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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_115238084_F | TCGTCGGCAGCGTCTGCGGTTCAAGCACAGGTAA | 60.1 | 1.00 |
| mm0_exon_Pop5_chr5_115238084_R | GTCTCGTGGGCTCGGCTCGCACAGAAGGTACCTGC | 60.7 | 1.00 |
| mm4_intergenic_BC052040|Meis2_chr2_115859177_F | TCGTCGGCAGCGTCAGCAAATGCATTCACAGGCA | 59.0 | 0.34 |
| mm4_intergenic_BC052040|Meis2_chr2_115859177_R | GTCTCGTGGGCTCGGTCCCCTCCTCTATCCACCAA | 58.9 | 0.34 |
| mm3_exon_Psma7_chr2_180042114_F | TCGTCGGCAGCGTCGCAGTGGGGAAGCCAGAAAA | 60.8 | 0.29 |
| mm3_exon_Psma7_chr2_180042114_R | GTCTCGTGGGCTCGGGAGCTGAATGGTGACGACGT | 60.3 | 0.29 |
| mm4_intron_Hdac2_chr10_36974826_F | Primer3: not found at this Tm | N.d. | 0.22 |
| mm4_intron_Hdac2_chr10_36974826_R | Primer3: not found at this Tm | N.d. | 0.22 |
| mm4_intergenic_Gm23822|4921504A21Rik_chr5_19024881_F | Primer3: not found at this Tm | N.d. | 0.21 |
| mm4_intergenic_Gm23822|4921504A21Rik_chr5_19024881_R | Primer3: not found at this Tm | N.d. | 0.21 |
| mm4_intergenic_Acot5|Gm8385_chr12_84086648_F | Primer3: not found at this Tm | N.d. | 0.18 |
| mm4_intergenic_Acot5|Gm8385_chr12_84086648_R | Primer3: not found at this Tm | N.d. | 0.18 |
| mm4_intergenic_Acot5|Gm8385_chr12_84086561_F | Primer3: not found at this Tm | N.d. | 0.18 |
| mm4_intergenic_Acot5|Gm8385_chr12_84086561_R | Primer3: not found at this Tm | N.d. | 0.18 |
| mm4_intergenic_Acot5|Gm8385_chr12_84086471_F | Primer3: not found at this Tm | N.d. | 0.18 |
| mm4_intergenic_Acot5|Gm8385_chr12_84086471_R | Primer3: not found at this Tm | N.d. | 0.18 |
| mm4_intron_Ephx4_chr5_107403457_F | Primer3: not found at this Tm | N.d. | 0.17 |
| mm4_intron_Ephx4_chr5_107403457_R | Primer3: not found at this Tm | N.d. | 0.17 |
| mm3_exon_Reps1_chr10_18055896_F | Primer3: not found at this Tm | N.d. | 0.17 |
| mm3_exon_Reps1_chr10_18055896_R | Primer3: not found at this Tm | N.d. | 0.17 |
| mm3_exon_Nudt9_chr5_104047124_F | Primer3: not found at this Tm | N.d. | 0.16 |
| mm3_exon_Nudt9_chr5_104047124_R | Primer3: not found at this Tm | N.d. | 0.16 |
| mm4_exon_Gm10657/Cd276_chr9_58555037_F | Primer3: not found at this Tm | N.d. | 0.16 |
| mm4_exon_Gm10657/Cd276_chr9_58555037_R | Primer3: not found at this Tm | N.d. | 0.16 |
| mm4_intron_6330403A02Rik_chr1_180483063_F | TCGTCGGCAGCGTCGACACATCCACGGGTCTCAG | 60.1 | 0.15 |
| mm4_intron_6330403A02Rik_chr1_180483063_R | GTCTCGTGGGCTCGGGTGCCGGGATTGGGTAAGAA | 60.0 | 0.15 |
| mm4_intron_Grlf1_chr7_16614283_F | Primer3: not found at this Tm | N.d. | 0.15 |
| mm4_intron_Grlf1_chr7_16614283_R | Primer3: not found at this Tm | N.d. | 0.15 |
| mm4_intergenic_Nfib|Gm11266_chr4_82506924_F | TCGTCGGCAGCGTCGAAAGAAAAGTGAGCGCCCG | 60.1 | 0.15 |
| mm4_intergenic_Nfib|Gm11266_chr4_82506924_R | GTCTCGTGGGCTCGGGTGCGAGGACTGGAGAAAGT | 59.6 | 0.15 |
| mm4_exon_Kdm5b_chr1_134560325_F | TCGTCGGCAGCGTCGGAGCCTGCCCTGTGCTC | 62.7 | 0.15 |
| mm4_exon_Kdm5b_chr1_134560325_R | GTCTCGTGGGCTCGGGGAGGCAGGAACTCTCCCA | 60.6 | 0.15 |
| mm4_exon_Pdgfb_chr15_80014043_F | Primer3: not found at this Tm | N.d. | 0.14 |
| mm4_exon_Pdgfb_chr15_80014043_R | Primer3: not found at this Tm | N.d. | 0.14 |
| mm3_intergenic_Chd6|Gm14243_chr2_161109342_F | TCGTCGGCAGCGTCCTAGATCTCCCCGCCTTGC | 59.6 | 0.14 |
| mm3_intergenic_Chd6|Gm14243_chr2_161109342_R | GTCTCGTGGGCTCGGGCTTGCAAAACAGAGCGCAG | 61.2 | 0.14 |
| mm4_exon_Prtg_chr9_72807282_F | TCGTCGGCAGCGTCCCCTCTACAGCCTCCCTCC | 60.4 | 0.14 |
| mm4_exon_Prtg_chr9_72807282_R | GTCTCGTGGGCTCGGCTCCTGCTGCAACCCGCT | 62.7 | 0.14 |
| mm4_intergenic_Gm22668|Thoc3_chr13_54445081_F | Primer3: not found at this Tm | N.d. | 0.14 |
