← 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 |
|---|---|---|---|
| mm0_exon_Pop5_chr5_115238035_F | TCGTCGGCAGCGTCGAGCGTGGAGATTGACAGGG | 60.4 | 1.00 |
| mm0_exon_Pop5_chr5_115238035_R | GTCTCGTGGGCTCGGCGCTGCTTACCTGTGCTTGA | 60.9 | 1.00 |
| mm4_intergenic_Adcy5|Gm25179_chr16_35197303_F | TCGTCGGCAGCGTCTTTGTGAAAGCTCCCTGGGG | 60.1 | 0.55 |
| mm4_intergenic_Adcy5|Gm25179_chr16_35197303_R | GTCTCGTGGGCTCGGCAAACAGCAGGAAAAGCCCC | 59.9 | 0.55 |
| mm4_intergenic_Dusp10|Gm23349_chr1_184261210_F | Primer3: not found at this Tm | N.d. | 0.30 |
| mm4_intergenic_Dusp10|Gm23349_chr1_184261210_R | Primer3: not found at this Tm | N.d. | 0.30 |
| mm4_intergenic_Csrp1|Phlda3_chr1_135752264_F | TCGTCGGCAGCGTCCTGTAGGCATGGGCTGTTGA | 60.0 | 0.23 |
| mm4_intergenic_Csrp1|Phlda3_chr1_135752264_R | GTCTCGTGGGCTCGGTGCTGAGATTGTTCTGGTCTGA | 59.3 | 0.23 |
| mm4_intergenic_Sox11|Gm24326_chr12_27342968_F | TCGTCGGCAGCGTCTCAAAAGAAATCCGCGAGTGC | 59.8 | 0.17 |
| mm4_intergenic_Sox11|Gm24326_chr12_27342968_R | GTCTCGTGGGCTCGGCTGGGGTTCAGTCCATCGTC | 60.1 | 0.17 |
| mm3_exon_Slc43a2_chr11_75532621_F | TCGTCGGCAGCGTCGGTGTCTGCAGAACCGGAG | 60.3 | 0.12 |
| mm3_exon_Slc43a2_chr11_75532621_R | GTCTCGTGGGCTCGGGGTTTTCCAACACAGCGGTG | 60.2 | 0.12 |
| mm3_exon_Suds3_chr5_117115953_F | TCGTCGGCAGCGTCGACTCCCCTCGGCTCCGA | 62.8 | 0.11 |
| mm3_exon_Suds3_chr5_117115953_R | GTCTCGTGGGCTCGGCTGATCAGGCTGTCACCGAG | 60.1 | 0.11 |
| mm4_intron_Ror2_chr13_53121182_F | TCGTCGGCAGCGTCGCAGTGGTAGGGTCCAAGAC | 60.0 | 0.09 |
| mm4_intron_Ror2_chr13_53121182_R | GTCTCGTGGGCTCGGCAGCGCTCCTCAGTCTCTTC | 60.1 | 0.09 |
| mm4_exon_Podxl_chr6_31563903_F | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_exon_Podxl_chr6_31563903_R | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_intergenic_Gm25905|Dcp1b_chr6_118989106_F | TCGTCGGCAGCGTCCACCAGGAGAGCAACCAGAG | 60.0 | 0.05 |
| mm4_intergenic_Gm25905|Dcp1b_chr6_118989106_R | GTCTCGTGGGCTCGGAGGCAAAACTGACTCGGAGG | 59.9 | 0.05 |
| mm4_intron_Bcor_chrX_12089895_F | TCGTCGGCAGCGTCGTTAGTGCCAGCCCCACTG | 60.6 | 0.05 |
| mm4_intron_Bcor_chrX_12089895_R | GTCTCGTGGGCTCGGAATAGATCTCGCAGGCCCTG | 59.3 | 0.05 |
| mm4_intron_4933426M11Rik_chr12_80793003_F | TCGTCGGCAGCGTCGCAAGACCTCAGCACTCTGT | 59.9 | 0.04 |
| mm4_intron_4933426M11Rik_chr12_80793003_R | GTCTCGTGGGCTCGGGCCCCAGACACAGTAGAGGA | 60.6 | 0.04 |
| mm4_exon_Katnal1_chr5_148928453_F | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_exon_Katnal1_chr5_148928453_R | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_intron_Lrrc8c_chr5_105519838_F | TCGTCGGCAGCGTCGATCCCGCTAACCCCAACC | 60.1 | 0.03 |
| mm4_intron_Lrrc8c_chr5_105519838_R | GTCTCGTGGGCTCGGTTCTCCTAGTACGCCCCTCC | 60.1 | 0.03 |
| mm4_intron_Hmgb3_chrX_71557164_F | TCGTCGGCAGCGTCTTATGGGTGTCCGGAGCAAC | 60.0 | 0.03 |
| mm4_intron_Hmgb3_chrX_71557164_R | GTCTCGTGGGCTCGGCTGAATTAAAGCCCAGCCGC | 59.8 | 0.03 |
