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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 |
|---|---|---|---|
| ontarget_mm0_exon_5730457N03Rik/Evx1_chr6_52313713_F | TCGTCGGCAGCGTCCGCATCACAAGGTGACCCTA | 59.7 | 1.00 |
| ontarget_mm0_exon_5730457N03Rik/Evx1_chr6_52313713_R | GTCTCGTGGGCTCGGCTCCTAATCCCAGGCTCCCT | 60.1 | 1.00 |
| mm2_intergenic_E130006D01Rik|Miat/MIAT_exon5_3/MIAT_exon5_2/Gm26953/MIAT_exon5_1_chr5_111870160_F | TCGTCGGCAGCGTCATTCGTGGGACCTGTGGAAC | 59.9 | 0.45 |
| mm2_intergenic_E130006D01Rik|Miat/MIAT_exon5_3/MIAT_exon5_2/Gm26953/MIAT_exon5_1_chr5_111870160_R | GTCTCGTGGGCTCGGCGTTCCAAGGGCACATTAGC | 59.5 | 0.45 |
| mm4_exon_Egfl7/Mir126/Agpat2_chr2_26590925_F | Primer3: not found at this Tm | N.d. | 0.30 |
| mm4_exon_Egfl7/Mir126/Agpat2_chr2_26590925_R | Primer3: not found at this Tm | N.d. | 0.30 |
| mm4_intron_Arid1b_chr17_5225423_F | TCGTCGGCAGCGTCGCAGAGTCACCCTCAACCTC | 60.0 | 0.28 |
| mm4_intron_Arid1b_chr17_5225423_R | GTCTCGTGGGCTCGGGCCATGATGAGCCTTGGACA | 60.3 | 0.28 |
| mm4_intergenic_Gm8935|Gm2464_chr3_13093116_F | Primer3: not found at this Tm | N.d. | 0.26 |
| mm4_intergenic_Gm8935|Gm2464_chr3_13093116_R | Primer3: not found at this Tm | N.d. | 0.26 |
| mm4_intergenic_Gm22815|Cntn5_chr9_9596759_F | Primer3: not found at this Tm | N.d. | 0.26 |
| mm4_intergenic_Gm22815|Cntn5_chr9_9596759_R | Primer3: not found at this Tm | N.d. | 0.26 |
| mm4_intergenic_Gm23891|1700018B24Rik_chr3_48239684_F | Primer3: not found at this Tm | N.d. | 0.26 |
| mm4_intergenic_Gm23891|1700018B24Rik_chr3_48239684_R | Primer3: not found at this Tm | N.d. | 0.26 |
| mm4_intergenic_Cadm1|Nxpe2_chr9_47930865_F | Primer3: not found at this Tm | N.d. | 0.22 |
| mm4_intergenic_Cadm1|Nxpe2_chr9_47930865_R | Primer3: not found at this Tm | N.d. | 0.22 |
| mm4_intron_Agap1_chr1_89850367_F | Primer3: not found at this Tm | N.d. | 0.22 |
| mm4_intron_Agap1_chr1_89850367_R | Primer3: not found at this Tm | N.d. | 0.22 |
| mm4_intron_Tmem132d_chr5_128432262_F | Primer3: not found at this Tm | N.d. | 0.21 |
| mm4_intron_Tmem132d_chr5_128432262_R | Primer3: not found at this Tm | N.d. | 0.21 |
| mm4_intron_Kat6b_chr14_21558695_F | TCGTCGGCAGCGTCGCCAGAACCCTTGTCTGGAA | 59.8 | 0.21 |
| mm4_intron_Kat6b_chr14_21558695_R | GTCTCGTGGGCTCGGCTGGATCTTAGGGCATGGCG | 60.6 | 0.21 |
| mm4_intergenic_B230206L02Rik|Tob1_chr11_94172602_F | TCGTCGGCAGCGTCAGGGGATGCAAAGTTAGCCC | 60.0 | 0.21 |
| mm4_intergenic_B230206L02Rik|Tob1_chr11_94172602_R | GTCTCGTGGGCTCGGCCTTCTCCATGTTTGCCCCT | 59.9 | 0.21 |
| mm4_intergenic_Gm9806|Foxb2_chr19_16827066_F | Primer3: not found at this Tm | N.d. | 0.20 |