| mm4_intergenic_Gm22668|Thoc3_chr13_54445081_R | Primer3: not found at this Tm | N.d. | 0.14 |
| mm4_intergenic_Gm12349|Eif1_chr11_100308616_F | Primer3: not found at this Tm | N.d. | 0.14 |
| mm4_intergenic_Gm12349|Eif1_chr11_100308616_R | Primer3: not found at this Tm | N.d. | 0.14 |
| mm4_exon_Lphn2_chr3_148989135_F | TCGTCGGCAGCGTCCCAAGTCCGTCAGTCAGTCC | 60.0 | 0.11 |
| mm4_exon_Lphn2_chr3_148989135_R | GTCTCGTGGGCTCGGGACCCGACATGTGAGGAAGG | 60.1 | 0.11 |
| mm4_intron_Nr5a1_chr2_38711806_F | TCGTCGGCAGCGTCCAGACAAAGCCACGCAGC | 59.7 | 0.11 |
| mm4_intron_Nr5a1_chr2_38711806_R | GTCTCGTGGGCTCGGTCTCCCACTCTCTGTACCCC | 59.6 | 0.11 |
| mm4_exon_Zbtb14_chr17_69383928_F | Primer3: not found at this Tm | N.d. | 0.10 |
| mm4_exon_Zbtb14_chr17_69383928_R | Primer3: not found at this Tm | N.d. | 0.10 |
| mm3_intergenic_Dpy19l1|Dpy19l2_chr9_24503222_F | TCGTCGGCAGCGTCCTCACTCTGGCCGGCGAG | 62.5 | 0.10 |
| mm3_intergenic_Dpy19l1|Dpy19l2_chr9_24503222_R | GTCTCGTGGGCTCGGCCCTGGCAACCCGAGAGC | 62.7 | 0.10 |
| mm4_intron_Wdr20a_chr12_110738493_F | TCGTCGGCAGCGTCGGGGCTTCGGGAGTGAGG | 61.7 | 0.09 |
| mm4_intron_Wdr20a_chr12_110738493_R | GTCTCGTGGGCTCGGGATCGGAACCTGACAGACCC | 59.8 | 0.09 |
| mm3_intron_Rala_chr13_17943813_F | TCGTCGGCAGCGTCCTTGAAAGCGAGGGAGGTCG | 60.7 | 0.09 |
| mm3_intron_Rala_chr13_17943813_R | GTCTCGTGGGCTCGGAAGGTCACCTGTATAGCGCC | 59.5 | 0.09 |
| mm3_exon_Peli1_chr11_21091605_F | TCGTCGGCAGCGTCCTGGTGCCTGCGTTCAAC | 59.3 | 0.09 |
| mm3_exon_Peli1_chr11_21091605_R | GTCTCGTGGGCTCGGCTCACCGGACGACTGCTG | 60.1 | 0.09 |
| mm4_exon_Rbm15_chr3_107332580_F | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_exon_Rbm15_chr3_107332580_R | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_intergenic_Prr14|Fbrs_chr7_127479113_F | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_intergenic_Prr14|Fbrs_chr7_127479113_R | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_intergenic_Hes1|n-R5s32_chr16_30070395_F | Primer3: not found at this Tm | N.d. | 0.07 |
| mm4_intergenic_Hes1|n-R5s32_chr16_30070395_R | Primer3: not found at this Tm | N.d. | 0.07 |
| mm4_intron_Syngap1_chr17_26953865_F | TCGTCGGCAGCGTCCTGGATTTGGGGCTGGAGG | 60.0 | 0.07 |
| mm4_intron_Syngap1_chr17_26953865_R | GTCTCGTGGGCTCGGTATAGCAGCCCCGTCATCAC | 59.3 | 0.07 |
| mm4_intergenic_Cacng4|Gm11650_chr11_107794592_F | Primer3: not found at this Tm | N.d. | 0.07 |
| mm4_intergenic_Cacng4|Gm11650_chr11_107794592_R | Primer3: not found at this Tm | N.d. | 0.07 |
| mm4_intron_Pmp22_chr11_63132536_F | Primer3: not found at this Tm | N.d. | 0.07 |
| mm4_intron_Pmp22_chr11_63132536_R | Primer3: not found at this Tm | N.d. | 0.07 |
| mm4_intergenic_Ppm1h|Mirlet7i_chr10_122985562_F | Primer3: not found at this Tm | N.d. | 0.07 |
| mm4_intergenic_Ppm1h|Mirlet7i_chr10_122985562_R | Primer3: not found at this Tm | N.d. | 0.07 |
| mm4_intergenic_Gm9727|Btbd8_chr5_107479358_F | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_intergenic_Gm9727|Btbd8_chr5_107479358_R | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_intron_Akap9_chr5_3928556_F | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_intron_Akap9_chr5_3928556_R | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_intron_St6galnac2_chr11_116694390_F | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_intron_St6galnac2_chr11_116694390_R | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_exon_Cdc34_chr10_79682350_F | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_exon_Cdc34_chr10_79682350_R | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_intron_Rab31_chr17_65729984_F | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_intron_Rab31_chr17_65729984_R | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_exon_Ccdc85b_chr19_5456862_F | TCGTCGGCAGCGTCCAGGCTAGGGGCAACTGATC | 60.1 | 0.05 |
