBI GCA_002611025.1 (ASM261102v1)
Bacillus subtilis subsp. subtilis str. 168 - Bacillus subtilis 168 - NCBI GCF_000009045.1 (ASM904v1)
Bacillus velezensis SQR9 - Bacillus amyloliquefaciens SQR9 - NCBI GCF_000685725.1 (ASM68572v1)
Bactrocera tryoni - Queensland fruit fly - NCBI GCA_000695345.1 (Assembly 2.2 of Bactrocera tryoni genome)
Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088 - Bifidobacterium longum bv. Infantis ATCC 15697 - NCBI GCF_000020425.1 (ASM2042v1)
Biomphalaria glabrata - B. glabrata - VectorBase 1
Blastomyces dermatitidis ATCC 26199 - Ajellomyces dermatitidis ATCC 26199 - NCBI GCA_000166155.1 (BD_ATCC26199_V2)
Blastomyces dermatitidis ER-3 - Ajellomyces dermatitidis ER-3 - NCBI GCA_000003525.2 (BD_ER3_V1)
Blastomyces gilchristii SLH14081 - Blastomyces gilchristii SLH14081 - NCBI GCA_000003855.2 (BD_SLH14081_V1)
Bombus terrestris - Buff-tailed bumblebee - Genbank Bter1.0
Bombyx mori - Bombyx mori - EnsemblMetazoa 76 (GCA_000151625.1)
Bos taurus - Cattle - Ensembl 76 (UMD3.1)
Bos taurus - domestic cow - NCBI GCF_000003205.7 (Btau_5.0.1)
Bos taurus - domestic cow - NCBI GCF_002263795.1 (ARS-UCD1.2)
Botrylloides leachii - B. leachii - Aniseed SBv3
Brachypodium distachyon - Brachypodium distachyon - Phytozome V9, Dec 2012
Brachypodium distachyon - Purple false brome - Bd21-3 v1.1
Branchiostoma lanceolatum - common lancelet - NCBI GCA_900088365.1 (Bl71nemr)
Brassica Napus - Rapeseed - Genoscope 4.1 Darmor-bzh
Brassica oleracea - Brassica oleracea - EnsemblPlants 92 (v2.1)
Brassica oleracea - wild cabbage - NCBI GCA_900416815.2 (Brassica_oleracea_HDEM)
Brassica rapa - Brassica rapa - Phytozome V9, Dec 2012, Chiifu-401_v2.5
Brassica rapa - field mustard - NCBI GCA_900412535.2 (Brassica_rapa_Z1)
Brugia malayi - B.malayi - EnsemblMetazoa 76 (B_malayi-3.0)
Burkholderia seminalis - Burkholderia seminalis - NCBI GCF_001742345.1 (ASM174234v1)
C. glutamicum ATCC 13032 - Corynebacterium glutamicum ATCC 13032 - NCBI GCA_000011325.1 (ASM1132v1)
Caenorhabditis brenneri - Brenneri - EnsemblMetazoa 76 (C_brenneri-6.0.1b)
Caenorhabditis briggsae - Briggsae - EnsemblMetazoa 76 (CB4)
Caenorhabditis elegans - C. elegans - UCSC Feb. 2013 (WBcel235/ce11)
Caenorhabditis elegans - C. elegans - UCSC Oct. 2010 (WS220/ce10)
Caenorhabditis japonica - Japonica - EnsemblMetazoa 76 (C_japonica-7.0.1)
Caenorhabditis remanei - Remanei - EnsemblMetazoa 76 (C_remanei-15.0.1)
Callithrix jacchus - white ear-tufted marmoset - NCBI GCF_000004665.1 (Callithrix jacchus-3.2)
Camelina Sativa - False flax - Camelinadb.ca V2 with genes
Camelina sativa - False Flax - Cs
Camelina sativa - False flax - Camelinadb.ca V2
Camelpox Virus - Camelpox Virus - Refseq GCF_000839105.1
Candida albicans SC5314 - Candida albicans SC5314 - NCBI GCF_000182965.3 (ASM18296v3)
Canis familiaris - Dog - Ensembl 79 (CanFam3.1)
Cannabis sativa - Marijuana, Purple Kush - canSat3, genome.ccbr.utoronto.ca
Cannabis sativa - marijuana - NCBI GCA_000230575.1 (canSat3)
Cannabis sativa - marijuana - NCBI GCA_001865755.1 (Phylos Biosc. 2016)
Capitella teleta - Capitella teleta - EnsemblMetazoa 76 (GCA_000328365.1)
Capra hircus - goat - RefSeq ARS1
Capsella rubella - Capsella rubella - Phytozome V9, Dec 2012
Capsicum annuum - Capsicum annuum - NCBI GCA_000710875.1 (Pepper Zunla 1 Ref_v1.0)
Carica papaya - Carica papaya - Phytozome V9, Dec 2012
Castanea mollissima - Chinese chestnut - NCBI GCA_000763605.1 (ASM76360v1)
Catharanthus roseus - rosy periwinkle - NCBI GCA_001292565.1 (BAC_SGD)
Cavia porcellus - Domestic guinea pig - Ensembl 76 (cavPor3)
Chiloscyllium plagiosum - Whitespotted bamboo shark - GCA_004010195.1 (merged < 3kbp)
Chlamydomonas reinhardtii - Chlamydomonas reinhardtii - NCBI v3.0
Chlamydomonas reinhardtii - Chlamydomonas reinhardtii - Phytozome V9, Dec 2012
Chlorella variabilis - Chlorella variabilis - NCBI GCA_000147415.1 (v 1.0)
Chlorocebus sabaeus - Green monkey - UCSC Mar. 2014 (Chlorocebus_sabeus 1.1/chlSab2)
