Query sequence, not found in the selected genome, Mus musculus (mm10)
Warning: The query sequence was not found in the selected genome. This can be a valid query, e.g. a GFP sequence.
If not, you might want to check if you selected the right genome for your query sequence.
Use a tool like BLAT to check if the sequence really has a 100% identical match in the target genome.

When reading the list of guide sequences and off-targets below, bear in mind that in case that the input sequence is really in the genome and just has a few differences, the software will use the first found match as the on-target as it cannot distinguish 0-mismatch off-targets from 0-mismatch on-targets. In this case, the specificity scores of guide sequences are too low. In other words, some guides may be fine, the problem may just be that the on-target is shown as an off-target.
Because there is no flanking sequence available, the guides in your sequence that are within 50bp of the ends will have no efficiency scores. The efficiency scores will instead be shown as '--'. Include more flanking sequence > 50bp to obtain these scores.

Your input sequence is 147 bp long. It contains 32 possible guide sequences.
Shown below are their PAM sites and the expected cleavage position located -3bp 5' of the PAM site.
Click on a match for the PAM NGG below to show its 20 bp-long guide sequence. (Need help? Look at the CRISPOR manual)
Colors green, yellow and red indicate high, medium and low specificity of the PAM's guide sequence in the genome.

Input sequence not in genome, cannot show genome variants.

Position  0         10        20        30        40        50        60        70        80        90        100       110       120       130       140       
Sequence  ACGCTGCCTGTCCGAGCCTAGTGCCGCCTTCCTCCCGCATCCGGCGCGGACGCCATGGTGCGGTTCAAGCACGGGTAAGCAGCGCTGTCCCCGCGCCGTCCCCGCGACCCGGGCCGCGCTCACCCCGCTGTCGCCGCAGGTACCTTC
                CCT---    CCT---    CCT---  CCG---   −−−CGG   CCA---          −−−CGG              CCC---     CCC---  CCC---         CCC---      −−−AGG
                     CCG---      CCG---    CCC---             −−−TGG           −−−GGG              CCC---     CCC---  CCG---         CCC---
                                        CCT---    CCG---           −−−CGG                           CCG---     CCG---      CCG---     CCG---
                                                −−−CGG                                                   CCG---     −−−CGG
                                                                                                                     −−−GGG

Download for: SerialCloner (free) - ApE (free) - GenomeCompiler - Benchling - SnapGene - Geneious - Vector NTI - LaserGene - Genbank - FASTA

Predicted guide sequences for PAMs
Ranked by default from highest to lowest specificity score (Hsu et al., Nat Biot 2013). Click on a column title to rank by a score.
If you use this website, please cite our paper in NAR 2018. Too much information? Look at the CRISPOR manual.

Download as Excel tables: Guides /  Guides, all scores /  Off-targets /  Saturating mutagenesis assistant
Position/
Strand
Guide Sequence + PAM
+ Restriction Enzymes
Only G- Only GG- Only A-
MIT Specificity Score CFD Spec. score Predicted Efficiency
Show all scores
Outcome Off-targets for
0-1-2-3-4 mismatches
+ next to PAM
Genome Browser links to matches sorted by CFD off-target score
exons only  No match, no chrom filter
34 / rev ATGGCGTCCGCGCCGGATGC GGG
Enzymes: BslI, MwoI, BtsCI
 Cloning / PCR primers
98 99 -- -- -- -- 0 - 0 - 0 - 2 - 7
0 - 0 - 0 - 0 - 0

9 off-targets
show all...
7 / rev AGGCGGCACTAGGCTCGGAC AGG
Enzymes: ApeKI, Hpy188I, Fsp4HI, BstV1I
 Cloning / PCR primers
96 97 -- -- -- -- 0 - 0 - 0 - 1 - 25
0 - 0 - 0 - 0 - 0

26 off-targets
show all...
35 / rev CATGGCGTCCGCGCCGGATG CGG
Enzymes: BslI, MwoI, BtsCI
 Cloning / PCR primers
96 99 -- -- -- -- 0 - 0 - 0 - 1 - 16
0 - 0 - 0 - 0 - 0

17 off-targets
show all...
41 / rev CCGCACCATGGCGTCCGCGC CGG
High GC content
Enzymes: MwoI, BtsCI, MspI, HinP1I, BspFNI, LpnPI, SsiI
 Cloning / PCR primers
95 98 -- -- -- -- 0 - 0 - 0 - 4 - 26
0 - 0 - 0 - 0 - 1

30 off-targets
show all...
56 / fw CGCATCCGGCGCGGACGCCA TGG
High GC content
Enzymes: BstDSI, AcyI, BseDI, ErhI, HgaI, BslI, NlaIII, Bsp19I
 Cloning / PCR primers
95 98 45 44 74 80 0 - 0 - 0 - 1 - 15
0 - 0 - 0 - 0 - 1