| mm4_exon_Ccdc85b_chr19_5456862_R | GTCTCGTGGGCTCGGAGTGGGCTCAGGTGCTGG | 61.6 | 0.05 |
| mm4_exon_Necab2_chr8_119446956_F | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_exon_Necab2_chr8_119446956_R | Primer3: not found at this Tm | N.d. | 0.05 |
| mm3_exon_Gm1673_chr5_33983854_F | TCGTCGGCAGCGTCGACTTTACTGCTGCTGCTGC | 59.8 | 0.05 |
| mm3_exon_Gm1673_chr5_33983854_R | GTCTCGTGGGCTCGGCGCTCAGGAAACAAAGACGC | 60.1 | 0.05 |
| mm4_exon_Ppp2r3d_chr9_124422716_F | TCGTCGGCAGCGTCCCCACATACCTTGGCAACCA | 60.2 | 0.04 |
| mm4_exon_Ppp2r3d_chr9_124422716_R | GTCTCGTGGGCTCGGCTACTTCCCTTGCGGTCGAC | 60.4 | 0.04 |
| mm4_intergenic_Tm2d3|Gm7551_chr7_65702965_F | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_intergenic_Tm2d3|Gm7551_chr7_65702965_R | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_intergenic_Pik3r1|Gm25808_chr13_101859418_F | TCGTCGGCAGCGTCGTCCCTCACTTCCCACCAAG | 59.9 | 0.04 |
| mm4_intergenic_Pik3r1|Gm25808_chr13_101859418_R | GTCTCGTGGGCTCGGTTCCTCTGGGTTGGACATGG | 59.3 | 0.04 |
| mm3_intergenic_Pde7a|Gm22282_chr3_19311445_F | Primer3: not found at this Tm | N.d. | 0.04 |
| mm3_intergenic_Pde7a|Gm22282_chr3_19311445_R | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_intron_Sar1a_chr10_61680480_F | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_intron_Sar1a_chr10_61680480_R | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_intergenic_Ren1|Etnk2_chr1_133363517_F | TCGTCGGCAGCGTCGCCCTTTGCGTCATTAAGGC | 60.1 | 0.04 |
| mm4_intergenic_Ren1|Etnk2_chr1_133363517_R | GTCTCGTGGGCTCGGATCATGGGTCGCAGTAACGC | 60.8 | 0.04 |
| mm4_exon_Sept9_chr11_117266364_F | TCGTCGGCAGCGTCAACAGCCAGTGCCGAGTC | 59.9 | 0.04 |
| mm4_exon_Sept9_chr11_117266364_R | GTCTCGTGGGCTCGGCACGGTCGGCTGAATGAATG | 59.6 | 0.04 |
| mm4_exon_Srpk1_chr17_28622502_F | TCGTCGGCAGCGTCCCCAAATCCCAGCTCTTCCT | 59.3 | 0.04 |
| mm4_exon_Srpk1_chr17_28622502_R | GTCTCGTGGGCTCGGTTGCCCTCCACTCTCGTACA | 60.5 | 0.04 |
| mm4_intergenic_Cenpf|Ptpn14_chr1_189728146_F | TCGTCGGCAGCGTCCTCCCCGGACGCATTCCT | 61.4 | 0.04 |
| mm4_intergenic_Cenpf|Ptpn14_chr1_189728146_R | GTCTCGTGGGCTCGGGTGGGAGGGGACGAGCAG | 61.7 | 0.04 |
| mm3_intron_Il17d_chr14_57525158_F | Primer3: not found at this Tm | N.d. | 0.04 |
| mm3_intron_Il17d_chr14_57525158_R | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_exon_Macrod2_chr2_140395402_F | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_exon_Macrod2_chr2_140395402_R | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_exon_Snta1_chr2_154408023_F | TCGTCGGCAGCGTCTCGAAGTCCCAGTACACTGC | 59.3 | 0.03 |
| mm4_exon_Snta1_chr2_154408023_R | GTCTCGTGGGCTCGGCTGTCCTCCGAAGCTCCG | 59.5 | 0.03 |
| mm4_intergenic_9430091E24Rik|Glg1_chr8_111145504_F | TCGTCGGCAGCGTCCTGAAGAGGGTCTGCGCC | 60.1 | 0.03 |
| mm4_intergenic_9430091E24Rik|Glg1_chr8_111145504_R | GTCTCGTGGGCTCGGCGTAAAGCGCGGAAGGTCG | 61.7 | 0.03 |
| mm4_exon_Pdpr_chr8_111094702_F | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_exon_Pdpr_chr8_111094702_R | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_intron_Sh3bp4_chr1_89070772_F | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_intron_Sh3bp4_chr1_89070772_R | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_intergenic_Eif4h|Limk1_chr5_134639367_F | TCGTCGGCAGCGTCGTCTCCGCTCCTTGAGGAAC | 60.1 | 0.03 |
| mm4_intergenic_Eif4h|Limk1_chr5_134639367_R | GTCTCGTGGGCTCGGGACTTGCGATCAGGCAGCG | 61.8 | 0.03 |