| mm4_intergenic_Nhsl2|Gm25828_chrX_101864982_F | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_intergenic_Nhsl2|Gm25828_chrX_101864982_R | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_exon_Gm26637/Eif2ak2_chr17_78882645_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_exon_Gm26637/Eif2ak2_chr17_78882645_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_exon_Adrbk1_chr19_4306164_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_exon_Adrbk1_chr19_4306164_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_exon_C3_chr17_57224326_F | TCGTCGGCAGCGTCAGTGCAGGATGACAGTGACG | 60.0 | 0.01 |
| mm4_exon_C3_chr17_57224326_R | GTCTCGTGGGCTCGGAGATTGAGGATGGTGTGGGG | 59.0 | 0.01 |
| mm4_intergenic_Ern1|Snord104_chr11_106489400_F | TCGTCGGCAGCGTCGAAGCTCCGACACTCCTGAG | 59.8 | 0.01 |
| mm4_intergenic_Ern1|Snord104_chr11_106489400_R | GTCTCGTGGGCTCGGGTCTCACAGGTCCCGTTGTC | 60.3 | 0.01 |
| mm4_intergenic_Gm13234|Gm13231_chr4_145641150_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Gm13234|Gm13231_chr4_145641150_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Gm13136|Gm13148_chr4_147738590_F | TCGTCGGCAGCGTCCTTGGAAGGCGCGCTCTC | 61.1 | 0.01 |
| mm4_intergenic_Gm13136|Gm13148_chr4_147738590_R | GTCTCGTGGGCTCGGCCAAGCTGCTTCCCTCGG | 60.4 | 0.01 |
| mm4_exon_Smarca5_chr8_80739080_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_exon_Smarca5_chr8_80739080_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_exon_Smarca5-ps_chr4_145464290_F | TCGTCGGCAGCGTCCCCAAGCCGCTTCTCTCG | 60.5 | 0.01 |
| mm4_exon_Smarca5-ps_chr4_145464290_R | GTCTCGTGGGCTCGGCTTGGAAGGCGCGCTCTT | 60.7 | 0.01 |
| mm4_exon_Gm13034_chr4_146067744_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_exon_Gm13034_chr4_146067744_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Gm26703|Dspp_chr5_104156812_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intergenic_Gm26703|Dspp_chr5_104156812_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm3_intron_Anp32e_chr3_95929865_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm3_intron_Anp32e_chr3_95929865_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intron_Itga9_chr9_118878794_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intron_Itga9_chr9_118878794_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intron_Galnt7_chr8_57652304_F | TCGTCGGCAGCGTCGACCACAGGAGAGGCTGGA | 60.6 | 0.00 |
| mm4_intron_Galnt7_chr8_57652304_R | GTCTCGTGGGCTCGGGTGCAGGCCTGAAGGAGG | 60.0 | 0.00 |
| mm4_intergenic_Aldh1l2|A230046K03Rik_chr10_83543837_F | TCGTCGGCAGCGTCGCCCTGAGAACAGTCGTGAA | 59.9 | 0.00 |
| mm4_intergenic_Aldh1l2|A230046K03Rik_chr10_83543837_R | GTCTCGTGGGCTCGGCTGGGAAAGCGAGTCGACC | 60.4 | 0.00 |
| mm3_intergenic_Gm24073|Mir17hg_chr14_115042223_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm3_intergenic_Gm24073|Mir17hg_chr14_115042223_R | Primer3: not found at this Tm | N.d. | 0.00 |
These only list off-targets that have primers in the table above. Primers underlined, off-targets in bold.