Ciona Intestinalis (formerly: C. intestinalis type B) - sea vase ascidian - ANISEED MTP2012
Ciona robusta (formerly C. intestinalis type A) - Sea squirt ciona intestinalis - Ensembl 76 (KH2008)
Ciona robusta (formerly: C. intestinalis type A) - sea vase ascidian - GHOST Joined, KH2008, KH2013 Genes + SNPs: Ghost SNPs
Ciona robusta (formerly: C. intestinalis, type A) - sea vase ascidian - UCSC JGI 2.1, Ci2, Mar. 2005
Citrus clementina - Citrus clementina - Phytozome V9, Dec 2012
Citrus sinensis - Citrus sinensis - Phytozome V9, Dec 2012
Clytia hemisphaerica - Jellyfish C.hem. - via Tsuyoshi Momose
Coccomyxa subellipsoidea C-169 - Coccomyxa subellipsoidea C-169 - Phytozome V9, Dec 2012
Coprinopsis cinerea okayama7#130 - Coprinus cinereus okayama7#130 - NCBI GCA_000182895.1 (CC3)
Corynebacterium glutamicum ATCC 13032 - Corynebacterium glutamicum ATCC 13032 - NCBI GCF_000011325.1 (ASM1132v1)
Corynebacterium pseudotuberculosis - Bacillus pseudotuberculosis - NCBI GCF_001433475.1 (ASM143347v1)
Corynebacterium pseudotuberculosis 1002 - Corynebacterium pseudotuberculosis 1002 - NCBI GCF_000144935.1 (ASM14493v2)
Coturnix japonica - Japanese quail - RefSeq V2.0 GCF_001577835
Crassostrea gigas - Crassostrea gigas - EnsemblMetazoa 76 (GCA_000297895.1)
Cricetulus griseus (CHO cells) - Chinese hamster CHO cells - NCBI GCA_900186095.1 (CHOK1S_HZDv1, Sep 2017)
Cricetulus griseus (CHO cells) - Chinese hamster ovary cells - UCSC Aug. 2011 (CHO K1 cell line/criGriChoV1)
Cricetulus griseus - Chinese hamster - UCSC Jul. 2013 (C_griseus_v1.0/criGri1)
Cryptococcus neoformans var. neoformans JEC21 - Filobasidiella neoformans var. neoformans strain JEC21 - NCBI GCA_000091045.1 (ASM9104v1)
Cryptosporidium parvum Iowa II - Cryptosporidium parvum strain Iowa type II - NCBI GCF_000165345.1 (ASM16534v1)
Cucumis melo L. - Muskmelon - Melonomics V3.5.1 Pseudo
Cucumis sativus - Cucumis sativus - Phytozome V9, Dec 2012
Cucurbita pepo subsp. pepo - field pumpkin - NCBI GCF_002806865.1 (ASM280686v2)
Culex quinquefasciatus - Southern house mosquito - EnsemblMetazoa 76 (CpipJ2)
Danaus plexippus - Danaus plexippus - EnsemblMetazoa 76 (DanPle_1.0)
Danio rerio - Zebrafish - Ensembl 76 (Zv9)
Danio rerio - Zebrafish - UCSC Jul. 2010 (Zv9/danRer7)
Danio rerio - Zebrafish - UCSC May 2017 (GRCz11/danRer11)
Danio rerio - Zebrafish - UCSC Sep. 2014 (GRCz10/danRer10)
Danio rerio - zebra fish - NCBI GCA_000002035.4 (GRCz11)
Daphnia magna - Daphnia magna - EnsemblMetazoa 95 (daphmag2.4)
Daphnia magna - Daphnia magna - NCBI GCA_003990815.1 (ASM399081v1)
Daphnia pulex - Daphnia pulex - EnsemblMetazoa 76 (GCA_000187875.1)
Daucus carota subsp. sativus - Daucus carota var. sativus - NCBI GCF_001625215.1 (ASM162521v1)
Dendroctonus ponderosae - Dendroctonus ponderosae - EnsemblMetazoa 76 (GCA_000355655.1)
Desulfovibrio vulgaris str. Hildenborough - Desulfovibrio vulgaris ATCC 29579 - NCBI GCA_000195755.1 (ASM19575v1)
Dictyostelium discoideum - Dictyostelium discoideum - Dictybase.org Apr 2017
Drosophila ananassae - Drosophila ananassae - EnsemblMetazoa 76 (dana_caf1)
Drosophila erecta - Drosophila erecta - EnsemblMetazoa 76 (dere_caf1)
Drosophila grimshawi - Drosophila grimshawi - EnsemblMetazoa 76 (dgri_caf1)
Drosophila melanogaster - D. melanogaster - UCSC Apr. 2006 (BDGP R5/dm3)
Drosophila melanogaster - D. melanogaster - UCSC Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6)
Drosophila melanogaster - Fruit fly - EnsemblMetazoa 76 (BDGP5)
Drosophila mojavensis - Drosophila mojavensis - EnsemblMetazoa 76 (dmoj_caf1)
Drosophila persimilis - Drosophila persimilis - EnsemblMetazoa 76 (dper_caf1)
Drosophila pseudoobscura - Drosophila pseudoobscura - EnsemblMetazoa 76 (HGSC2)
Drosophila sechellia - Drosophila sechellia - EnsemblMetazoa 76 (dsec_caf1)
Drosophila simulans - Drosophila simulans - EnsemblMetazoa 76 (WUGSC1)
Drosophila suzukii - Spotted-Wing Drosophila - SpottedWingFlybase V1
