← return to the list of all guides
Contents:In the table below, Illumina Nextera Handle sequences have been added and highlighted in bold. Primers for the on-target have been added for convenience. The table below is sorted by the CFD off-target score. Sites with very low CFD scores < 0.02 are unlikely to be cleaved, see our study Haeussler et al. 2016, Figure 2.
In the protocol by Matthew Canver, Harvard, two PCRs are run: one PCR to amplify the potential off-target, then a second PCR to extend the handles with Illumina barcodes. Please click here to download the protocol. Alternatively, you can have a look at Fu et al, 2014.
If a primer was not found, the reason is usually that the region around the off-target is too repetitive. To avoid unspecific primers, all repeats are masked for the primer design (not for off-target search). If you think that we should change the parameters here or should use different primer3 settings, please let us know.
Name | Primer Sequence | Tm | CFD Score |
---|---|---|---|
ontarget_mm0_exon_5730457N03Rik/Evx1_chr6_52314238_F | Primer3: not found at this Tm | N.d. | 1.00 |
ontarget_mm0_exon_5730457N03Rik/Evx1_chr6_52314238_R | Primer3: not found at this Tm | N.d. | 1.00 |
mm4_intergenic_Zswim6|Smim15_chr13_107938155_F | TCGTCGGCAGCGTCGCTCCTCGCTGACTTGCTAA | 60.1 | 0.57 |
mm4_intergenic_Zswim6|Smim15_chr13_107938155_R | GTCTCGTGGGCTCGGTGTGTGCAATATCATTTGGCCA | 59.1 | 0.57 |
mm4_intron_1110057K04Rik_chr12_8243745_F | TCGTCGGCAGCGTCCGGGATTTACTTGGTGCTTGG | 59.5 | 0.53 |
mm4_intron_1110057K04Rik_chr12_8243745_R | GTCTCGTGGGCTCGGTCTGAAACAGCGCGGTTACT | 59.9 | 0.53 |
mm4_exon_Cdh6_chr15_13053929_F | TCGTCGGCAGCGTCTCGGCATCACTGGCTTTGAT | 60.0 | 0.34 |
mm4_exon_Cdh6_chr15_13053929_R | GTCTCGTGGGCTCGGAGTGTCTGCCTCACCATGTG | 59.9 | 0.34 |
mm3_exon_Tmem65_chr15_58822997_F | Primer3: not found at this Tm | N.d. | 0.31 |
mm3_exon_Tmem65_chr15_58822997_R | Primer3: not found at this Tm | N.d. | 0.31 |
mm4_exon_Itpkb/Gm5069_chr1_180330579_F | TCGTCGGCAGCGTCGCGGTAGTGTCTCCAACCAA | 59.9 | 0.28 |
mm4_exon_Itpkb/Gm5069_chr1_180330579_R | GTCTCGTGGGCTCGGGGGTGCAACGAAGCTGAATG | 60.1 | 0.28 |
mm4_exon_Vps37b_chr5_124004774_F | TCGTCGGCAGCGTCCCCCTTTACTGCATCCACCC | 60.3 | 0.18 |
mm4_exon_Vps37b_chr5_124004774_R | GTCTCGTGGGCTCGGACCCTACTGGAACCACTCTGT | 60.1 | 0.18 |
mm4_intergenic_Gm25660|Slc27a6_chr18_58387266_F | TCGTCGGCAGCGTCCAGTTCAGATTGCGCACAGG | 59.8 | 0.16 |
mm4_intergenic_Gm25660|Slc27a6_chr18_58387266_R | GTCTCGTGGGCTCGGGGACTTGTGGGTAGGACAGG | 59.3 | 0.16 |
mm4_intergenic_Cat|Gm13996_chr2_103538154_F | TCGTCGGCAGCGTCCAACCAGAGCCTGCTACACA | 59.9 | 0.15 |
