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Target
RefSeq/ENSEMBL/gene ID or genomic coordinates.
Target
Paste fasta entry here.
In
Homo sapiens (hg38/GRCh38) GENCODEv29
Mus musculus (mm10/GRCm38) GENCODEvM19
In
Aedes aegypti (AaegL3)
Aedes aegypti (AaegL5)
Aedes albopictus (GCA_001876365.2)
Anopheles funestus (AfunF1)
Anopheles gambiae (anoGam1)
Anopheles gambiae (AgamP4)
Acyrthosiphon pisum (Acyr_2.0)
Anopheles stephensi (Indian, AsteI2)
Anopheles stephensi (SDA-500, AsteS1)
Apis mellifera (HAv3.1)
Anopheles albimanus (AalbS2)
Bactrocera cucurbitae (ASM80634v1)
Bactrocera dorsalis (ASM78921v2)
Bactrocera oleae (GCA_001188975.2)
Bombyx mori (release 31)
Camponotus floridanus (GCF_003227725.1)
Ceratitis capitata (Ccap1.0)
Ceratitis capitata (Ccap_2.1)
Clitarchus hookeri (GCA_002778355.1)
Cimex lectularius (GCF_000648675.2)
Culex quinquefasciatus (CpipJ2)
Dalotia coriaria (Dcor_v1)
Diaphorina Citri (GCF_000475195.1)
Drosophila melanogaster (dm3)
Drosophila melanogaster (dm6)
Drosophila suzukii (Dsuz 1.0)
Harpegnathos saltator (GCF_003227715.1)
Mayetiola destructor (v1.0)
Ixodes scapularis (IscaW1)
Lasius niger (GCA_001045655.1)
Lutzomyia longipalpis (LlonJ1.5)
Manduca sexta (Mansex1.0)
N. vitripennis (Nvit1.0)
Nasonia vitripennis (Nvit2.1)
Phlebotomus papatasi (Ppapl1.5)
Papilio polytes (Ppolytes v1)
Rhodnius prolixus (RproC3)
Tetranychus urticae (Sept 2009)
Tribolium castaneum (Tcas5)
Astatotilapia burtoni (AstBur1.0)
Austrofundulus limnaeus (GCF_001266775.1)
Astyanax mexicanus (AstMex102)
Betta splendens (v1.1)
Betta splendens (fBetSpl5.2)
Betta splendens (BetSpl5)
Bos taurus (Btau 5.0)
Bos taurus (bosTau9)
Bos taurus indicus (GCF_000247795.1)
Bubalus bubalis (GCF_003121395.1)
Chinese Hamster Ovary CHO-K1 (GCF_003668045.3_CriGri-PICRH-1.0)
Canis familiaris (CanFam3)
Ciona intestinalis (KH2012)
Callithrix jacchus (C_jacchus3.2.1)
Capra hircus (GCF_001704415.1)
Coturnix japonica (GCF_001577835.1)
Carcharodon carcharias (GCA_003604245.1)
Cyprinodon variegatus (GCF_000732505.1)
Danio rerio (danRer10/GRCz10)
Danio rerio (danRer11/GRCz11)
Equus caballus (EquCab2)
Felis Catus (felCat9)
Gasterosteus aculeatus (gasAcu1)
Gallus gallus (galGal4)
Gallus gallus (galGal5)
Gallus gallus (galGal6)
Homo sapiens (hg19/GRCh37)
Homo sapiens (hg38/GRCh38)
Larimichthys crocea (GCA_900246015.1)
Lepisosteus oculatus (LepOcu1)
Maylandia zebra (M_zebra_UMD2a/GCA_000238955.5)
Mus musculus (mm10/GRCm38)
Mus musculus (mm39)
Mustela putorius furo (MusPutFur1.0/musFur1)
Macaca mulatta (Mmul_10)
Nothobranchius furzeri (NotFur1/Stanford)
Nothobranchius furzeri (Nfu_20140520/Jena)
Oryctolagus cuniculus (GCA_000003625.1)
Oikopleura dioica (Odioica)
Oryzias latipes (oryLat2)
Oryzias latipes (ASM223467v1)
Oncorhynchus mykiss (Omyk_1.0)
Oreochromis niloticus (ASM185804v2)
Ovis aries (Oar_v3.1)
Rattus norvegicus (rn6)
Salmo salar (GCF_000233375.1)