| mm4_exon_Setd8_chr5_124445668_F | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_exon_Setd8_chr5_124445668_R | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_intergenic_Gm11746|Slc24a3_chr2_145167691_F | TCGTCGGCAGCGTCTCCTCTCGCCGGTCCTTC | 60.7 | 0.03 |
| mm4_intergenic_Gm11746|Slc24a3_chr2_145167691_R | GTCTCGTGGGCTCGGGGGGTCCCTCTCCTGCTC | 60.7 | 0.03 |
| mm4_intron_1810013L24Rik_chr16_8830747_F | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_intron_1810013L24Rik_chr16_8830747_R | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_intergenic_Zfp853|E130309D02Rik_chr5_143293438_F | TCGTCGGCAGCGTCCCGGCACAGGAAGTCCCC | 62.4 | 0.03 |
| mm4_intergenic_Zfp853|E130309D02Rik_chr5_143293438_R | GTCTCGTGGGCTCGGCGCGGCCTAGAGAGACTATG | 59.4 | 0.03 |
| mm4_exon_Nfatc2_chr2_168590141_F | TCGTCGGCAGCGTCAAAGTCCAGCTCGTCTTGGG | 59.9 | 0.03 |
| mm4_exon_Nfatc2_chr2_168590141_R | GTCTCGTGGGCTCGGCCGCGACTCTATACGAACCC | 60.0 | 0.03 |
| mm4_intron_Gata4_chr14_63255790_F | TCGTCGGCAGCGTCTGTCGTACTCTGCTGGAGA | 57.3 | 0.03 |
| mm4_intron_Gata4_chr14_63255790_R | GTCTCGTGGGCTCGGCCGCGGCCATCCATCAAG | 61.2 | 0.03 |
| mm4_exon_C78339_chr13_46670180_F | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_exon_C78339_chr13_46670180_R | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_intergenic_1700019O17Rik|Ptma_chr1_86526244_F | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_intergenic_1700019O17Rik|Ptma_chr1_86526244_R | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_exon_Bag5_chr12_111713156_F | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_exon_Bag5_chr12_111713156_R | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_intergenic_Tac2|Zbtb39_chr10_127739501_F | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_intergenic_Tac2|Zbtb39_chr10_127739501_R | Primer3: not found at this Tm | N.d. | 0.03 |
| mm3_intergenic_Gm9755|Nat3_chr8_67523120_F | Primer3: not found at this Tm | N.d. | 0.03 |
| mm3_intergenic_Gm9755|Nat3_chr8_67523120_R | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_exon_Onecut3_chr10_80495769_F | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_exon_Onecut3_chr10_80495769_R | Primer3: not found at this Tm | N.d. | 0.02 |
| mm3_exon_Nrxn2_chr19_6498310_F | Primer3: not found at this Tm | N.d. | 0.02 |
| mm3_exon_Nrxn2_chr19_6498310_R | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_exon_Tm9sf3_chr19_41263989_F | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_exon_Tm9sf3_chr19_41263989_R | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_exon_Cpeb2/Gm7854_chr5_43234704_F | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_exon_Cpeb2/Gm7854_chr5_43234704_R | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_exon_Btbd2_chr10_80656426_F | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_exon_Btbd2_chr10_80656426_R | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_exon_Pafah1b1_chr11_74724129_F | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_exon_Pafah1b1_chr11_74724129_R | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_exon_Map2k7_chr8_4240713_F | TCGTCGGCAGCGTCTGTGATCACTCTAAGCCCTGC | 59.7 | 0.02 |
| mm4_exon_Map2k7_chr8_4240713_R | GTCTCGTGGGCTCGGAGCGGTTAGGTCAATGTGCA | 59.9 | 0.02 |
| mm4_exon_Gm8770_chrX_78785864_F | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_exon_Gm8770_chrX_78785864_R | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_intron_Slc2a1_chr4_119109248_F | TCGTCGGCAGCGTCGCTAAAAGAGCCGAGCCCC | 60.8 | 0.01 |
| mm4_intron_Slc2a1_chr4_119109248_R | GTCTCGTGGGCTCGGGAAGTGCCTTCTCCTCCTGG | 59.7 | 0.01 |