mm4_intergenic_Cat|Gm13996_chr2_103538154_R | GTCTCGTGGGCTCGGAAGTTGGTAACTGGGATATTGGA | 57.2 | 0.15 |
mm4_intergenic_Fkrp|Strn4_chr7_16816908_F | TCGTCGGCAGCGTCCAAGCCCAGAGAGCCTGTC | 60.0 | 0.15 |
mm4_intergenic_Fkrp|Strn4_chr7_16816908_R | GTCTCGTGGGCTCGGTTTATTCGCGCAGACCCCAT | 60.1 | 0.15 |
mm4_exon_Dmgdh_chr13_93674520_F | TCGTCGGCAGCGTCCACTGCCACCTCGCCATG | 61.1 | 0.14 |
mm4_exon_Dmgdh_chr13_93674520_R | GTCTCGTGGGCTCGGCCTGCTCCTCTTCCCACCC | 61.6 | 0.14 |
mm3_exon_Hoxb1_chr11_96366824_F | TCGTCGGCAGCGTCCTGACGTGGCTTTTCTCCCT | 59.9 | 0.11 |
mm3_exon_Hoxb1_chr11_96366824_R | GTCTCGTGGGCTCGGTGGTGAAGTTTGTGCGGAGA | 59.8 | 0.11 |
mm4_exon_BC025920/Gm26896_chr10_81608927_F | TCGTCGGCAGCGTCATGTGTCGTGAGTGGAGCAG | 60.0 | 0.11 |
mm4_exon_BC025920/Gm26896_chr10_81608927_R | GTCTCGTGGGCTCGGTAGGCTTGGGAGTGGAAGGT | 60.1 | 0.11 |
mm4_intergenic_Fbxl2|Susd5_chr9_114047563_F | Primer3: not found at this Tm | N.d. | 0.05 |
mm4_intergenic_Fbxl2|Susd5_chr9_114047563_R | Primer3: not found at this Tm | N.d. | 0.05 |
mm4_intron_Ubr4_chr4_139420618_F | TCGTCGGCAGCGTCTTAGCGGTGGAGGAGGAAGA | 59.9 | 0.04 |
mm4_intron_Ubr4_chr4_139420618_R | GTCTCGTGGGCTCGGAGAAGGCAGCAGGACTCAAC | 59.9 | 0.04 |
mm4_intergenic_Nek2|1700034H15Rik_chr1_191841216_F | TCGTCGGCAGCGTCACAAGCTATGCCTCAGCCTG | 60.1 | 0.03 |
mm4_intergenic_Nek2|1700034H15Rik_chr1_191841216_R | GTCTCGTGGGCTCGGTGCCTTGTGTGAGTTCTGCT | 59.8 | 0.03 |
mm4_intergenic_Ccl25|Cers4_chr8_4405092_F | TCGTCGGCAGCGTCCTGGGCCAGTATATGCAGGG | 59.9 | 0.03 |
mm4_intergenic_Ccl25|Cers4_chr8_4405092_R | GTCTCGTGGGCTCGGTCTCAGGCGTGGTACTGAGA | 59.9 | 0.03 |
mm4_intergenic_Vash2|Mfsd7b_chr1_190988237_F | TCGTCGGCAGCGTCTTTTGAGTGTCTCTCCCAGAAA | 57.2 | 0.02 |
mm4_intergenic_Vash2|Mfsd7b_chr1_190988237_R | GTCTCGTGGGCTCGGTGGGGAATTGGTGCTCAGT | 58.8 | 0.02 |
mm4_intron_Gabbr2_chr4_46881504_F | Primer3: not found at this Tm | N.d. | 0.02 |
mm4_intron_Gabbr2_chr4_46881504_R | Primer3: not found at this Tm | N.d. | 0.02 |
mm4_intergenic_Itpkb/Gm5069|Itpkb_chr1_180331025_F | Primer3: not found at this Tm | N.d. | 0.00 |
mm4_intergenic_Itpkb/Gm5069|Itpkb_chr1_180331025_R | Primer3: not found at this Tm | N.d. | 0.00 |
mm4_exon_Grin2c_chr11_115250438_F | Primer3: not found at this Tm | N.d. | 0.00 |
mm4_exon_Grin2c_chr11_115250438_R | Primer3: not found at this Tm | N.d. | 0.00 |
mm4_exon_Dync1li2_chr8_104442831_F | TCGTCGGCAGCGTCCAACTGCAGCCACAAAGAGG | 59.6 | 0.00 |
mm4_exon_Dync1li2_chr8_104442831_R | GTCTCGTGGGCTCGGCGCTGGATAACGGAGCTTCT | 59.8 | 0.00 |
These only list off-targets that have primers in the table above. Primers underlined, off-targets in bold.