16 off-targets
show all...
124 / rev AAGGTACCTGCGGCGACAGC GGG
Enzymes: AsuHPI, MspA1I, MwoI
 Cloning / PCR primers
95 97 -- -- -- -- 0 - 0 - 0 - 1 - 40
0 - 0 - 0 - 0 - 0

41 off-targets
show all...
47 / fw CCTTCCTCCCGCATCCGGCG CGG
Enzymes: AcyI, MwoI, MspI, HinP1I, HgaI, LpnPI, BslI, BspFNI
 Cloning / PCR primers
94 96 -- -- -- -- 0 - 0 - 0 - 2 - 50
0 - 0 - 0 - 0 - 0

52 off-targets
show all...
138 / fw GCTCACCCCGCTGTCGCCGC AGG
High GC content
Enzymes: TauI, MwoI, Csp6I, BanI, Asp718I, NlaIV, SsiI, Fsp4HI
 Cloning / PCR primers
94 96 -- -- -- -- 0 - 0 - 0 - 7 - 49
0 - 0 - 0 - 0 - 0

56 off-targets
show all...
31 / rev GCGTCCGCGCCGGATGCGGG AGG
High GC content
Enzymes: BslI
 Cloning / PCR primers
92 97 -- -- -- -- 0 - 0 - 0 - 4 - 47
0 - 0 - 0 - 1 - 0

51 off-targets
show all...
123 / rev AGGTACCTGCGGCGACAGCG GGG
Enzymes: AsuHPI, MspA1I, MwoI
 Cloning / PCR primers
92 96 -- -- -- -- 0 - 0 - 0 - 4 - 35
0 - 0 - 0 - 1 - 0

39 off-targets
show all...
100 / rev TGAGCGCGGCCCGGGTCGCG GGG
High GC content
Enzymes: BspFNI, BceAI, MwoI, BslFI, BslI
 Cloning / PCR primers
90 94 -- -- -- -- 0 - 0 - 0 - 5 - 56
0 - 0 - 0 - 0 - 1

61 off-targets
show all...
61 / fw CCGGCGCGGACGCCATGGTG CGG
High GC content
Enzymes: BstDSI, ErhI, BseDI, AgsI, BslI, Bsp19I
 Cloning / PCR primers
89 95 59 86 73 79 0 - 0 - 0 - 1 - 40
0 - 0 - 0 - 0 - 0

41 off-targets
show all...
125 / rev GAAGGTACCTGCGGCGACAG CGG
Enzymes: AsuHPI, MspA1I, MwoI
 Cloning / PCR primers
89 94 -- -- -- -- 0 - 0 - 0 - 2 - 69
0 - 0 - 0 - 0 - 0

71 off-targets
show all...
109 / rev ACAGCGGGGTGAGCGCGGCC CGG
Inefficient
High GC content
Enzymes: BshFI, BmeT110I, TauI, MwoI, MspI, BseDI, PspPI, NciI, LpnPI, StyD4I, Cfr9I, Fsp4HI
 Cloning / PCR primers
87 93 -- -- -- -- 0 - 0 - 0 - 8 - 67
0 - 0 - 0 - 0 - 2

75 off-targets
show all...
27 / rev CCGCGCCGGATGCGGGAGGA AGG
High GC content
Enzymes: TauI, Fsp4HI
 Cloning / PCR primers
86 96 -- -- -- -- 0 - 0 - 0 - 3 - 61
0 - 0 - 0 - 1 - 0

64 off-targets
show all...
42 / fw TGCCGCCTTCCTCCCGCATC CGG
Enzymes: LweI, MwoI, MspI, HinP1I, LpnPI, BslI, BspFNI
 Cloning / PCR primers
86 94 -- -- -- -- 0 - 0 - 1 - 9 - 85
0 - 0 - 0 - 1 - 2

95 off-targets
show all...
90 / rev CCGGGTCGCGGGGACGGCGC GGG
High GC content
Enzymes: HinP1I, BspFNI, MwoI, BceAI, BslFI
 Cloning / PCR primers
86 92 28 78 74 70 0 - 0 - 0 - 17 - 93
0 - 0 - 0 - 2 - 2

110 off-targets
show all...
101 / rev GTGAGCGCGGCCCGGGTCGC GGG
High GC content
Enzymes: BspFNI, MwoI, BslFI, BslI
 Cloning / PCR primers
85 95 -- -- -- -- 0 - 0 - 1 - 6 - 52
0 - 0 - 0 - 0 - 0

59 off-targets
show all...
72 / fw GCCATGGTGCGGTTCAAGCA CGG
Enzymes: MwoI
 Cloning / PCR primers
84 93 55 46 66 88 0 - 0 - 2 - 7 - 64
0 - 0 - 0 - 0 - 2