| mm4_intergenic_4930519P11Rik/Zfp341|Zfp341_chr2_154613475_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_4930519P11Rik/Zfp341|Zfp341_chr2_154613475_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Nr1d1|Msl1_chr11_98795432_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Nr1d1|Msl1_chr11_98795432_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Rgs9bp|Ankrd27_chr7_35585650_F | TCGTCGGCAGCGTCGTTTCCTAGGACACGCCTCC | 60.1 | 0.01 |
| mm4_intergenic_Rgs9bp|Ankrd27_chr7_35585650_R | GTCTCGTGGGCTCGGGGGAGAAGAGGGAAAGCCAC | 60.0 | 0.01 |
| mm4_exon_Tbc1d4_chr14_101608149_F | TCGTCGGCAGCGTCTGCTCGAAGATGAACACCCC | 60.0 | 0.01 |
| mm4_exon_Tbc1d4_chr14_101608149_R | GTCTCGTGGGCTCGGGAGGTGATCCTGGTGCTCAG | 59.8 | 0.01 |
| mm4_exon_D830050J10Rik/Raf1_chr6_115676153_F | TCGTCGGCAGCGTCAAATCTGAGCAGGGGTGTGG | 59.9 | 0.01 |
| mm4_exon_D830050J10Rik/Raf1_chr6_115676153_R | GTCTCGTGGGCTCGGTCCCTCAGGTAGGCCACAG | 60.3 | 0.01 |
| mm4_intron_Wdr41_chr13_94976603_F | TCGTCGGCAGCGTCGCTGGCTGATCGGAGGAG | 59.5 | 0.01 |
| mm4_intron_Wdr41_chr13_94976603_R | GTCTCGTGGGCTCGGTTCTTAGCAGAGGCCAGGTG | 59.3 | 0.01 |
| mm4_intergenic_Gm12249|Larp1_chr11_58008806_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Gm12249|Larp1_chr11_58008806_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_exon_Ppp2r5a_chr1_191396781_F | TCGTCGGCAGCGTCGAGTCCGGACAGGTCTTCAG | 59.4 | 0.01 |
| mm4_exon_Ppp2r5a_chr1_191396781_R | GTCTCGTGGGCTCGGCATCGCTGACAGGAGAACGA | 59.8 | 0.01 |
| mm4_intergenic_Col12a1|Cox7a2_chr9_79719360_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Col12a1|Cox7a2_chr9_79719360_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_C230037L18Rik|Shank3_chr15_89499578_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_C230037L18Rik|Shank3_chr15_89499578_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intron_Stau2_chr1_16519765_F | TCGTCGGCAGCGTCGGTCGAGCGGCCATTGTT | 60.7 | 0.01 |
| mm4_intron_Stau2_chr1_16519765_R | GTCTCGTGGGCTCGGCCGAGACCCCAGGCCTAA | 60.3 | 0.01 |
| mm4_exon_Rnd2_chr11_101468190_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_exon_Rnd2_chr11_101468190_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_1700128E19Rik|Arhgef7_chr8_11727861_F | TCGTCGGCAGCGTCCCGCCCTACCCACAAAGG | 60.0 | 0.01 |
| mm4_intergenic_1700128E19Rik|Arhgef7_chr8_11727861_R | GTCTCGTGGGCTCGGTCACCGGAGAAGAAAGACGC | 60.0 | 0.01 |
| mm4_exon_Dbp_chr7_45706907_F | TCGTCGGCAGCGTCGGACCTGGACGCCTTCTTG | 60.3 | 0.00 |
| mm4_exon_Dbp_chr7_45706907_R | GTCTCGTGGGCTCGGGGGAAGAGGAGCTGCAAGAG | 60.1 | 0.00 |
| mm4_intron_Trib2_chr12_15815107_F | TCGTCGGCAGCGTCGACTTGAGAGCTTTCCGACCT | 59.7 | 0.00 |
| mm4_intron_Trib2_chr12_15815107_R | GTCTCGTGGGCTCGGCCAGCCCAGCTTTGCTTTTG | 60.6 | 0.00 |
| mm4_exon_Dtx1_chr5_120694845_F | TCGTCGGCAGCGTCCCAGGATTGCGACTTGGGAA | 60.3 | 0.00 |
| mm4_exon_Dtx1_chr5_120694845_R | GTCTCGTGGGCTCGGAGCATGTCCCAGATGAACCG | 60.1 | 0.00 |
| mm4_exon_Slc7a10_chr7_35186550_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_exon_Slc7a10_chr7_35186550_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_exon_Smad6_chr9_64020813_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_exon_Smad6_chr9_64020813_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intron_Lrp4_chr2_91457770_F | TCGTCGGCAGCGTCCTCTGCGCACACGGTAAGC | 61.7 | 0.00 |
| mm4_intron_Lrp4_chr2_91457770_R | GTCTCGTGGGCTCGGCGACCAGTCTCAGGGACAAA | 59.3 | 0.00 |
| mm4_intron_Eif5a2_chr3_28781427_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intron_Eif5a2_chr3_28781427_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_exon_Zer1_chr2_30124393_F | TCGTCGGCAGCGTCAGGAGGTCGGATCCGGTC | 60.1 | 0.00 |
| mm4_exon_Zer1_chr2_30124393_R | GTCTCGTGGGCTCGGCCGAGGGCAAGGGAACGG | 62.7 | 0.00 |
These only list off-targets that have primers in the table above. Primers underlined, off-targets in bold.
