CCTop - CRISPR/Cas9 target online predictor

Supported species

This is the list of species available in CCTop to identify CRISPR/Cas9 off-target sites. Notice the assembly version of the genome and the gene model used.

If you would like additional species contact us through the forum or a direct email to

Species Genome Gene model
Anopheles gambiae MOZ2 ENSEMBL version 22 (downloaded from UCSC browser)
Arabidopsis TAIR10 ENSEMBLPlants version 30
Arabidopsis lyrata JGI v1.0 MPIPZ v2.1 (Phytozome 12)
Aspergillus flavus JCVI-afl1-v2.0 ENSEMBLFungi version 38
Axolotl ASM291563v1
Bacillus megaterium (Strain ATCC 14581) GCA_000832985.1 GCA_000832985.1
Bacillus sp. strain RZ2MS9 Provided by Everthon Figueredo (Esalq/USP) Provided by Everthon Figueredo (Esalq/USP)
Brassica napus AST_PRJEB5043_v1 ENSEMBLPlants version 38
Broom-corn version 3.1 Phytozome 11 Phytozome 11
C. elegans WBcel235 ENSEMBL version 83
C. intestinalis KH2012 aniseed KH2012 aniseed
Candida albicans (SC5314) CGD version 22 CGD version 22
Cannabis sativa GCA_900626175.1 NA
Cardamine hirsuta v1.0 MPIPZ v1.0 MPIPZ
Caulobacter crescentus ASM2200v1 ENSEMBLBacteria version 32
Cavefish AstMex102 ENSEMBL version 83
Chickpea GCA_000331145.1 GCA_000331145.1
Chickpea Desi School of Plant Biology, University of Western Australia School of Plant Biology, University of Western Australia
Chinese hamster ovary cell line CHO-K1-v1 refseq 2014 v101
Chlamydomonas reinhardtii v3.1 ENSEMBLPlants version 38
Chromochloris zofingiensis v5 v5.2.3.2
Clavibacter cf. michiganensis LMG 26808 GCA_000698005.1 GCA_000698005.1
Cow UMD_3.1 ENSEMBL version 83
E.coli str. K-12 substr. MG1655 (GCA_000801205) ASM80120v1 ENSEMBL version 43
Eucalyptus grandis JGI v2.0 JGI v2.0
European hop GCA_000831365.1 NA
Foxtail millet JGI v2.2 JGI v2.2
Fruit fly BDGP5/dm3 ENSEMBL version 77
Fruit fly BDGP6/dm6 ENSEMBL version 83
Goat ARS1 ENSEMBL version 93
Green foxtail JGI v1.1 JGI v1.1
Human GRCh38/hg38* ENSEMBL version 83
Human GRCh37/hg19* ENSEMBL version 84
Japanese medaka HdrR GCA_002234675.1 ENSEMBL version 95
Kluyveromyces marxianus GCA_001417885.1 GCA_001417885.1
Lettuce JGI v8 JGI v5
Medaka oryLat2 ENSEMBL version 83 plus unpublished transcriptome based on RNA-seq**
Medicago truncatula (Barrel Medic) Medtr4 ENSEMBLPlants version 30
Mouse GRCm38/mm10* ENSEMBL version 83
Nannochloropsis gaditana (B-31) GCA_000569095.1 ENSEMBL Protists version 38
Nannochloropsis oceanica 1779 (CCMP1779 v2.0) CCMP1779 v2.0 (2018) CCMP1779 v2.0 (2018, filtered model)
Oidiodendron maius GCA_000827325.1 ENSEMBLFungi version 43
Paenibacillus larvae subsp. larvae DSM 25430 GCA_000511405.1 GCA_000511405.1
Paenibacillus larvae subsp. larvae DSM 25719 GCA_000511115.1 GCA_000511115.1
Panicum virgatum (V1.0) Phytozome V12 Phytozome V12
Pantoea agglomerans (FDAARGOS_160) GCA_001558735.1 GCA_001558735.1
Papaya ASGPBv0.4 ASGPBv0.4