Drosophila virilis - Drosophila virilis - EnsemblMetazoa 76 (dvir_caf1)
Drosophila willistoni - Drosophila willistoni - EnsemblMetazoa 76 (dwil_caf1)
Drosophila yakuba - Drosophila yakuba - EnsemblMetazoa 76 (dyak_r1.3_FB2008_07)
Ectocarpus sp. - Ectocarpus sp. - V2 ugent.be
Eimeria tenella - Eimeria tenella - NCBI GCF_000499545.2 (ETH001)
Equus caballus - Horse - UCSC Sep. 2007 (Broad/equCab2)
Escherichia coli - E.coli - strain K-12/MG1655 (ASM584v2)
Escherichia coli W - Escherichia coli ATCC 9637 - NCBI GCF_000184185.1 (ASM18418v1)
Escherichia coli str. K-12 substr. DH10B - Escherichia coli str. K-12 substr. DH10B - NCBI GCF_000019425.1 (ASM1942v1)
Escherichia virus Lambda - Bacteriophage lambda - NCBI GCF_000840245.1 (ViralProj14204)
Eucalyptus grandis - Eucalyptus grandis - Phytozome V9, Dec 2012
Exaiptasia pallida - Aiptasia pallida - NCBI GCA_001417965.1 (Aiptasia genome 1.1)
Felis catus - Domestic cat - Ensembl 89 (Felis_catus_6.2)
Fonsecaea monophora - Botrytoides monophora - NCBI GCF_001642475.1 (ASM164247v1)
Fragaria vesca - Fragaria vesca - Phytozome V9, Dec 2012
Fragaria vesca subsp. vesca - wild strawberry - NCBI GCA_000184155.1 (FraVesHawaii_1.0)
Fragaria_vesca - wild strawberry - rosaceae.org v4.0.1a
Fusarium graminearum - Gibberella zeae - NCBI GCA_900044135.1 (GZPH1RResV1)
Gadus morhua - Atlantic cod - EnsemblVertebrates 95 (gadMor1)
Gallid alphaherpesvirus 1 - Infectious laryngotracheitis virus - NCBI GCA_000847005.2 (ViralProj14566)
Gallid herpesvirus 2 strain CVI988 - Gallid herpes 2 CVI988 - Genbank DQ530348.1
Gallus gallus - Chicken - UCSC Dec 2015 (Gallus_gallus-5.0/galGal5)
Gallus gallus - Chicken - UCSC Nov. 2011 (ICGSC Gallus_gallus-4.0/galGal4)
Ganoderma lucidum BCRC 37177 - Ganoderma lucidum BCRC 37177 - NCBI GCA_000338035.1 (Glu37177_1.0)
Ganoderma sinense ZZ0214-1 - Ganoderma sinense ZZ0214-1 - NCBI GCA_002760635.1 (GanSi1.6)
Gasterosteus aculeatus - Stickleback - UCSC Feb. 2006 (Broad/gasAcu1)
Glossina morsitans - G. moritans - VectorBase Yale 1.6
Glycine max - Glycine max - Phytozome V9, Dec 2012
Goatpox virus Pellor - Goatpox virus Pellor - NCBI GCF_000840165.1 (ViralProj14197)
Gossypium hirsutum - American upland cotton - NCBI GCF_000987745.1 (ASM98774v1)
Gossypium raimondii - Gossypium raimondii - Phytozome V9, Dec 2012
HBV genotype D DNA - AB554016.1 - NCBI Genbank
Halocynthia aurantium - sea peach - ANISEED MTP2014
Halocynthia roretzi - sea pineapple - ANISEED MTP2014
Helianthus annuus - Helianthus annuus - NCBI HanXRQr1.0
Heliconius melpomene - Heliconius melpomene - EnsemblMetazoa 76 (Hmel1)
Helicoverpa armigera - tobacco budworm - NCBI GCA_002156985.1 (Harm_1.0)
Helobdella robusta - Helobdella robusta - EnsemblMetazoa 76 (GCA_000326865.1)
Heterocephalus glaber - Naked Mole Rat - NCBI HetGla_female_1.0
Histoplasma capsulatum G217B - Ajellomyces capsulatus G217B - NCBI GCA_000170615.1 (ASM17061v1)
Homo sapiens - Human - UCSC Dec. 2013 (GRCh38/hg38) + SNPs: dbSNP148, Kaviar
Homo sapiens - Human - UCSC Feb. 2009 (GRCh37/hg19) + SNPs: 1000Genomes, ExaC
Homo sapiens - Human - UCSC Mar. 2006 (NCBI36/hg18) + SNPs: HEK293
Homo sapiens - human - UCSC Dec 2013 (hg38 analysis set) + SNPs: dbSNP148, Kaviar
Hordeum vulgare - Two-rowed barley - EnsemblPlants 95 (IBSC_v2)
Human alphaherpesvirus 1 - Herpes simplex virus 1 - NCBI GCF_000859985.2 (ViralProj15217)
Human alphaherpesvirus 2 - Herpes simplex virus 2 - NCBI GCF_000858385.2 (ViralProj15218)
Human betaherpesvirus 5, Merlin strain - Human cytomegalovirus - NCBI GCF_000845245.1 (ViralProj14559)
Human betaherpesvirus 6A - Human herpesvirus 6A - NCBI GCA_000845685.2 (ViralProj14462)
Human betaherpesvirus 6B - Human herpes virus 6B - NCBI GCF_000846365.1 (ViralProj14422)
Human betaherpesvirus 7 - Herpes simplex virus 7 - NCBI GCF_000848125.1 (ViralProj14625)
Human herpesvirus-7 - HHV7 - Genbank U43400.1