| mm0_exon_Pop5_chr5_115238035 |
GAGCGTGGAGATTGACAGGGCACGCTGCCTGTCCGAGCCTAGTGCCGCCTTCCTCCCGCATCCGGCGCGGACGCCATGGT GCGGTTCAAGCACAGGTAAGCAGCG |
| mm4_intergenic_Adcy5|Gm25179_chr16_35197303 |
TTTGTGAAAGCTCCCTGGGGGAGGGCCGCACCATGACATCCATGCAGGGACCACATGGTACTTGGACGCACCTAGACACC AGGAGGTAGAACATGCAAGGGGGAACATGAGCGGGGGCTTTTCCTGCTGTTTG |
| mm4_intergenic_Csrp1|Phlda3_chr1_135752264 |
CTGTAGGCATGGGCTGTTGAAGCTGATTTATCATCTGATCAATAAAGCAATTTAGAACTGAACTCTGCTTTCCTGTCTGT CTATGGGGGCCCGGCCACACCCTGGAGTCAGCGCTGGATCAGACCAGAACAATCTCAGCA |
| mm4_intergenic_Sox11|Gm24326_chr12_27342968 |
TCAAAAGAAATCCGCGAGTGCGCACAGCTGCGCGTGTCCCCCGGGCGGATGCAGGACGGAGCGAGAGACGCCAGCGCGGA CTCAAGGGCGCGGGACGATGGACTGAACCCCAG |
| mm3_exon_Slc43a2_chr11_75532621 |
GGTGTCTGCAGAACCGGAGCCCGACCACCGCCACACCGCACCATGGCGCCCACCCTGGCCACTGCCCATCGGCGCCGCTG GTGGATGGCCTGCACCGCTGTGTTGGAAAACC |
| mm3_exon_Suds3_chr5_117115953 |
GACTCCCCTCGGCTCCGAGCTCCGCCCCCCACCCCGCACCCCGGCGCCCGCGCTGGGCAACGGGGGCCTCGCGCAGCCGG CTACTTCCGGGTCGTGGGCTGCTCGGTGACAGCCTGATCAG |
| mm4_intron_Ror2_chr13_53121182 |
GCAGTGGTAGGGTCCAAGACTAACAGATTTCCTTCCTAAAGCGTCTTCTAGTAAAAATCCCTCACCATGGAGCCCACGCT GGGCTGCTGAAAGCTCACGGCCAGCCAGAAAACTCCCGAAGAGACTGAGGAGCGCTG |
| mm4_intergenic_Gm25905|Dcp1b_chr6_118989106 |
CACCAGGAGAGCAACCAGAGCACCAAGTGATTGGCCTCACCATAGCGTCCAGGCTGGCAGATGCAAAACTGAAGCAGCAG AGACAGAGGTGTGCACTGGAGCGCTGGCCCCTCCGAGTCAGTTTTGCCT |
| mm4_intron_Bcor_chrX_12089895 |
GTTAGTGCCAGCCCCACTGCACCGGAGCCAGCGCGGGCCCCGAGGTGCGGGATTGACGCCCCCCCCCCGCCCCCTGGTGG GGCGCCCGCGTCCCTCCTCCTCCCGCCCCTCTCCAGGGCCTGCGAGATCTATT |
| mm4_intron_4933426M11Rik_chr12_80793003 |
GCAAGACCTCAGCACTCTGTGGTTTCCTGCCCGGTCTCCATGGTGTGGCGATTGAACTGGAGCACTTATGTAATGATGCA TCTTCTGACAGGGGATTTCCTCCTCTACTGTGTCTGGGGC |
| mm4_intron_Lrrc8c_chr5_105519838 |
GATCCCGCTAACCCCAACCCCACCCAACCCACGCGGGCCCTGGCGTCCGCGCCAGGGACCCCCAGCCGGGAGCCCAGTAC AGCCTGGCCGCTAGGTTCTGGGGACTGGGGGAGGGGCGTACTAGGAGAA |
| mm4_intron_Hmgb3_chrX_71557164 |
TTATGGGTGTCCGGAGCAACGGGGACGTGGCCCGACACGGGCTGTCTGCTGCCGGCCTGGACGCCCGGGTGCGGGGGCCC GCCCCACCCGGGATACCGCGGCTGGGCTTTAATTCAG |
| mm4_exon_C3_chr17_57224326 |
AGTGCAGGATGACAGTGACGGAGACATACAGGGACTTCCCCACCAGGGCGTCGGCGTTGGAAGGCCGTACCCCCTCCATC AGCACCTTCCGGGTCAGCACTGCATCCCCCACACCATCCTCAATCT |
| mm4_intergenic_Ern1|Snord104_chr11_106489400 |
GAAGCTCCGACACTCCTGAGCATGCTNNNNNNNNNNNNNNNNNNNNNNNAAGCCATGGAGCTGGCCAATGATGCAAGCTG ACAACGGGACCTGTGAGAC |
| mm4_intergenic_Gm13136|Gm13148_chr4_147738590 |
CTTGGAAGGCGCGCTCTCGGGAGGCGGGAGCGGCGGAGGCTCCACCGCGGACGACATGTTCCGGCTGCGTCACCCGCCGC GGCCACGGGCAGGCGCGGCGCCGAGGGAAGCAGCTTGG |
| mm4_exon_Smarca5-ps_chr4_145464290 |
CCCAAGCCGCTTCTCTCGGCGCCGCGCCTGCCCATGGCCGCGGCGGGTGACGCAGCCGGAACATGTCGTCCGCGGTGGAG CCTCCGCCGCTCCCGCCTCCCAAGAGCGCGCCTTCCAAG |
| mm4_intron_Galnt7_chr8_57652304 |
GACCACAGGAGAGGCTGGACCGCGGGGCCTGCTCCACCGGACCACGGCGGCGGCGCCGGCATCTCGCCTCCTTCAGGCCT GCAC |
| mm4_intergenic_Aldh1l2|A230046K03Rik_chr10_83543837 |
GCCCTGAGAACAGTCGTGAACGGCAGCGAGACCAGGAAAGGATGCAGGATGCCAACGGCAGCCATCACTATGGCGGCCGC GCCGGGAGCAGGCGGTCGACTCGCTTTCCCAG |