| mm0_exon_Pop5_chr5_115238084 |
TGCGGTTCAAGCACAGGTAAGCAGCGCTGTCCCCGCGCCGTCCCCGCGACCCGGGCCGCGCTCACCCCGCTGTCGCCGCA GGTACCTTCTGTGCGAG |
| mm4_intergenic_BC052040|Meis2_chr2_115859177 |
AGCAAATGCATTCACAGGCAAAATTGCATCCTCTGTGAACGAAACAAACCTAGGTCTATTTTGTTACTTTATTCCCGGGT CTTGGGGAGGGGGCGGGGTGTACAGAATCCATTGGTGGATAGAGGAGGGGA |
| mm3_exon_Psma7_chr2_180042114 |
GCAGTGGGGAAGCCAGAAAAAATCGCCCGGCTCTCCGGGAAGCGCGGCGCGGTCCCCGCGACCTGGTGCCCTTCCTACGT CGTCACCATTCAGCTC |
| mm4_intron_6330403A02Rik_chr1_180483063 |
GACACATCCACGGGTCTCAGCCAGTGCCTACCTCTGCCCTGCCTGGTCTCCATCAGGCAGCCCAGGTCGCAGGGACCGCA GGGGTTAAAGGGGTCACAAGGGTCGCCCACACACACACTTCTTACCCAATCCCGGCAC |
| mm4_intergenic_Nfib|Gm11266_chr4_82506924 |
GAAAGAAAAGTGAGCGCCCGGGGCTCCATGTCGCCCTAGCTTGGGGCCGCCGAGCGTTTCCAGGCCCCCCGCGGCCTCCC GCTCCCACCCCGCGTCCTGGACTTTCCCCCCCTCAACTTTCTCCAGTCCTCGCAC |
| mm4_exon_Kdm5b_chr1_134560325 |
GGAGCCTGCCCTGTGCTCGCCCCTGCCCAGGTCGCGGTGATGGAGCCGGCCACCACGCTGCCCCCANNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNTGGGAGAGTTCCTGCCTCC |
| mm3_intergenic_Chd6|Gm14243_chr2_161109342 |
CTAGATCTCCCCGCCTTGCAGACAGCGCAGCTCCCGGCCCGCCCCCCCGGAATGAAGCGGCCGGGCCGCGNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTGCGCTCTGTTTTGCAAGC |
| mm4_exon_Prtg_chr9_72807282 |
CCCTCTACAGCCTCCCTCCGCCCCCGGCTGGACGCGGCGCGCGTGGTCCCCGCGGCCTGGCGCACTCGCGGGGCTCCGTG CGCCTGCAAGCGGCGCGTCGCCTTCCCACGCCGGAGCAGCGGGTTGCAGCAGGAG |
| mm4_exon_Lphn2_chr3_148989135 |
CCAAGTCCGTCAGTCAGTCCGGAGGAGCCCGGTGCGCGCGGGCAGCGGCGGCAGGACCTGCATCCGGCGCACGCGCCGCC CCTGCGGCCTGGGGCACGACTCTGCCGCCAGCCCTTCCTCACATGTCGGGTC |
| mm4_intron_Nr5a1_chr2_38711806 |
CAGACAAAGCCACGCAGCGACGGCACCCACCGGCGAGCCGAGACGTCGGGCCGGGAGCGGGCGTTGAGGGCGCAGCCGGG TCGCGGGAGCGGGGCGGAGACCTCCGGCGGAGAAGGGGTACAGAGAGTGGGAGA |
| mm3_intergenic_Dpy19l1|Dpy19l2_chr9_24503222 |
CTCACTCTGGCCGGCGAGGGCGGGCCGGGAGGCGGGGACAGCGCGGGCCGTGTGGCCGCTGCCTACCGCGTGGCGGCCGA GAGGCGGCGCCGGACTCCCGCGCCTCCGCCGTTGCCGCTCTCGGGTTGCCAGGG |
| mm4_intron_Wdr20a_chr12_110738493 |
GGGGCTTCGGGAGTGAGGCGCCGGCGGCAGCGCTGCCTCCTAGGGGAGGAGGGGGCTCTGGAGCCGGGTCGCGGAGATGC CCCGGGAGTAGCCGGTCGCCTCCTCCCCCGGCGGGGTCTGTCAGGTTCCGATC |
| mm3_intron_Rala_chr13_17943813 |
CTTGAAAGCGAGGGAGGTCGGGGTGGAGTGCGGCGCAGGGACTNNNNNNNNNNNNNNNNNNNNCCCAGGTCGCGGGCACC GCCCGGGCACAGCCCTGGGAGCCACCGGCGCTATACAGGTGACCTT |
| mm3_exon_Peli1_chr11_21091605 |
CTGGTGCCTGCGTTCAACCGGTGCTNNNNNNNNNNNNNNNNNNNNNNTGTCCGTGCGGCGGGCCGAGCTGGCGTTCCGGC CACCAGCAGTCGTCCGGTGAG |
| mm4_intron_Syngap1_chr17_26953865 |
CTGGATTTGGGGCTGGAGGGGGGGGGGTGAGGGCATGGTATTCCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAG CGTGGTGCTGACGGCAGCCAGAGCCTGTGATGACGGGGCTGCTATA |