Hydra Vulgaris - Fresh Water Poly - RP 1.0 RefSeq GCA_000004095.1
Hypsibius dujardini - water bear - tardigrades.org 3.15
Ixodes scapularis - Black-legged tick - EnsemblMetazoa 76 (IscaW1)
Juglans regia - English walnut - NCBI GCF_001411555.1 (wgs.5d)
Klebsiella aerogenes KCTC 2190 - Enterobacter aerogenes KCTC 2190 - NCBI GCA_000215745.1 (ASM21574v1)
Klebsiella pneumoniae subsp. pneumoniae 1158 - Klebsiella pneumoniae 1158 - NCBI GCF_000814805.1 (ASM81480v1)
Klebsormidium nitens - Klebsormidium nitens - NCBI GCA_000708835.1 (ASM70883v1)
Kluyveromyces lactis - Kluyveromyces drosophilarum - NCBI GCA_002151565.1 (ASM215156v1)
Kluyveromyces marxianus DMKU3-1042 - Kluyveromyces marxianus DMKU3-1042 - NCBI GCA_001417885.1 (Kmar_1.0)
Lactuca sativa - garden lettuce - NCBI GCF_002870075.1 (Lsat_Salinas_v7)
Leishmania major strain Friedlin - Leishmania major MHOM/IL/81/Friedlin - NCBI GCA_000002725.2 (ASM272v2)
Leishmania mexicana MHOM/GT/2001/U1103 - Leishmania mexicana MHOM/GT/2001/U1103 - NCBI GCF_000234665.1 (ASM23466v4)
Leptosphaeria maculans - Blackleg of oilseed - JN3 via Colin Clairet
Linum usitatissimum - Linum usitatissimum - Phytozome V9, Dec 2012
Loa loa - Eye worm - EnsemblMetazoa 76 (Loa_loa_V3)
Lolium perenne - Perennial Rye-Grass - V1.0 L. Fuchs
Lottia gigantea - Lottia gigantea - EnsemblMetazoa 76 (GCA_000327385.1)
Lotus japonicus - Lotus japonicus - kazusa.or.jp V3
Lumpy skin disease KSGP 0240 - LSDV virus - Genbank KX683219.1
Lumpy skin disease virus NI-2490 - Lumpy skin disease virus NI-2490 - NCBI GCF_000839805.1 (ViralProj14122)
Lutzomyia longipalpis - Sand fly - VectorBase LionJ1
Lysinibacillus sphaericus C3-41 - Bacillus sphaericus C3-41 - NCBI GCA_000017965.1 (ASM1796v1)
Macaca fascicularis - Crab-eating macaque - RefSeq 5.0
Macaca mulatta - Rhesus - UCSC Jan. 2006 (MGSC Merged 1.0/rheMac2)
Macrostomum lignano - Macrostomum lignano - Genbank GCA_001188465.1_ML2
Macrostomum lignano - Macrostomum lignano - NCBI GCA_002269645.1 (Mlig_3_7)
Malus domestica - Apple - INRA GDDH13 Version 1.1
Malus domestica - Malus domestica - ASM211411v1
Malus domestica - Malus domestica - Phytozome V9, Dec 2012
Manihot esculenta - Manihot esculenta - Phytozome V9, Dec 2012
Marchantia polymorpha - Common liverwort - Phytozome 12, V3.1
Medicago truncatula - Medicago truncatula - Phytozome V9, Dec 2012
Medicago truncatula - barrel medic - NCBI GCA_002024945.1 (R108 v. 1.0)
Medicago truncatula - barrel medic - medicagogenome.org V4.3
Medicago truncatula - barrelclover - Medicohapmap.org R108 0.95
Medicago truncatula A17 - barrelclover - INRA A17r5.0 r1.6 Pascal Gamas
Megaselia scalaris - Megaselia scalaris - EnsemblMetazoa 76 (Msca1)
Meleagris gallopavo - Domestic turkey - Ensembl 76 (UMD2)
Mentha longifolia - horsemint - NCBI GCA_001642375.1 (Mlong1.0)
Mesocricetus auratus - Syrian hamster - NCBI GCF_000349665.1 (MesAur1.0)
Methylococcus capsulatus str. Bath - Methylococcus capsulatus ATCC 33009 - NCBI GCF_000008325.1 (ASM832v1)
Micractinium conductrix - Micractinium conductrix - NCBI GCA_002245815.2 (ASM224581v2)
Microtus ochrogaster - prairie vole - NCBI GCF_000317375.1 (MicOch1.0)
Mimulus guttatus - Mimulus guttatus - Phytozome V9, Dec 2012
Minuartia pusilla 299 - Minuartia pusilla 299 - Phytozome V9, Dec 2012
Miscanthus sinensis - Chinese silver grass - Phytozome12, Msin v7.1
Mizuhopecten yessoensis - ezo giant scallop - NCBI GCF_002113885.1 (ASM211388v2)
Moesziomyces aphidis DSM 70725 - Moesziomyces aphidis DSM 70725 - NCBI GCA_000517465.1 (PseuAph1.0)
Molgula occidentalis - Sandy Sea Grape - ANISEED EL_v1.2
Molgula occulta - Tail-less Sea Grape - ANISEED EL_v1.2
Molgula oculata - Tailed Sea Grape - ANISEED EL_v1.2
Mortierella alpina ATCC 32222 - Mortierella alpina ATCC 32222 - NCBI GCA_000240685.2 (ASM24068v2)
Murine cytomegalovirus - CMV - AM886412.1, Strain K181
Mus musculus - Mouse (reference) - UCSC Dec. 2011 (mm10=C57BL/6J) + SNPs: C57BL/10J, C57BR/cdJ,...
