SugarcaneOmics
The SugarCane multi-Omics Database

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Home

Genome

Genome Genes Pan-Gene

Transcriptome

Dataset ExpProfile DegPattern

Variome

FeatureGenes

Transcription Factor Functional Genes

Varieties

Tools

BLAST

BLASTN BLASTP BLASTX TBLASTN

SeqFetch GO Enrichment KEGG Enrichment CRIOff PrimerServer PIN Miner Visualization

Downloads

About

Documentation Statistics News About Us

Home

Tools

CRIOff

CRIOff can search potential off-target sites of CRISPR/Cas-derived RNA-guided endonucleases (RGEN), and predict the off-targets activities. It employs Cas-OFFinder to find the off-target sites, then uses CRISPR-Net to quantify the activities of the off-target with Indels and Mismatches.

CRISPR/Cas-derived RNA-guided Endonucleases (RGENs): PAM type

Select Protospacer Adjacent Motif (PAM) type

SpCas9 from Streptococcus pyogenes: 5'-NGG-3'

SpCas9 from Streptococcus pyogenes: 5'-NRG-3' (R = A or G)

StCas9 from Streptococcus thermophilus: 5'-NNAGAAW-3' (W = A or T)

NmCas9 from Neisseria meningitidis: 5'-NNNNGMTT-3' (M = A or C)

SaCas9 from Staphylococcus aureus: 5'-NNGRRT-'3 (R=A or G)

CjCas9 from Campylobacter jejuni: 5'-NNNVRYAC-3' (V = G or C or A, R = A or G, Y = C or T)

CjCas9 from Campylobacter jejuni: 5'-NNNNRYAC-3' (R=A or G, Y= C or T)

AsCpf1 from Acidaminococcus or LbCpf1 from Lachnospiraceae: 5'-TTTN-3'

AsCpf1 from Acidaminococcus or LbCpf1 from Lachnospiraceae: 5'-TTTV-3'(V = G or C or A)

SpCas9 from Streptococcus pasteurianus: 5'-NNGTGA-3'

FnCpf1 from Francisella: 5'-TTN-3'

SaCas9 from Staphylococcus aureus: 5'-NNNRRT-'3 (R=A or G)

FnCpf1 from Francisella: 5'-KYTV-3'

VRER SpCas9 from Streptococcus pyogenes: 5'-NGCG-3'

VQR SpCas9 from Streptococcus pyogenes: 5'-NGA-3'

XCas9 3.7 (TLIKDIV SpCas9) from Streptococcus pyogenes: 5'-NGT-3'

XCas9 3.7 (TLIKDIV SpCas9) from Streptococcus pyogenes: 5'-NG-3'

BhCas12b from Bacillus hisashii: 5'-TTN-3'

BhCas12b v4 from Bacillus hisashii: 5'-ATTN-3'

BhCas12b v4 from Bacillus hisashii: 5'-DTTN-3'

Spy-macCas9 from Streptococcus pyogenes and Streptococcus macacae: 5'-NAAN-3'

Nme2Cas9 from Neisseria meningitidis: 5'-NNNNCC-3'

RR AsCpf1 from Acidaminococcus: 5'-TYCV-3'

RVR AsCpf1 from Acidaminococcus: 5'-TATV-3'

CcCas9 from Clostridium cellulolyticum: 5'-NNNNGNA-3'

MAD7 nuclease: 5'-YTTV-3'

Complementary SpCas9 from Streptococcus pyogenes: 5'-NCC-3'

ThermoCas9 from Geobacillus thermodenitrificans T1: 5'-NNNNCNR-3'

ThermoCas9 from Geobacillus thermodenitrificans T1: 5'-NNNNCNAA-3'

SpRY Cas9 from Streptococcus pyogenes: 5'-NNN-3'

SpRY Cas9 from Streptococcus pyogenes: 5'-NRN-3'

SpCas9 Variant from Streptococcus pyogenes: 5'-NGC-3'

Cas12f1 from Acidibacillus sulfuroxidans: 5'-TTTR-3'

Cas12f1 from Acidibacillus sulfuroxidans: 5'-NTTR-3'

DpbCasX (Cas12e) from Deltaproteobacteria: 5'-TTCN-3'

SpCas9 Variant (TAT.P5-1) from Streptococcus pyogenes: 5'-NRTH-3' (R=G or A, H=A or C orT)

SpCas9 from Staphylococcus Auricularis: 5'-NNGG-3'

St3Cas9 from Streptococcus Thermophilus: 5'-NGGNG-3'

Frcas9 from Faecalibaculum rodentium: 5’-NRTA-3’ for target (R=A or G)

Frcas9 from Faecalibaculum rodentium: 5’-NNNA-3’

LtCas12a from Cas12a family: 5’-TTNA-3’

SpCas9: 5’-NRNH-3’

VRQR SpCas9 from Streptococcus pyogenes: 5'-NGNG-3'

SpCas9 Variant from Streptococcus pyogenes: 5'-NRCH-3'

Target genome

Saccharum spontaneum Np-X

Saccharum spontaneum AP85-441

Saccharum spontaneum Np-X

Saccharum officinarum LA-purple

Saccharum hybrid cultivar CC-01-1940

Saccharum hybrid cultivar GT42

Saccharum hybrid cultivar R570

Saccharum hybrid cultivar ROC22

Saccharum hybrid cultivar ZZ1

Erianthus fulvus (Ness)

Erianthus rockii (YN83-224)

Erianthus rufipilus (Yunnan2009-3)

Query sequences

Note: Query sequences (5' to 3'), one sequence per line. Mixed bases are allowed.
Please write crRNA sequences without PAM sequences (e.g. without NGG for SpCas9).
The length of each query sequence should be between 15 and 25 nt, and all be the same length!

Optional parameters

Mismatch Number ≤

DNA Bulge Size ≤

RNA Bulge Size ≤

Run

Reset

Help

Codes of bases

Code	Base	Code	Base	Code	Base
A	Adenine	R	A or G	B	C or G or T
C	Cytosine	Y	C or T	D	A or G or T
G	Guanine	S	G or C	H	A or C or T
T	Thymine	W	A or T	V	A or C or G
		K	G or T	N	any base
		M	A or C

Bulge size

Note: Large number of bulge size will significantly increase the calculation time!

CRIOff Result

Summary

Sequence ID	Target Sequence	Bulge Type	Bulge Size	Mismatch	Number of Found Targets

Details

SeqID	Target	Chromosome	Position	Direction	Mismatches	Bulge Type	Bulge Size

SugarcaneOmics The SugarCane multi-Omics Database

SugarcaneOmics The SugarCane multi-Omics Database

CRIOff

Optional parameters

Codes of bases

Bulge size

SugarcaneOmics
The SugarCane multi-Omics Database

SugarcaneOmics
The SugarCane multi-Omics Database