| mm4_exon_Ccdc85b_chr19_5456862 |
CAGGCTAGGGGCAACTGATCCGGGCTGCCCACACTGCCAGTGCTGGAACTTCCATCGCCTAGGTCGCGGGGCCCGCACGG TGGCAGGGCGAGCTCGGGTGTGGGCCCAGCACCTGAGCCCACT |
| mm3_exon_Gm1673_chr5_33983854 |
GACTTTACTGCTGCTGCTGCTGAGCCTGGCGCTGCTGGGCGCCCGCGCCGAGCCCGCCACCGGGAGCGCTGTCCCCGCTC AGAGTAGGTGCCCGCGGAGGGGGCGTGCGGGAGGCGTCTTTGTTTCCTGAGCG |
| mm4_exon_Ppp2r3d_chr9_124422716 |
CCCACATACCTTGGCAACCACGGCCATGTCGCCCAGACCCGCCCTCCCACGAGGCAGCCCCTCGAACGCGCACTCCACGA GGGCGATGGCATCCTCCGTGTCCTGGGGACGGGGCGGGGGTCGACCGCAAGGGAAGTAG |
| mm4_intergenic_Pik3r1|Gm25808_chr13_101859418 |
GTCCCTCACTTCCCACCAAGCCCAATTTTGTGAAGGGCCAGGGCGGGGGGACGGTGTGGGGGGGGGGGAGATGATCACAG ACATTCTGATTAAAGATTACTGTTGGCCATGTCCAACCCAGAGGAA |
| mm4_intergenic_Ren1|Etnk2_chr1_133363517 |
GCCCTTTGCGTCATTAAGGCGGGGCATCCCCCACCCAGAGCTCCAGGTAGCGGTGGAGCCAGCAACGGGAGATGGCGGGC TGCACTCGCCCGGAGGCGGGGGCGGGGCGGGCAAGGGGCGTTACTGCGACCCATGAT |
| mm4_exon_Sept9_chr11_117266364 |
AACAGCCAGTGCCGAGTCGCGGAGGCCGGCTGGGGTACGGGAACCTGATCCAGCCGGGANNNNNNNNNNNNNNNNNNNNN NNNNTGCTTGGGGAGGGGCCGGCGCCCGCCTTCCTCCCCCATTCATTCAGCCGACCGTG |
| mm4_exon_Srpk1_chr17_28622502 |
CCCAAATCCCAGCTCTTCCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNACCACGCCCCACACGGCGTCGCGC GCCTGCGTGGTGAACACAGAGCCTACCACCTGCTCCGGGGTGTACGAGAGTGGAGGGCAA |
| mm4_intergenic_Cenpf|Ptpn14_chr1_189728146 |
CTCCCCGGACGCATTCCTGGCCCGCCCAGCGAGCGCCCCGCGCGCTCCCCGCCTCCTGGCCCCCAGCACTGCGGAGCAGA GCCCGGGGCGGGGGAGCGCGGCCAGCGGCGCCTGCTCGTCCCCTCCCAC |
| mm4_exon_Snta1_chr2_154408023 |
TCGAAGTCCCAGTACACTGCGCTCGCCCGGTCCCGCCGTACCCGGCCCGCTCCGACCCAGCGCCCAGGGCAGAGGGCGGC GGGGCAGCAGAGCCAGTCGCCACCCTACCCCGGCCTCGGGGGCGGAGCTTCGGAGGACAG |
| mm4_intergenic_9430091E24Rik|Glg1_chr8_111145504 |
CTGAAGAGGGTCTGCGCCGGCCGGAAAGGGGGCCAGGGCATGGGGACGGGGCGGGACGCGGAGCGCAGAGTTCCGGGACC GCGGGGGCCTGCGACCTTCCGCGCTTTACG |
| mm4_intergenic_Eif4h|Limk1_chr5_134639367 |
GTCTCCGCTCCTTGAGGAACCAGCGGGCCAGCGAGGAAGGACCCCGCAATATAACTCCTCCTCCCCCCGCCCGCCCCGCT ACCGGGGCTGTCCGCCGCGCTGCCTGATCGCAAGTC |
| mm4_intergenic_Gm11746|Slc24a3_chr2_145167691 |
TCCTCTCGCCGGTCCTTCCCCGCTCCTCCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNC CAGGCCGAACGCGGGCGCGGAGCGTGGGAGCCATGGCGCGCGAGCAGGAGAGGGACCCC |
| mm4_intergenic_Zfp853|E130309D02Rik_chr5_143293438 |
CCGGCACAGGAAGTCCCCCCGGCATCCGCATCCTGTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNTAAGCCATAGTCTCTCTAGGCCGCG |
| mm4_exon_Nfatc2_chr2_168590141 |
AAAGTCCAGCTCGTCTTGGGGACTGCCCCCGGGCTCGTGGCCGGGGCCGTCCCCGCCATCGGGGTCGGGCTGCGGCTCCG GGACGTCCATGGCTCGGGGCGTTCGGGATGCGGGTTCGTATAGAGTCGCGG |