Sus scrofa (Sscrofa11.1)
Sparus aurata (GCA_900880675.1)
Xenopus laevis (Xenla9.1/JGI v9.1)
Xenopus laevis (v9.2)
Xenopus tropicalis (xenTro9.0/JGI v9.0)
Xenopus tropicalis (v9.1)
Exaiptasia pallida isolate CC7 (GCA_001417965.1)
Nematostella vectensis (nemVec1)
Mnemiopsis leidyi (GCA_000226015.1)
Lytechinus variegatus (Lvar_2.2)
Strongylocentrotus purpuratus (EchinoBase v3.1)
Biomphalaria glabrata (BglaB1)
Octopus bimaculoides (PRJNA270931)
Ancylostoma ceylanicum (PRJNA231479)
Caenorhabditis elegans (ce10/WS220)
Pristionchus pacificus (TAU2011)
Acidovorax citrulli str. M6 (CP029373.1)
Anabaena (PCC 7120)
Azotobacter vinelandii DJ (NC_012560.1)
Bdellovibrio bacteriovorus (ASM19617v1)
Bacteroides fragilis 638R (FQ312004.1)
Bacteroides fragilis 9343 (NC_003228.3)
Bacillus RZ2MS9 (MJBF01)
Bacillus RZ2MS9 (CP049978.1)
Bacillus cereus ATCC14579 (NC_004722.1)
Bacillus subtilis 168 (NC_000964.3)
Bacteroides thetaiotaomicron (FR901300.1)
Bifidobacterium longum (GCA_000196555)
Candidatus Carsonella ruddii (NC_018417.1)
Caulobacter crescentus (NA1000)
Chlamydia psittaci (GCA_000204255.1)
Clostridium acetobutylicum ATCC 824 (GCF_000008765.1)
Clostridium beijerinckii 6423 (GCF_900010805.1)
Clostridium botulinum ATCC 19397 (NC_009697.1)
Corynebacterium glutamicum ATCC 13032 (GCF_000011325.1)
Corynebacterium pseudotuberculosis 1002 (GCF_000144935.1)
Coxiella burnetii RSA 493 (GCF_000007765.2)
Cupriavidus malaysiensis USMAA1020 chr1 (CP017754.1)
Cupriavidus malaysiensis USMAA1020 chr2 (CP017754.1)
Cyanobacterium aponinum PCC 10605 (CP003947.1)
Campylobacter jejuni NCTC11168 (GCF_000009085.1)
Dermacoccus abyssi str. HZAU 226 (CP043031.1)
Escherichia coli (str. CFT073/ASM744v1)
Escherichia coli (str. K-12/MG1655)
Escherichia coli (Nissle 1917/CP007799.1)
Escherichia coli (C321.ΔA/GCA_000474035.1)
Escherichia coli BW25113 (NZ_CP009273.1)
Enterococcus faecalis (GCF_000007785.1)
Enterococcus faecalis OG1RF (GCA_000172575.2)
Eubacterium limosum ATCC 8486 (NZ_CP019962.1)
Francisella tularensis sp. holarctica FSC200 (GCA_000168775.2)
Klebsiella pneumoniae str. SGH10 (CP025080)
Lactobacillus delbrueckii (ATCC 11842)
Lactobacillus casei (GCA_000829055.1)
Lactobacillus plantarum WCFS1 (firmicutes) (GCF_000203855.3)
Legionella pneumophila (GCF_000008485.1)
Leptospira biflexa (GCF_000017685.1)
Listeria monocytogenes EGD-e (GCF_000196035.1)
Lysobacter enzymogenes (NZ_CP013140.1)
Mycobacterium marinum M (ASM1834v1)
Mycobacteroides abscessus ATCC 19977(MAb) (GCA_000069185.1)
Mycobacterium smegmatis MC2 155 (GCF_000015005.1)
Mycoplasma genitalium (NC_000908.2)
Neisseria gonorrhoeae FA 1090 (NC_002946.2)
Nocardia terpenica strain NC_YFY_NT001 (NZ_CP023778.1)
Mycobacterium tuberculosis H37Rv (ASM19595v2)
Orientia tsutsugamushi (GCF_900327275.1)
Paenibacillus thiaminolyticus (GCF_002161855.1)
Pseudomonas aeruginosa (UCBPP-PA14)
Pseudomonas syringae pv. tomato str. DC3000 (NC_004578.1)
