Eukaryotic Pathogen CRISPR guide RNA Design Tool

with (1) custom genome upload, (2) off-target analysis, (3) on-targets searching (for targeting gene families), (4) efficiency/activity prediction, (5) assisted oligo repair template design , (6) guide RNA transcription problem identification, (7) flanking microhomology searching (for predicting deletions)

batch mode available here

Gene tagging batch mode available here (?)

Our CRISPR/Cas9 gRNA design tool has a new look!!

Job Name:

RNA guided nuclease selection: (?)

choose one to automatically configure gRNA and PAM settings for each nuclease

custom (please manually enter PAM requirement)

Additional option settings: (click to expand a category)

guide RNA search parameters

guide RNA length:  

PAM motif(s):
(use comma to separate multiple PAM motifs
use IUPAC code for degenerate base)

on-target search parameters

(Default settings
recommended for most users)

homology arm length:

off-target search parameters

(Default settings
recommended for most users)

seed sequence length (including PAM):

maximum number
of mismatches:

off-target PAM motif(s)(?):
(comma separated if more than one,
use IUPAC code for degenerate base)

HDR repair template parameters

(Default settings
recommended for most users)

homology arm length:(?)     


Genome (expand a category and choose one):

genome naming paradigm:
specie strain database-version


A. castellanii Neff AmoebaDB-26
E. dispar SAW760 AmoebaDB-26
E. histolytica (Amoeba) HM1IMSS AmoebaDB v26
E. histolytica (Amoeba) HM1IMSS AmoebaDB v28
E. histolytica HM1IMSS-A AmoebaDB-26
E. histolytica HM1IMSS-B AmoebaDB-26
E. histolytica HM3IMSS AmoebaDB-26
E. histolytica KU27 AmoebaDB-26
E. invadens IP1 AmoebaDB-26
E. moshkovskii Laredo AmoebaDB-26
E. nuttalli P19 AmoebaDB-26
N. fowleri ATCC30863 AmoebaDB-26


C. hominis TU502 CryptoDB-26
C. muris RN66 CryptoDB-26
C. parvum IowaII CryptoDB-26
C. parvum IowaII CryptoDB-28
C. velia CCMP2878 CryptoDB-26
G. niphandrodes Unknown CryptoDB-26
V. brassicaformis CCMP3155 CryptoDB-26


A. aculeatus ATCC16872 FungiDB-26
A. capsulatus G186AR FungiDB-26
A. capsulatus NAm1 FungiDB-26
A. carbonarius ITEM5010 FungiDB-26
A. clavatus NRRL1 FungiDB-26
A. flavus NRRL3357 FungiDB-26
A. fumigatus Af293 FungiDB-26
A. macrogynus ATCC38327 FungiDB-26
A. nidulans FGSCA4 FungiDB-26
A. niger ATCC1015 FungiDB-26
A. niger CBS513-88 FungiDB-26
A. oryzae RIB40 FungiDB-26
A. terreus NIH2624 FungiDB-26
B. dendrobatidis JEL423 FungiDB-26
B. fuckeliana B05-10 FungiDB-26
C. albicans SC5314 FungiDB-26
C. cinerea okay7-130 FungiDB-26
C. gattii R265 FungiDB-26
C. gattii WM276 FungiDB-26
C. glabrata CBS138 FungiDB-26
C. immitis H538-4 FungiDB-26
C. immitis RS FungiDB-26
C. neoformans B-3501A FungiDB-26
C. neoformans H99 FungiDB-26
C. neoformans JEC21 FungiDB-26
C. posadasii C735deltSOWgp FungiDB-26
C. posadasii RMSCC3488 FungiDB-26
C. posadasii Silveira FungiDB-26
F. graminearum PH-1 FungiDB-26
F. oxysporum 4287 FungiDB-26
F. verticillioides 7600 FungiDB-26
M. circinelloides CBS277-49 FungiDB-26
M. globosa CBS7966 FungiDB-26
M. larici-populina 98AG31 FungiDB-26
M. oryzae 70-15 FungiDB-26
N.crassa OR74A FungiDB-26
N. discreta FGSC8579 FungiDB-26
N. fischeri NRRL181 FungiDB-26
N. tetrasperma FGSC2508 FungiDB-26
P. blakesleeanus NRRL1555- FungiDB-26
P. chrysosporium RP-78 FungiDB-26
P. graminis CRL75-36-700-3 FungiDB-26
P. jirovecii SE8 FungiDB-26
R. delemar RA99-880 FungiDB-26
S. cerevisiae S288c FungiDB-26
S. japonicus yFS275 FungiDB-26
S. macrospora k-hell FungiDB-26
S. octosporus yFS286 FungiDB-26
S. pombe 972h- FungiDB-26
S. punctatus DAOMBR117 FungiDB-26
S. reilianum SRZ2 FungiDB-26
S. sclerotiorum 1980UF-70 FungiDB-26
T. marneffei ATCC18224 FungiDB-26
T. mesenterica DSM1558 FungiDB-26
T. reesei QM6a FungiDB-26
T. stipitatus ATCC10500 FungiDB-26
U. maydis 521 FungiDB-26
Y. lipolytica CLIB122 FungiDB-26