Mus musculus - Mouse (reference) - UCSC July 2007 (NCBI37/mm9)
Mus musculus - Mouse strain C57BL/6NJ - NCBI GCA_001632555.1 (C57BL_6NJ_v1)
Mus musculus c3hhej - Mouse - Ensembl 90 (C3H_HeJ_v1)
Musa acuminata subsp. malaccensis - true apple banana - NCBI GCF_000313855.2 (ASM31385v2)
Musca domestica - house fly - NCBI GCF_000371365.1 (Musca_domestica-2.0.2)
Mustela putorius furo - Ferret - UCSC Apr. 2011 (MusPutFur1.0/musFur1)
Mycobacterium abscessus - Mycobacterium chelonae subsp. abscessus - NCBI GCF_000069185.1 (ASM6918v1)
Myotis lucifugus - Microbat - UCSC Jul. 2010 (Broad Institute Myoluc2.0/myoLuc2)
Myxoma virus - myxoma virus MYX - NCBI GCF_000843685.1 (ViralProj14396)
Nannochloropsis gaditana - Nannochloropsis gaditana - NCBI GCA_002838785.1 (we3730_nuc)
Nannochloropsis oceanica CCMP1779 - microalgae - JGI Nanoce1779_2
Nasonia vitripennis - Nasonia vitripennis - EnsemblMetazoa 76 (GCA_000002325.2)
Neisseria meningitidis Z2491 - Neisseria meningitidis serogroup A strain Z2491 - NCBI GCA_000009105.1 (ASM910v1)
Nematostella vectensis - Nematostella vectensis - EnsemblMetazoa 76 (GCA_000209225.1)
Neovison vison - mink - NCBI GCA_900108605.1 (NNQGG.v01)
Nicotiana_benthamiana - N. benthamiana - SolGenomics.net V1.01
Nicotiana_tabacum - N. tabacum - SolGenomics.net V4.5 Edwards et al 2017
Nocardia terpenica - Nocardia terpenica - NCBI GCF_001625105.1 (ASM162510v1)
Nostoc sp. PCC 7120 - Anabaena sp. PCC 7120 - NCBI GCF_000009705.1 (ASM970v1)
Nothobranchius furzeri - turquoise killifish - NCBI GCA_001465895.2 (Nfu_20140520)
Onchocerca volvulus - O.volvulus - EnsemblMetazoa 76 (Cameroon_v3)
Oncorhynchus kisutch - coho salmon - NCBI GCF_002021735.1 (Okis_V1)
Oncorhynchus mykiss - rainbow trout - NCBI GCF_002163495.1 (Omyk_1.0)
Oncorhynchus tshawytscha - king salmon - NCBI GCF_002872995.1 (Otsh_v1.0)
Oreochromis niloticus - Nile tilapia - Ensembl 76 (Orenil1.0)
Oryctolagus cuniculus - Rabbit - Ensembl 76 (OryCun2.0)
Oryza sativa - Oryza sativa - Phytozome V9, Dec 2012
Oryzias latipes - Medaka - UCSC Oct. 2005 (NIG/UT MEDAKA1/oryLat2)
Ostreococcus lucimarinus - Ostreococcus lucimarinus - Phytozome V9, Dec 2012
Ostreococcus tauri - O. tauri - Genbank 140606
Ovis aries - Domestic sheep - Ensembl 76 (Oar_v3.1)
Paenibacillus larvae subsp. larvae - Paenibacillus larvae subsp. larvae - NCBI GCF_002951875.1 (ASM295187v1)
Paenibacillus larvae subsp. larvae - Paenibacillus larvae subsp. larvae - NCBI GCF_002951915.1 (ASM295191v1)
Paenibacillus larvae subsp. larvae - Paenibacillus larvae subsp. larvae - NCBI GCF_002951935.1 (ASM295193v1)
Paenibacillus larvae subsp. larvae DSM 25430 - Paenibacillus larvae subsp. larvae 04-309 - NCBI GCF_002951895.1 (ASM295189v1)
Paenibacillus larvae subsp. larvae DSM 25719 - Paenibacillus larvae subsp. larvae 08-100 - NCBI GCF_000511115.1 (ASM51111v1)
Pan troglodytes - Chimp - UCSC Feb. 2011 (CSAC 2.1.4/panTro4)
Panicum virgatum - Panicum virgatum - Phytozome V9, Dec 2012
Pantoea agglomerans - P. agg. FDAARGOS_160 - Refseq GCF_001558735.1
Papio anubis - Baboon - UCSC Mar. 2012 (Baylor Panu_2.0/papAnu2)
Paramecium bursaria Chlorella virus 1 - Chlorella PBCV-1 virus - NCBI GCF_000847045.1 (ViralProj14564)
Parhyale hawaiensis - P. hawaiensis - GCA_001587735.2 but merged short contigs (PE Gallindo Torres)
Passiflora edulis chloroplast - Passionfruit, chloroplast genome - Genbank KX290855.1
Penaeus vannamei - white shrimp - NCBI GCF_003789085.1 (ASM378908v1)
Penicillium digitatum Pd1 - Penicillium digitatum Pd1 - NCBI GCA_000315645.2 (PdigPd1_v1)
Penicillium expansum - Penicillium expansum - NCBI GCA_000769755.1 (PEX1)