Pantoea agglomerans (NZ_CP014129.1)
Pseudomonas cichorii JBC1 (PRJNA232591)
Rhodobacter capsulatus SB 1003 (CP001312.1)
Rhodobacter sphaeroides 2.4.1 (NZ_CP030271.1 (chr1))
Rhodobacter sphaeroides 2.4.1 (NZ_CP030272.1 (chr2))
Rhodobacter sphaeroides (KD131)
Rhodopseudomonas palustris CGA009 (NC_005296.1)
Salmonella enterica subsp. (GCF_000022165.1)
Salmonella enterica subsp. Typhimurium str. LT2 (GCF_000006945.2)
Shewanella oneidensis MR-1 (AE014299.2)
Shigella flexneri 1c (CP020753)
Shigella flexneri 5a M90T (NZ_CP037923.1)
Staphylococcus aureus (MSSA-GP01, v1.0)
Staphylococcus aureus (MRSA-ATCC 43300, v1.0)
Streptomyces coelicolor M145 (ASM20383v1)
Streptomyces platensis (DSM-40041)
Streptococcus pyogenes M1 GAS (GCA_000321355.1)
Synechococcus sp. PCC 7002 (CP000951.1)
Thalassomonas viridans (GCF_000948985.1)
Thermoanaerobacter ethanolicus JW 200 (GCF_003722315.1)
Treponema caldarium (GCF_000219725.1)
Vibrio natriegens (NZ_CP009977.1)
Xenorhabdus nematophila (GCF_000252955.1)
Aspergillus fumigatus (Af293)
Arthrobotrys oligospora (GCF_000225545.1)
Aspergillus niger (ATCC 1015)
Botrytis cinerea (ASM83294v1)
Candida albicans (A22)
Candida auris (GCA_002759435.2)
Candida glabrata (CBS138)
Candida krusei (GCA_003054445.1)
Candida lusitaniae (GCA_000003835.1)
Candida parapsilosis (GCA_000182765.2)
Collectotrichum graminicola M1.001 (Colgr1)
Cochliobolus heterostrophus C5 (v2.0)
Candida tropicalis (MYA-3404)
Grifola frondosa (GCA_001683735.1)
Metarhizium anisopliae (MAN 1.0)
Mortierella alpine ATCC 32222 (GCA_000240685.2)
Neurospora crassa (GCA_000182925.2)
Ogataea polymorpha NCYC495 leu1.1 (Hanpo2)
Paecilomyces variotii (CBS101075)
Penicillium roqueforti (FM164)
Pochonia chlamydosporia (GCF_001653235.2)
Puccinia triticina (GCA_000151525.1)
Purpureocillium lilacinum (GCA_001653205.1)
Pichia pastoris (PRJEA62483)
Saccharomyces cerevisiae (sacCer3/S288c)
Schizosaccharomyces pombe (ASM294v2.30)
Starmerella bombicola (JCM_9596_assembly_v001)
Trichoderma brevicrassum TC967
Trichoderma harzianum T22 (TriharT22)
Trichoderma reesei (GCA_000167675.2)
Trichophyton interdigitale MR816 (GCA_000622975)
Trichophyton rubrum CBS 118892 (GCA_000151425)
Yarrowia lipolytica (GCF_000002525.2)
Yarrowia lipolytica (W29)
Zymoseptoria tritici (GCA_000219625.1)
Leishmania braziliensis (MHOM/BR/75/M2904)
Leishmania major Friedlin (LmjF.01)
Leishmania major Friedlin (TritrypDB 46)
Plasmodium berghei (ANKA v2.0)
Plasmodium cynomolgi (GCF_000321355.1)
Plasmodium falciparum (3D7 v3.0)
Opisthorchis viverrini (GCF_000715545.1)
Schistosoma haematobium (GCF_000699445.2)
Schistosoma mansoni (Smansoni_v7)
Trypanosoma cruzi (TcruziSylvioX10-1-2012)
Trypanosoma brucei (TREU927)
Toxoplasma gondii GT1 (ToxoDB-28)
Toxoplasma gondii ME49 (ToxoDB-28)
Aquilegia coerulea (v3.1)
Arachis hypogaea (GCA_003086295.2)
Arachis duranensis (Aradu 1.0)
Arachis ipaensis (Araip 1.0)