mm4_intergenic_Zswim6|Smim15_chr13_107938155 |
GCTCCTCGCTGACTTGCTAAATAGCAAAAATTGGTACTTGGCATTCCCAGTGGATGTGGGAAAAGATAATAAGTACCCCA AATGTAAAGAAAATCGAAATGAAACTAATTATGGCCAAATGATATTGCACACA |
mm4_intron_1110057K04Rik_chr12_8243745 |
CGGGATTTACTTGGTGCTTGGGGGTCGTATCTCTCAGAGATAGCAGATCCTAATCCTGTGGTACCTGGCGTTCCCTGGGG AAAGTGCACAGTAACCGCGCTGTTTCAGA |
mm4_exon_Cdh6_chr15_13053929 |
TCGGCATCACTGGCTTTGATCCTGCCAATTGGCGTTCCCGGTGGAGAGGACTCGGGGGTCTTAAACTGGTAGGTACCTGT CAATCACCAAACACATGGTGAGGCAGACACT |
mm4_exon_Itpkb/Gm5069_chr1_180330579 |
GCGGTAGTGTCTCCAACCAAGCACAGAGCAACGCAGGGTCGGCCTGGCGGTGTCCCCTCCGGGATCGCCTAGTCCCTGCG CCGGTACATTCAGCTTCGTTGCACCC |
mm4_exon_Vps37b_chr5_124004774 |
CCCCTTTACTGCATCCACCCGGAGCTCCCATGTGGCTGCGGCCCGAGACTGGCAGTGGGCGTTCCTGGTGGCAGAGGTAC TGAAGTGGCACATACAGCTTTGTCTCTTTACAGAGTGGTTCCAGTAGGGT |
mm4_intergenic_Gm25660|Slc27a6_chr18_58387266 |
CAGTTCAGATTGCGCACAGGGGCTGTTATGACACCTGGTATTCGGGGATCCCAGCGGGGCAGTATCGAGTAGACACCTTC TGAGAGGCTGATTGGTATTTCTGAAACTTTCCTGTCCTACCCACAAGTCC |
mm4_intergenic_Cat|Gm13996_chr2_103538154 |
CAACCAGAGCCTGCTACACATACTGGGGTAGCGATTCCAACACAATCTGTCTACTCCTGGTTATCGGGGTTCCTGGGGGC ATTGCTGGATGTAATCCAATATCCCAGTTACCAACTT |
mm4_intergenic_Fkrp|Strn4_chr7_16816908 |
CAAGCCCAGAGAGCCTGTCTGGGCGATGCGACTCGGGGTTCCCGGGGGACAGAGTGCTGAGAAAGTGGATGGGGTCTGCG CGAATAAA |
mm4_exon_Dmgdh_chr13_93674520 |
CACTGCCACCTCGCCATGCTCCGCCCGGGCGCGCTGCGGCTGCGGGGCCTCGCGCTGCGGGGCTCCCCCAGGCGCCCAAG CTCCGCTGGCCTCCGGGAAGGGTGAGTACCCGATGGCTGCCGGGTGGGAAGAGGAGCAGG |
mm3_exon_Hoxb1_chr11_96366824 |
CTGACGTGGCTTTTCTCCCTGCCCCGCCCCTAGCGAAGGTGTCCGAGCTGGGACTGGGCGCTCCCGGCGGTCTCCGCACA AACTTCACCA |
mm4_exon_BC025920/Gm26896_chr10_81608927 |
ATGTGTCGTGAGTGGAGCAGAGCCTTCTGGTACTCTGTGTCCCCGAGGGCACACTGGATGACACATTTGGGAACCAGTCC TTACTATGTGAGCAGTGTGGGAAAACCTTCCACTCCCAAGCCTA |
mm4_intron_Ubr4_chr4_139420618 |
TTAGCGGTGGAGGAGGAAGACTCCCAGGCTGAGGACTCTGTAAGTGCTCTAGGGAAGGGAATGGCTCTTCAGCCTGTCCA GTGTGCTCTGGTACTCTGCCTCCTCGGTGGGCTTGAGGACGTTGAGTCCTGCTGCCTTCT |
mm4_intergenic_Nek2|1700034H15Rik_chr1_191841216 |
ACAAGCTATGCCTCAGCCTGGGGCAGGTCCCCAGCACCTTGGCCTCCGAGGACGCCCAGTACAAGCTTGGTACATCCTCT GACATTTAGACAGCAGAACTCACACAAGGCA |
mm4_intergenic_Ccl25|Cers4_chr8_4405092 |
CTGGGCCAGTATATGCAGGGCTGCAGACAAAGGAATCCCTGGCCGGGTCCCAGTCGGTCAGGCGCCCTCTGGCAACTTCT GGACCTCTCCTCCTCCGCGTTCCCGGTGGTCACCCCTTCTCAGTACCACGCCTGAGA |
mm4_intergenic_Vash2|Mfsd7b_chr1_190988237 | TTTTGAGTGTCTCTCCCAGAAACTGGTACTCGTCGTTTCAGCTGGACTGAGCACCAATTCCCCA |
mm4_exon_Dync1li2_chr8_104442831 |
CAACTGCAGCCACAAAGAGGGCCCTCCCCCGGGCCCGCCGAGGACCCGCAAGGANNNNNNNNNNNNNNNNNNNNNNNNNN NNAACGCCGCAGAAGCTCCGTTATCCAGCG |