Petromyzon marinus - Sea lamprey - Ensembl 76 (Pmarinus_7.0)
Petromyzon marinus - marine lamprey - NCBI GCA_002833325.1 (Pmar_germline 1.0)
Petunia axillaris - While moon petunia - Solgenomics V1.6.2
Petunia inflata - Petunia inflata - Solgenomics V1
Phaeodactylum tricornutum - Phaeodactylum tricornutum - EnsemblProtists 79 (ASM15095v2_bd)
Phalaenopsis equestris - Phalaenopsis equestris - NCBI GCF_001263595.1 (ASM126359v1)
Phallusia fumigata - P. fumigata - ANISEED - MTP 2014
Phallusia mammillata - white sea squirt - ANISEED MTP 2014
Phaseolus vulgaris - Phaseolus vulgaris - Phytozome V9, Dec 2012
Physcomitrella patens - A moss - EnsemblPlants 76 (ASM242v1)
Physcomitrella patens - Physcomitrella patens - Phytozome V9, Dec 2012
Physcomitrella patens - Spreading Earthmoss - Phytozome V11
Pimelobacter simplex - Arthrobacter simplex - NCBI GCF_000785495.1 (ASM78549v1)
Pimephales promelas - Fathead minnow - Genbank FHM_SOAPdenovo
Pinctada martensii - Akoya pearl oyster - NCBI GCA_002216045.1 (PinMar1.0)
Plasmodium berghei ANKA - Plasmodium berghei ANKA - PlasmoDB 3.1
Plasmodium falciparum 3D7 - Plasmodium falciparum 3D7 - PlasmoDB 3.1
Plasmodium knowlesi H - Plasmodium knowlesi H - PlasmoDB 3.1
Plasmodium vivax - malaria parasite P. vivax - NCBI GCF_000002415.2 (ASM241v2)
Plasmodium vivax North Korean - North Korean strain of Plasmodium vivax - NCBI GCA_000320685.2 (PV_N_Korean_V1)
Populus trichocarpa - Populus trichocarpa - Phytozome V9, Dec 2012
Pristionchus pacificus - Pristionchus - EnsemblMetazoa 76 (P_pacificus-5.0)
Prunus persica - Prunus persica - Phytozome V9, Dec 2012
Pseudocercospora fijiensis CIRAD86 - Mycosphaerella fijiensis CIRAD86 - NCBI GCF_000340215.1 (Mycfi2)
Pseudomonas aeruginosa PAO1 - Pseudomonas aeruginosa str. PAO1 - NCBI GCF_000006765.1 (ASM676v1)
Pseudomonas aeruginosa UCBPP-PA14 - P. aer. UCBPP-PA14 - MW Azam
Pseudomonas putida KT2440 - Pseudomonas putida (strain KT2440) - NCBI GCF_000007565.2 (ASM756v2)
Pseudonitzschia multistriata - P.m. diatom algae - bioinfo.szn.it, unknown version
Pyropia yezoensis - Susabi Nori, Marine Red Alga - NRIFS.fra.affrc..go.jp V1
Python bivittatus - Burmese python - NCBI GCF_000186305.1 (Python_molurus_bivittatus-5.0.2)
Ramazzottius varieornatus - water bear - tardigrades.org 1.01
Rattus norvegicus - Norway rat - Ensembl 76 (Rnor_5.0)
Rattus norvegicus - Rat - UCSC Jul. 2014 (RGSC 6.0/rn6)
Rattus norvegicus - Rat - UCSC Mar. 2012 (RGSC 5.0/rn5)
Rhabditophanes sp. KR3021 - Rhabditophanes sp. KR3021 - NCBI GCA_000944355.1 (Rhabditophanes_sp_KR3021)
Rhodnius prolixus - Rhodnius prolixus - EnsemblMetazoa 76 (RproC1)
Rhodococcus opacus PD630 - Rhodococcus opacus PD630 - NCBI GCF_000599545.1 (ASM59954v1)
Ricinus communis - Ricinus communis - Phytozome V9, Dec 2012
Rosa chinensis - Rose - HapOB_Angers genome V1.0
S. boulardii - Saccharomyces sp. 'boulardii' - NCBI GCA_000769245.1 (ASM76924v1)
Saccharomyces cerevisiae - S. cerevisiae - UCSC Apr. 2011 (SacCer_Apr2011/sacCer3)
Salmo salar - Atlantic salmon - NCBI GCF_000233375.1 (ICSASG_v2)
Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S - Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S - NCBI GCA_000022165.1 (ASM2216v1)
Schistosoma mansoni - Schistosoma mansoni - EnsemblMetazoa 76 (ASM23792v2)
Schizosaccharomyces pombe - fission yeast - NCBI GCF_000002945.1 (ASM294v2)
Schmidtea Mediterranea - freshwater planarian - smedgd.stowers.org 1.1
Schmidtea Mediterranea - freshwater planarian - smedgd.stowers.org 4.0
Schmidtea mediterranea - freshwater planarian - NCBI GCA_002600895.1 (ASM260089v1)