Penicillium chrysogenum ASM71027v1 ENSEMBLFungi version 37
Petunia axillaris Provided by Dr. Robert Schuurink Provided by Dr. Robert Schuurink
Pig susScr3 ENSEMBL version 83
Populus alba AspenDB v2 AspenDB v2
Populus tremula AspenDB v2 AspenDB v2
Populus trichocarpa JGI v3.0 JGI v3.1
Potato DM1-3 v4.04 Spud DB DM1-3 v4.03 Spud DB
Pseudomonas aeruginosa (UCBPP-PA14) GCF_000006765.1 GCF_000006765.1
Rainbow trout (Oncorhynchus mykiss Omyk_1.0)) GCF_002163495.1 CF_002163495.1
Ralstonia solanacearum GMI1000 ENSEMBLBacteria version 29
Rat rn6 ENSEMBL version 83
Rhesus macaque rheMac2 ENSEMBL version 83
Rice (Oryza sativa Japonica) GCA_001433935.1 ENSEMBL Plants version 38
Saccharomyces cerevisiae S288c GCA_000146045.2 ENSEMBL Fungi version 38
Salmon GCF_000233375.1 GCF_000233375.1
Salt cress version 1.0 Phytozome 12 Phytozome 12
Sheep oviAri3 ENSEMBL version 83
Silk worm SilkDB v2.0 ENSEMBL metazoa version 26
Soybean Wm82.a2.v1 Wm82.a2.v1
Spotted gar LepOcu1 ENSEMBL version 83
Starlet sea anemone GCA_000209225.1 ENSEMBL metazoa version 33
Stickleback BROADS1/gasAcu1 ENSEMBL version 83
Streptomyces acidiscabies NCPPB 4445 ASM118901v1 ENSEMBLBacteria version 32
Streptomyces acidiscabies 84-104 ASM24271v2 ASM24271v2
Streptomyces mobaraensis GCF_000342125.1 GCF_000342125.1
Streptomyces scabiei ASM9130v1 ENSEMBLBacteria version 32
Streptomyces turgidiscabies Sturgcar8v1 ENSEMBLBacteria version 32
Tobacco (Nicotiana benthamiana) Niben101 BTI Niben101 BTI
Tobacco (Nicotiana tabacum) Ntab-BX solgenomics Blat alignments from the Tomato annotation version ITAG 2.4 solgenomics
Tomato Solyc2.5 solgenomics Solyc2.5 solgenomics
Trypanosoma cruzi (CL-Brener) TriTrypDB Release 42 TriTrypDB-42_TcruziCLBrener_Genome.fasta TriTrypDB Release 42 TriTrypDB-42_TcruziCLBrener.gff
Utricularia gibba v4.1, id19477 CoGe v4.1, id19477 CoGe
Xenopus laevis Xenla7.1 JGI 7.2
Xenopus tropicalis JGI4.2/xenTro3 ENSEMBL version 83
Water Flea (Daphnia pulex) JGI 2006-09-05 JGI 060905 V11
Wild sugarcane (Saccharum spontaneum AP85-441) The Ming Laboratory The Ming Laboratory
Yersinia enterocolitica (strain KNG22703) GCA_001305635.1 GCA_001305635.1
Yersinia enterocolitica (strain WA) GCF_000834195.1 GCF_000834195.1
Zymomonas mobilis subsp. mobilis Zm4 ENSEMBLBacteria version 30
Zebrafish Zv9/danRer7 ENSEMBL version 83
Zebrafish danRer10 ENSEMBL version 83
* Only chromosome sequences, no haplotype or unplaced sequences.
**As gene model, for Medaka we use the ENSEMBL genes version 83 plus genes identified from an unpublished work based on RNA-seq data from different embryonic stages. The gene annotation derived from this second set have identifiers with the prefix "XLOC". As gene name in this case the ENSEMBL name or ENSEMBL ID is given if the gene overlaps with an ENSEMBL gene, otherwise we use the description from an automated annotation pipeline based on blast alignments.