Arabidopsis thaliana (Araport11)
Cicer arietinum (ASM33114v1)
Cannabis sativa (v2)
Cardamine hirsuta (v1.0)
Chrysanthemum seticuspe (CSE_r1.0)
Chlorella sorokiniana (CSI2_1230)
Coffea canephora (v1.0)
Dendrobium catenatum (ASM160598v2)
Eucalyptus grandis (v2.0)
Emiliania huxleyi (CCMP1516)
Eutrema salsugineum (v1.0)
Eragrostis tef (1.1.2)
Glycine max (GCA_000004515.3)
Gossypium hirsutum (v1.1)
Lupinus angustifolius (GCF_001865875.1)
Marchantia polymorpha (MpTak1v5.1)
Nannochloropsis oceanica (IMET1.v2)
Nymphaea thermarum (ASM1179976v1)
Oryza sativa (MSU-version_7.0)
Petunia axillaris (v1.6.2)
Panicum virgatum (Panicum virgatum-v4)
Physcomitrella patens (Ppatens_318_v3)
Phalaenopsis equestris (ASM126359v1)
Populus deltoides (WV94 v2.1)
Populus trichocarpa (v3.1)
Sesamum indicum (GCF_000512975.1)
Solanum lycopersicum (SL3.0)
Sorghum bicolor (Phytozome v3.1.1)
Utricularia gibba (v1.1F)
Triticum aestivum (IWGSC v1.1) Chr 1 & 2 only!
Zea mays (B73 AGPv4)
African Swine Fever Virus Kenya (IX 1033)
Autographa californica nucleopolyhedrovirus (AcMNPV) (NC_001623.1)
Bovine diarrhea virus (NC_001461.1)
Enterobacteria phage lambda (J02459.1)
Gallid herpesvirus 1 (NC_006623.1)
Gallid herpesvirus 2 (str. CVI988, DQ530348.1)
Gallid herpesvirus 3 (str. SB-1, HQ840738.1)
Hepatitis B (AB602818.1)
Hepatitis C (M58335.1)
Human herpesvirus 1 (str. 17, JN555585.1)
Human herpesvirus 2 (str. 333)
Human herpesvirus 2 (str. HG52)
Human herpesvirus 2 (str. SD90e)
Human herpesvirus 4 (str. Akata)
Human herpesvirus 6A (U1102_X83413)
Human herpesvirus 6B (Z29_NC000898)
Human T-cell lymphotropic virus type I (J02029.1)
HIV-1 (AF033819.3)
Meleagrid herpesvirus 1 strain FC126 (AF291866.1)
Monkeypox virus Zaire -96-I-16 (NC_003310)
Myxoma Virus (GCA_000843685.1)
Simian foamy virus isolate BAK74 (JQ867464)
Vaccinia virus (str. WR/AY243312.1)
Wuhan Coronavirus (nCORV-2019)
Acanthamoeba castellanii (GCF_000313135.1)
Amphimedon queenslandica (GCF_000090795.1)
Aurantiochytrium limacinum ATCC MYA-1381 (Aurli1)
Babesia bovis T2Bo (BbovisT2Bo)
Chlamydomonas reinhardtii (v5.6)
Corallochytrium limacisporum (Hawaii) (v01)
Ectocarpus (EctsiV2)
Naegleria gruberi (GCF_000004985.1)
Phaeodactylum tricornutum (ASM15095v2)
Pseudonitzschia multistriata (PsnmuV1.4)
Schmidtea mediterranea (schMed4)
Tetrahymena thermophila (MAC)
Tetrahymena thermophila (MIC)
Add
new species.
Using
CRISPR/Cas9
CRISPR/Cas9 nickase
CRISPR/Cpf1 or CasX
CRISPR/Cas13 (eg. C2C2)
TALEN
Change default PAM and guide length in Options.
For
knock-out
knock-down
knock-in
activation
repression
nanopore enrichment
Presets can be adjusted in Options.
General
Cas9
Cpf1
Cas13
Cas9 nickase
TALEN
Primers
Target specific region of gene:
Coding region
All exons (inc. UTRs)
Splice sites
5' UTR
3' UTR
Promoter
Only target exon(s):
Restrict targeting:
Search exons and immediate short flanking regions.
Only search within the exon.