73 off-targets
show all...
110 / fw CCCGCGCCGTCCCCGCGACC CGG
High GC content
Enzymes: BshFI, BmeT110I, TauI, MwoI, MspI, BseDI, PspPI, NciI, LpnPI, BslI, StyD4I, SsiI, Cfr9I, Fsp4HI
 Cloning / PCR primers
84 94 -- -- -- -- 0 - 0 - 0 - 12 - 87
0 - 0 - 0 - 1 - 0

99 off-targets
show all...
12 / rev GAGGAAGGCGGCACTAGGCT CGG
Enzymes: Hpy188I
 Cloning / PCR primers
81 89 -- -- -- -- 0 - 0 - 0 - 12 - 113
0 - 0 - 0 - 0 - 0

125 off-targets
show all...
17 / rev TGCGGGAGGAAGGCGGCACT AGG
Enzymes: MaeI
 Cloning / PCR primers
81 90 -- -- -- -- 0 - 0 - 2 - 12 - 133
0 - 0 - 0 - 4 - 2

147 off-targets
show all...
114 / rev CGGCGACAGCGGGGTGAGCG CGG
High GC content
Enzymes: BshFI, TauI, MwoI, NciI, MspI, PspPI, HinP1I, BspFNI, LpnPI, StyD4I, Fsp4HI
 Cloning / PCR primers
81 93 -- -- -- -- 0 - 0 - 0 - 17 - 88
0 - 0 - 0 - 1 - 1

105 off-targets
show all...
102 / rev GGTGAGCGCGGCCCGGGTCG CGG
High GC content
Enzymes: BspFNI, MwoI, BslFI, BslI
 Cloning / PCR primers
80 92 -- -- -- -- 0 - 0 - 3 - 7 - 101
0 - 0 - 1 - 0 - 0

111 off-targets
show all...
91 / rev CCCGGGTCGCGGGGACGGCG CGG
High GC content
Enzymes: HinP1I, BspFNI, MwoI, BceAI, BslFI
 Cloning / PCR primers
79 86 26 62 78 77 0 - 0 - 1 - 12 - 102
0 - 0 - 0 - 2 - 5

115 off-targets
show all...
96 / rev CGCGGCCCGGGTCGCGGGGA CGG
High GC content
Enzymes: HinP1I, BspFNI, MwoI, BceAI, BslFI
 Cloning / PCR primers
79 89 -- -- -- -- 0 - 0 - 0 - 8 - 119
0 - 0 - 0 - 1 - 1

127 off-targets
show all...
89 / rev CGGGTCGCGGGGACGGCGCG GGG
High GC content
Enzymes: HinP1I, BspFNI, MwoI, BslFI
 Cloning / PCR primers
78 93 30 78 74 87 0 - 0 - 2 - 9 - 109
0 - 0 - 0 - 2 - 2

120 off-targets
show all...
108 / rev CAGCGGGGTGAGCGCGGCCC GGG
High GC content
Enzymes: BshFI, BmeT110I, TauI, MwoI, NciI, MspI, BseDI, PspPI, BspFNI, LpnPI, StyD4I, Cfr9I, Fsp4HI
 Cloning / PCR primers
77 90 -- -- -- -- 0 - 0 - 2 - 11 - 105
0 - 0 - 0 - 0 - 0

118 off-targets
show all...
111 / fw CCGCGCCGTCCCCGCGACCC GGG
High GC content
Enzymes: BshFI, BmeT110I, TauI, MwoI, NciI, MspI, BseDI, PspPI, BspFNI, LpnPI, BslI, StyD4I, SsiI, Cfr9I, Fsp4HI
 Cloning / PCR primers
76 94 -- -- -- -- 0 - 0 - 2 - 25 - 85
0 - 0 - 0 - 16 - 0

112 off-targets
show all...
24 / rev CGCCGGATGCGGGAGGAAGG CGG
Enzymes: TauI, Fsp4HI
 Cloning / PCR primers
66 86 -- -- -- -- 0 - 0 - 0 - 8 - 114
0 - 0 - 0 - 2 - 8

122 off-targets
show all...
73 / fw CCATGGTGCGGTTCAAGCAC GGG
Enzymes: MwoI
 Cloning / PCR primers
59 93 51 54 67 77 0 - 1 - 0 - 5 - 43
0 - 0 - 0 - 1 - 0

49 off-targets
show all...
53 / rev CCCGTGCTTGAACCGCACCA TGG
Enzymes: BstDSI, AcyI, BseDI, ErhI, NlaIII, BslI, Bsp19I
 Cloning / PCR primers
49 97 70 54 74 76 0 - 1 - 1 - 1 - 20
0 - 1 - 0 - 0 - 1

23 off-targets
show all...
Download as Excel tables: Guides /  Guides, all scores /  Off-targets /  Saturating mutagenesis assistant
Tab-sep format: Guides /  Off-targets

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