G. intestinalis Assemblage_A GiardiaDB-26
G. intestinalis Assemblage_A GiardiaDB-28
G. intestinalis AssemblageADH GiardiaDB-26
G. intestinalis Assemblage_B GiardiaDB-26
G. intestinalisAssemblageBGS B GiardiaDB-26
G. intestinalis AssemblageE GiardiaDB-26
S. salmonicida ATCC50377 GiardiaDB-26


A. algerae PRA109 MicrosporidiaDB-26
A. algerae PRA339 MicrosporidiaDB-26
E. aedis USNM41457 MicrosporidiaDB-26
E. bieneusi H348 MicrosporidiaDB-26
E. cuniculi1 EC1 MicrosporidiaDB-26
E. cuniculi EC2 MicrosporidiaDB-26
E. cuniculi EC3 MicrosporidiaDB-26
E. cuniculi GBM1 MicrosporidiaDB-26
E. hellem ATCC50504 MicrosporidiaDB-26
E. hellem Swiss MicrosporidiaDB-26
E. intestinalis ATCC50506 MicrosporidiaDB-26
E. romaleae SJ2008 MicrosporidiaDB-26
M. daphniae UGP3 MicrosporidiaDB-26
N. bombycis CQ1 MicrosporidiaDB-26
N. ceranae BRL01 MicrosporidiaDB-26
N. ematocida Sp1ERTm2 MicrosporidiaDB-26
N. parisii ERTm1 MicrosporidiaDB-26
N. parisii ERTm3 MicrosporidiaDB-26
N. sp 1ERTm6 MicrosporidiaDB-26
O. colligata OC4 MicrosporidiaDB-26
S. lophii42 110 MicrosporidiaDB-26
T. hominis Unknown MicrosporidiaDB-26
V. corneae ATCC50505 MicrosporidiaDB-26
V. culicisfloridensis MicrosporidiaDB-26


A. astaci APO3 FungiDB-26
A. candida 2VRR FungiDB-26
A. invadans NJM9701 FungiDB-26
A. laibachii Nc14 FungiDB-26
H. arabidopsidis Emoy2 FungiDB-26
P. aphanidermatum DAOMBR444 FungiDB-26
P. arrhenomanes ATCC12531 FungiDB-26
P. capsici LT1534 FungiDB-26
P. cinnamomi CBS144-22 FungiDB-26
P. infestans T30-4 FungiDB-26
P. irregulare DAOMBR486 FungiDB-26
P. iwayamai DAOMBR242034 FungiDB-26
P. parasitica INRA-310 FungiDB-26
P. ramorum Pr-102 FungiDB-26
P. sojae P6497 FungiDB-26
P. ultimum BR650 FungiDB-26
P. ultimum DAOMBR144 FungiDB-26
P. vexans DAOMBR484 FungiDB-26
S. diclina VS20 FungiDB-26
S. parasitica CBS223-65 FungiDB-26


B. bigemina BOND PiroplasmaDB-26
B. bovis T2Bo PiroplasmaDB-26
B. microti RI PiroplasmaDB-26
C. felis Winnie PiroplasmaDB-26
T. annulata Ankara PiroplasmaDB-26
T. equi WA PiroplasmaDB-26
T. orientalis Shintoku PiroplasmaDB-26
T. parva Muguga PiroplasmaDB-26


P. berghei ANKA PlasmoDB-26
P. berghei ANKA PlasmoDB-28
P. chabaudichabaudi PlasmoDB-26
P. cynomolgi B PlasmoDB-26
P. falciparum 3D7 PlasmoDB-26
P. falciparum 3D7 PlasmoDB-28
P. falciparum IT PlasmoDB-26
P. gallinaceum 8A PlasmoDB-26
P. knowlesi H PlasmoDB-26
P. reichenowi CDC PlasmoDB-26
P. vivax SaI1 PlasmoDB-26
P. yoeliiyoelii 17X PlasmoDB-26
P. yoeliiyoelii 17X PlasmoDB-28
P. yoeliiyoelii 17XNL PlasmoDB-26
P. yoeliiyoelii YM PlasmoDB-26
P. yoeliiyoelii YM PlasmoDB-28