Isoform consensus determined by:
Intersection (only searches regions present in all isoforms)
Union (searches all exons in all isoforms)
Pre-filtering:
Minimum required GC [%] content has to be between min:
and max:
Self-complementarity has to be below:
Restriction enzymes:
Company preference:
Life Technologies
Minotech Biotechnology
Agilent Technologies
SibEnzyme Ltd.
Nippon Gene Co., Ltd.
Takara Bio Inc.
Roche Applied Science
New England Biolabs
Toyobo Biochemicals
Molecular Biology Resources - CHIMERx
Promega Corporation
Sigma Chemical Corporation
EURx Ltd.
SinaClon BioScience Co.
Minimum size of restriction enzyme binding site:
Fasta input:
Color scoring should ignore one off-target without mismatches.
Displayed flanking sequence length in detailed view:
sgRNA length without PAM:
PAM-3':
NGG
NAG
NGA
NRG (R = A or G)
NNAGAAW (W = A or T)
NNNNGMTT (M = A or C)
NNGRRT (R = A or G)
Custom PAM:
Method for determining off-targets in the genome:
Off-targets with up to
mismatches in protospacer
(Hsu et al., 2013)
Off-targets may have no more than
mismatches in the protospacer seed region
(Cong et al., 2013)
Efficiency score:
Doench et al. 2014 - only for NGG PAM
Doench et al. 2016 - only for NGG PAM
Chari et al. 2015 - only NGG and NNAGAAW PAM's in hg19 and mm10
Xu et al. 2015 - only for NGG PAM, but can be used with other PAMs
Moreno-Mateos et al. 2015 - only for NGG PAM
G20
Repair profile prediction (Shen et al. 2018):
mESC (recommended when you don't know which cell type)
U2OS
HEK293
HCT116
K562
Don't calculate (saves time)
5' requirements for sgRNA:
GN or NG
GG
No requirements
Self-complementarity (Thyme et al.):
Check for self-complementarity
I intend to replace the leading nucleotides with "GG"
Check for complementarity versus backbone:
Standard backbone (AGGCTAGTCCGT)
Extended backbone (AGGCTAGTCCGT,ATGCTGGAA)
Custom backbone:
sgRNA length without PAM:
PAM-3':
NGG
NAG
NGA
NRG (R = A or G)
NNAGAAW (W = A or T)
NNNNGMTT (M = A or C)
NNGRRT (R = A or G)
Custom PAM:
Method for determining off-targets in the genome:
Off-targets with up to
mismatches in protospacer
(Hsu et al., 2013)
Off-targets may have no more than
mismatches in the protospacer seed region
(Cong et al., 2013)
Efficiency score:
Doench et al. 2014 - only for NGG PAM
Doench et al. 2016 - only for NGG PAM
Chari et al. 2015 - only for NGG and NNAGAAW PAM's in hg19 and mm10
Xu et al. 2015 - only for NGG PAM, but can be used with other PAMs
Moreno-Mateos et al. 2015 - only for NGG PAM
G20
5' requirements for sgRNA:
GN or NG
GG
No requirements
Self-complementarity (Thyme et al.):
Check for self-complementarity
I intend to replace the leading nucleotides with "GG"
Check for complementarity versus backbone:
Standard backbone (AGGCTAGTCCGT)
Extended backbone (AGGCTAGTCCGT,ATGCTGGAA)
Custom backbone:
Distance between guides:
to:
Max distance between offtargets:
sgRNA length without PAM:
PFS:
5' end of target (like in Cpf1) e.g. Cas13a:
3' end of target (like in Cas9):
sgRNA length without PAM:
5'-PAM:
TTN
TTTN
TTCN (CasX)
Non-standard:
Efficiency score:
Kim et al. 2018
None (will display zeros in "Efficiency" column)
Self-complementarity (Thyme et al.):
Check for self-complementarity
Check for complementarity versus backbone:
Standard backbone (AGGCTAGTCCGT)
Extended backbone (AGGCTAGTCCGT,ATGCTGGAA)
Custom backbone:
Distance between TALENs:
to:
Size of TALENs:
Number of mismatches to search for when finding off-targets:
0
1
2
G repeat variable diresidue (RVD):
NN
NH
Design primers
Product size:
From:
to:
Primer size:
From:
to:
Optimal:
Primer Tm:
From:
to:
Optimal:
Minimum distance from primer to target site:
Paste Target
Options
Reset Options
Find Target Sites!
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