Scotinomys teguina - Alston's brown mouse - Paul Frazel NYU email
Selaginella kraussiana - Selaginella kraussiana - NCBI GCA_001021135.1 (ASM102113v1)
Selaginella moellendorffii - Selaginella moellendorffii - Phytozome V9, Dec 2012
Serendipita indica DSM 11827 - Serendipita indica DSM 11827 - NCBI GCA_000313545.1 (ASM31354v1)
Setaria italica - Setaria italica - Phytozome V9, Dec 2012
Setaria viridis - Green foxtail - Phytozome 11/v1.1
Sheeppox virus - sheep pox virus - NCBI GCF_000840205.1 (ViralProj14196)
Shewanella oneidensis MR-1 - Shewanella oneidensis ATCC 700550 - NCBI GCF_000146165.2 (ASM14616v2)
Solanum lycopersicum - Solanum lycopersicum - Phytozome V9, Dec 2012
Solanum lycopersicum - Tomato - Solgenomics.net SL3.0 ITAG3.0
Solanum melongena - eggplant/aubergine - NCBI GCA_000787875.1 (SME_r2.5.1)
Solanum tuberosum - Solanum tuberosum - Phytozome V9, Dec 2012
Solenopsis invicta - Red fire ant - EnsemblMetazoa 76 (GCA_000188075.1)
Sorghum bicolor - Sorghum bicolor - Phytozome V9, Dec 2012
Sorghum bicolor - milo - NCBI GCF_000003195.3 (Sorghum_bicolor_NCBIv3)
Spodoptera frugiperda - Fall Armyworm - Genouest V3.1
Spodoptera litura - Spodoptera litura - NCBI GCF_002706865.1 (ASM270686v1)
Staphylococcus aureus - Micrococcus aureus - NCBI GCA_002085525.1 (ASM208552v1)
Staphylococcus aureus subsp. aureus - Staphylococcus aureus subsp. aureus - NCBI GCF_002310395.1 (ASM231039v1)
Staphylococcus aureus subsp. aureus MRSA252 - Staphylococcus aureus subsp. aureus MRSA252 - NCBI GCF_000011505.1 (ASM1150v1)
Staphylococcus pseudintermedius - Staphylococcus pseudintermedius - NCBI GCF_001685665.2 (ASM168566v2)
Staphylococcus pseudintermedius - Staphylococcus pseudintermedius - NCBI GCF_002847235.2 (ASM284723v2)
Staphylococcus pseudintermedius ED99 - Staphylococcus pseudintermedius ED99 - NCBI GCF_000189495.1 (ASM18949v1)
Streptomyces bingchenggensis BCW-1 - Streptomyces bingchenggensis BCW-1 - NCBI GCF_000092385.1 (ASM9238v1)
Streptomyces bottropensis ATCC 25435 - Streptomyces bottropensis DSM 40262 - NCBI GCA_000383595.1 (ASM38359v1)
Streptomyces coelicolor A3(2) - Streptomyces coelicolor A3(2) - NCBI GCF_000203835.1 (ASM20383v1)
Streptomyces noursei ATCC 11455 - Streptomyces noursei ATCC 11455 - NCBI GCF_001704275.1 (ASM170427v1)
Streptomyces parvulus - Streptomyces parvulus - ASM166004v1
Strongylocentrotus purpuratus - Pacific purple sea urchin - EnsemblMetazoa 76 (GCA_000002235.2), not Echinobase
Suid alphaherpesvirus 1, strain: Becker - Alphaherpesvirus pseudorabies virus PRV (PRV, SuHV-1) - Genbank JF797219.1
Sus scrofa - Pig - Ensembl 76 (Sscrofa10.2)
Sus scrofa - Pig - NCBI GCF_000003025.6 (Sscrofa11.1)
Synechococcus elongatus PCC 7942 - Anacystis nidulans R2 - NCBI GCF_000012525.1 (ASM1252v1)
Taeniopygia guttata - Zebra finch - Ensembl 76 (taeGut3.2.4)
Tetranychus urticae - Tetranychus urticae - EnsemblMetazoa 76 (GCA_000239435.1)
Thellungiella halophila - Thellungiella halophila - Phytozome V9, Dec 2012
Theobroma cacao - Theobroma cacao - Phytozome V9, Dec 2012
Thermoascus aurantiacus - soil fungus T. aurant. - JGI Theau1
Tribolium castaneum - Red flour beetle - EnsemblMetazoa 76 (Tcas3)
Trichoderma atroviride - T. atroviride - JGI 2.0
Trichoderma harzianum - Trichoderma harzianum - NCBI GCA_001990665.1 (ASM199066v1)
Trichoderma harzianum - Trichoderma harzianum - NCBI GCA_002838845.1 (ASM283884v1)
Trichoderma reesei - T. reesei - JGI V2 Oct 2006
Trichoplusia ni - Cabbage looper - tn1 Github:weng-lab
Triticum aestivum - Bread wheat - EnsemblPlants 89 (TGACv1)
Triticum aestivum - Bread wheat - IWGSC RefSeq 1.0