E. acervulina Houghton ToxoDB-26
E. brunetti Houghton ToxoDB-26
E. falciformis BayerHaberkorn1970 ToxoDB-26
E. maxima Weybridge ToxoDB-26
E. mitis Houghton ToxoDB-26
E. necatrix Houghton ToxoDB-26
E. praecox Houghton ToxoDB-26
E. tenella Houghton ToxoDB-26
H. hammondi HH34 ToxoDB-26
N.caninum LIV ToxoDB-26
S. neurona SN1 ToxoDB-26
S. neurona SN3 ToxoDB-26
T. gondii GT1 ToxoDB-26
T. gondii GT1 ToxoDB-28
T. gondii ME49 ToxoDB-26
T. gondii ME49 ToxoDB-28
T. gondii RH ToxoDB-26(limited annotation)
T. gondii RH ToxoDB-28
T. gondii VEG ToxoDB-26
T. gondii VEG ToxoDB-28


T. vaginalis TrichDB v1.3
T. vaginalis G3 TrichDB-26


C. fasciculata CfCl TriTrypDB-26
E. monterogeii LV88 TriTrypDB-26
L. aethiopica L147 TriTrypDB-26
L. arabica LEM1108 TriTrypDB-26
L. braziliensis MHOMBR75M2903 TritrypDB-26
L. braziliensis MHOMBR75M2903 TritrypDB-28
L. braziliensis MHOMBR75M2904 TriTrypDB-26
L. donovani BPK282A1 TritrypDB-26
L. donovani BPK282A1 TritrypDB-28
L. enriettii LEM3045 TriTrypDB-26
L. gerbilli LEM452 TriTrypDB-26
L. infantum JPCM5 TritrypDB-26
L. infantum JPCM5 TritrypDB-28
L. major Friedlin TritrypDB-26
L. major Friedlin TritrypDB-28
L. major LV39c5 TriTrypDB-26
L. major LV39c5 TriTrypDB-28
L. major SD75.1 TriTrypDB-26
L. major SD75.1 TriTrypDB-28
L. mexicana MHOMGT2001U1103 TritrypDB-26
L. mexicana MHOMGT2001U1103 TritrypDB-28
L. panamensis MHOMCOL81L13 TriTrypDB-26
L. pyrrhocoris H10 TriTrypDB-26
L. seymouri ATCC30220 TriTrypDB-26
L. seymouri ATCC30220 TriTrypDB-28
L. sp MARLEM2494 TriTrypDB-26
L. tarentolae ParrotTarII TriTrypDB-26
L. tropica L590 TriTrypDB-26
L. turanica LEM423 TriTrypDB-26
T. brucei Lister427 TriTrypDB-26
T. brucei Lister427 TriTrypDB-28
T. brucei TREU927 TritrypDB-28
T. bruceigambiense DAL972 TriTrypDB-26
T. congolense IL3000 TriTrypDB-26
T. cruzi CLBrener TritrypDB-28 (hybrid diploid)
T. cruzi CLBrener TritrypDB-29 (hybrid diploid, including unassigned contigs)
T. cruzi CLBrener Esmeraldo-like TriTrypDB-28
T. cruzi CLBrener Non-Esmeraldo-like TriTrypDB-28
T. cruzi Dm28c TritrypDB-26
T. cruzi Dm28c TritrypDB-28
T. cruzi SylvioX10-1 TritrypDB-26
T. cruzi SylvioX10-1 TritrypDB-28
T. cruzi marinkellei B7 TriTrypDB-26
T. evansi STIB805 TriTrypDB-26
T. grayi ANR4 TriTrypDB-26
T. rangeli SC58 TriTrypDB-26
T. vivax Y486 TriTrypDB-26
A. deanei European Nucleotide Archive GCA_000442575.2 Dec 2014 v83.1
L. passim (Crithidia mellificae) Lotmaria passim whole genome shotgun (WGS) project, accession number AHIJ01000000, last update 2015-03-11

 Courtesy Uploads

Paramecium tetraurelia Stock d4-2 strain (repeat masked)
Biomphalaria glabrata BB02 strain released 2013.4 (repeat masked)
Canis_familiaris v3.1 (repeat masked)
D. melanogaster r6.04 FB2015_01
Enterobacteria phage T4
Mus musculus BALB/c
Mus musculus C57BL/6J

 Custom genome

upload your custom genome

 request more default genomes here


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