| mm4_intron_Gata4_chr14_63255790 |
TGTCGTACTCTGCTGGAGAGCAGAGCGCTGCCCGCCACCCAGCGGTGCGAGCATCGCGAGCCTCCGGGAGGCTGCGGCTC CCACCCCGCGTGCCCGCCGCCCTCGCCGCCCTCGCCACCCGGCTTGATGGATGGCCGCGG |
| mm4_exon_Map2k7_chr8_4240713 |
TGTGATCACTCTAAGCCCTGCTCCTGCCCCGTCCCAGCGAGCAGGTACCAGCCTTTTTATCATTGCTGCTTGCATATCTG CACATTGACCTAACCGCT |
| mm4_intron_Slc2a1_chr4_119109248 |
GCTAAAAGAGCCGAGCCCCCGGCCGGGCCCCGGCTAGGAGCGGAGGAGGCGGGACCCGCCCGGAGCCCGCGCCGCGCCCG GAACCCGGGCCATGGGGGTGGCCAGGAGGAGAAGGCACTTC |
| mm4_intergenic_Rgs9bp|Ankrd27_chr7_35585650 |
GTTTCCTAGGACACGCCTCCAGCCACCAGTCCAGGCCCGGGGCTTCCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNAGGGGTAGGCGGGGCCCAGCCCAGGTAGATCAAGTGTGGCTTTCCCTCTTCTCCC |
| mm4_exon_Tbc1d4_chr14_101608149 |
TGCTCGAAGATGAACACCCCGGTGTTGGGCTGCACAGCCCCGGAGCCTGCGCCCCCGCCGACCCCGGCACCCGGCGCAGG GACACAACGCAGAAAGGGGGCGCTGAGCACCAGGATCACCTC |
| mm4_exon_D830050J10Rik/Raf1_chr6_115676153 |
AAATCTGAGCAGGGGTGTGGAAACTGGCTCGCCGGCCATGACANNNNNNNNNNNNNNNNNNNNNNACCAGGATGACAGCG GCCTGGCCGACCCTGCGCCCCACGGTCGCACCGTCAGCCCTGTGGCCTACCTGAGGGA |
| mm4_intron_Wdr41_chr13_94976603 |
GCTGGCTGATCGGAGGAGGCCGCGAGCCGCAGGGCCTAGCCGAGGTAATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNAAGCGGCTGCTCAGGGCCACCTGGCCTCTGCTAAGAA |
| mm4_exon_Ppp2r5a_chr1_191396781 |
GAGTCCGGACAGGTCTTCAGCGGCTGCCGCCCGCGCTGTCCGCCCGGCCGGGAGCCTCCTCCCGGGGCGCTTCCATCGCG GGTCCGCGCGAGCCGCTGCCGAGCGCTCGTTCTCCTGTCAGCGATG |
| mm4_intron_Stau2_chr1_16519765 |
GGTCGAGCGGCCATTGTTCGCCGCGCCGTTCCCGCCCCCTGGCGGCTTCTGGGACCCCCGCATCCCGGGGCGCTGCGGGG CTTAGGCCTGGGGTCTCGG |
| mm4_intergenic_1700128E19Rik|Arhgef7_chr8_11727861 |
CCGCCCTACCCACAAAGGCGCGCAGCCCCGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCGCGTCTTTCTTCTCCGGTGA |
| mm4_exon_Dbp_chr7_45706907 |
GGACCTGGACGCCTTCTTGCTGGAGCACGGGCTACCGCCGANNNNNNNNNNNNNNNNNNNNNTGTCGCCGGCACCCTCTC CAGCGCGCACTCCCGCGCCCTCCCCCGGGCCCGGCTCTTGCAGCTCCTCTTCCC |
| mm4_intron_Trib2_chr12_15815107 |
GACTTGAGAGCTTTCCGACCTCCCGCACCGTCCCCGGCCCCTGGCAAAAGACCCAGGATGNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNGCAAAAAAACAAAACGCAAAAGCAAAGCTGGGCTGG |
| mm4_exon_Dtx1_chr5_120694845 |
CCAGGATTGCGACTTGGGAATGGAGCCGACAGTGAGCGGGTAAGCCAGGTCCAGGCGACGGCGCAGGCGGCGGCGGCGGC GCGTCTGGCGGTTCATCTGGGACATGCT |
| mm4_intron_Lrp4_chr2_91457770 | CTCTGCGCACACGGTAAGCGGCGTCGCAGCGCCCGCGCCGACCGGGCCACCGGGAAAGTTTGTCCCTGAGACTGGTCG |
| mm4_exon_Zer1_chr2_30124393 |
AGGAGGTCGGATCCGGTCCGGGTCCGGGTCNNNNNNNNNNNNNNNNNNNNNNNNNNAATGCTGCGACCGGAGCCCCGGAC GGAGGCCGTTCCCTTGCCCTCGG |