Triticum turgidum ssp. dicoccoides - Wild Emmer Wheat Zavitan - wheat.pw.usda.gov, Zavitan V2
Trypanosoma brucei 427 - T. brucei 427 - TriTrypDb 32
Trypanosoma cruzi - Chaga's disease - tritrypdb.org 4.1 CLBrenerEsmeraldo
Trypanosoma cruzi - Trypanosoma cruzi - NCBI GCF_000209065.1 (ASM20906v1)
Ulva prolifera - Enteromorpha prolifera - NCBI GCA_004138255.1 (ASM413825v1)
Ursus arctos horribilis - Grizzly bear - NCBI GCA_003584765.1 (ASM358476v1)
Ursus arctos horribilis - Ursus arctos horribilis - NCBI GCF_003584765.1 (ASM358476v1)
Vaccinia virus - vaccinia virus VV - NCBI GCF_000860085.1 (ViralProj15241)
Vaccinia virus strain Lister clone VACV107 - VV - Genbank DQ121394.1
Vibrio vulnificus - Beneckea vulnifica - NCBI GCF_002215135.1 (ASM221513v1)
Vigna radiata var. radiata - green gram - NCBI GCA_000741045.2 (Vradiata_ver6)
Vitis vinifera - Vitis vinifera - Phytozome V9, Dec 2012
Vitis vinifera - wine grape - NCBI GCA_002922885.1 (Chkhaveri_assembly01)
Volvox carteri - Volvox carteri - Phytozome V9, Dec 2012
Xanthomonas oryzae pv. oryzae PXO99A - Xanthomonas oryzae pv. oryzae PXO99A - NCBI GCF_000019585.2 (ASM1958v2)
Xanthophyllomyces dendrorhous - Xanthophyllomyces dendrorhous - NCBI GCA_001007165.2 (Xden1)
Xenopus laevis - African Clawed Frog - Xenbase 9.1
Xenopus laevis - X. laevis - Xenbase V7.1
Xenopus tropicalis - Western Clawed Frog - Xenbase 9.0
Xenopus tropicalis - X. tropicalis - UCSC Nov. 2009 (JGI 4.2/xenTro3)
Yarrowia lipolytica - Y. lipolytica - CLIB122 CR382127 Genolevures 2008
Zea mays - Maize - Gramene AGPv4
Zea mays - Zea mays - Phytozome V9, Dec 2012
Zymoseptoria tritici IPO323 - Mycosphaerella graminicola IPO323 - NCBI GCA_000219625.1 (MYCGR v2.0)
[Nectria] haematococca mpVI 77-13-4 - [Nectria] haematococca mpVI 77-13-4 - NCBI GCF_000151355.1 (v2.0)
Note: pre-calculated exonic guides for this species are on the
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Step 3
Select a Protospacer Adjacent Motif (PAM)
20bp-NGG - Sp Cas9, SpCas9-HF1, eSpCas9 1.1
20bp-NNG - Cas9 S. canis
20bp-NNGT - Cas9 S. canis - high efficiency PAM, recommended
20bp-NAA - iSpyMacCas9
21bp-NNG(A/G)(A/G)T - Cas9 S. Aureus
20bp-NNG(A/G)(A/G)T - Cas9 S. Aureus with 20bp-guides
20bp-NG(G/T) - xCas9, high efficiency PAM, recommended
20bp-NGN or GA(A/T) - xCas9, low efficiency PAM
21bp-NNN(A/G)(A/G)T - KKH SaCas9
20bp-NNN(A/G)(A/G)T - KKH SaCas9 with 20bp-guides
20bp-NGA - Cas9 S. Pyogenes mutant VQR
24bp-NNNNCC - Nme2Cas9
20bp-NGCG - Cas9 S. Pyogenes mutant VRER
20bp-NNAGAA - Cas9 S. Thermophilus
20bp-NGGNG - Cas9 S. Thermophilus
20bp-NNNNG(A/C)TT - Cas9 N. Meningitidis
20bp-NNNNACA - Cas9 Campylobacter jejuni, original PAM
22bp-NNNNRYAC - Cas9 Campylobacter jejuni, revised PAM
22bp-NNNVRYAC - Cas9 Campylobacter jejuni, opt. efficiency
20bp-TTCN - CasX
TTT(A/C/G)-23bp - Cas12a (Cpf1) - recommended, 23bp guides
TTT(A/C/G)-21bp - Cas12a (Cpf1) - 21bp guides recommended by IDT
TTTN-23bp - Cas12a (Cpf1) - low efficiency
ATTN-23bp - BhCas12b v4
NGTN-23bp - ShCAST/AcCAST, Strecker et al, Science 2019
T(C/T)C(A/C/G)-23bp - TYCV As-Cpf1 K607R
TAT(A/C/G)-23bp - TATV As-Cpf1 K548V
TTTA-23bp - TTTA LbCpf1
TCTA-23bp - TCTA LbCpf1
TCCA-23bp - TCCA LbCpf1
CCCA-23bp - CCCA LbCpf1
GGTT-23bp - CCCA LbCpf1
YTTV-20bp - MAD7 Nuclease, Lui, Schiel, Maksimova et al, CRISPR J 2020
TTYN- or VTTV- or TRTV-23bp - enCas12a E174R/S542R/K548R - Kleinstiver et al Nat Biot 2019
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CRISPR/Cas9 Guide Designer for chordate vertebrate ecdysozoans lophotrochozoans protostomes spongi corals plants butterflies metazoans genomes fruitflies insects nematodes mammals.