| mm4_intergenic_Gm9806|Foxb2_chr19_16827066_R | Primer3: not found at this Tm | N.d. | 0.20 |
| mm4_intron_Wfs1_chr5_36982676_F | TCGTCGGCAGCGTCCACAGAGGCTTAGGCTGGTC | 60.1 | 0.20 |
| mm4_intron_Wfs1_chr5_36982676_R | GTCTCGTGGGCTCGGGGCTGTCAGTCCTTGGTGTT | 60.1 | 0.20 |
| mm4_intergenic_Celsr1|Gramd4_chr15_86034077_F | Primer3: not found at this Tm | N.d. | 0.19 |
| mm4_intergenic_Celsr1|Gramd4_chr15_86034077_R | Primer3: not found at this Tm | N.d. | 0.19 |
| mm4_intergenic_Gm24248|Rybp_chr6_99898251_F | TCGTCGGCAGCGTCAACAAGAGCAGGTACCAGGC | 59.9 | 0.19 |
| mm4_intergenic_Gm24248|Rybp_chr6_99898251_R | GTCTCGTGGGCTCGGGTGCCAGACAGCATTTAGGC | 59.5 | 0.19 |
| mm4_intron_Gm11184_chr4_83383515_F | Primer3: not found at this Tm | N.d. | 0.18 |
| mm4_intron_Gm11184_chr4_83383515_R | Primer3: not found at this Tm | N.d. | 0.18 |
| mm4_exon_Ddx54/Ccdc42b_chr5_120627299_F | TCGTCGGCAGCGTCCCAGGAAGGGCAAGATGAGG | 60.1 | 0.16 |
| mm4_exon_Ddx54/Ccdc42b_chr5_120627299_R | GTCTCGTGGGCTCGGGGACATAGTCCCTGACGTCC | 59.2 | 0.16 |
| mm4_intron_Lpin2_chr17_71183756_F | Primer3: not found at this Tm | N.d. | 0.16 |
| mm4_intron_Lpin2_chr17_71183756_R | Primer3: not found at this Tm | N.d. | 0.16 |
| mm4_intron_Tshz1_chr18_84026506_F | TCGTCGGCAGCGTCAGCCTGGGACCCACTATGAA | 60.2 | 0.16 |
| mm4_intron_Tshz1_chr18_84026506_R | GTCTCGTGGGCTCGGCTTCCTCCGAGTGCTTCCTG | 60.1 | 0.16 |
| mm4_intergenic_Gm26883|Gm26883/Tshz2_chr2_169815159_F | TCGTCGGCAGCGTCTTCTCCACTTATGCTCCCGG | 59.1 | 0.16 |
| mm4_intergenic_Gm26883|Gm26883/Tshz2_chr2_169815159_R | GTCTCGTGGGCTCGGCAGAGTTGCCTGGGCTAACA | 59.9 | 0.16 |
| mm4_intergenic_Plch2|Pex10_chr4_155066885_F | TCGTCGGCAGCGTCCCTGTCATTACCCGCCACTT | 60.0 | 0.15 |
| mm4_intergenic_Plch2|Pex10_chr4_155066885_R | GTCTCGTGGGCTCGGATCTGTGGAGGCGGAGTAGT | 60.0 | 0.15 |
| mm4_intron_Gm14280_chr2_131692088_F | Primer3: not found at this Tm | N.d. | 0.14 |
| mm4_intron_Gm14280_chr2_131692088_R | Primer3: not found at this Tm | N.d. | 0.14 |
| mm4_intron_Drd2_chr9_49392725_F | TCGTCGGCAGCGTCGGTGTTGCAGGACCATGACT | 60.2 | 0.12 |
| mm4_intron_Drd2_chr9_49392725_R | GTCTCGTGGGCTCGGTCCCCTCCCATGATCCTCAG | 60.1 | 0.12 |
| mm4_intergenic_A530020G20Rik|A730020M07Rik_chr3_121615281_F | Primer3: not found at this Tm | N.d. | 0.12 |
| mm4_intergenic_A530020G20Rik|A730020M07Rik_chr3_121615281_R | Primer3: not found at this Tm | N.d. | 0.12 |
| mm4_intron_Ralgds_chr2_28548638_F | TCGTCGGCAGCGTCATCACTGTTGCCTGGTGACA | 59.5 | 0.12 |
| mm4_intron_Ralgds_chr2_28548638_R | GTCTCGTGGGCTCGGCTCCAGCTCACACGACAGG | 60.0 | 0.12 |
| mm4_intergenic_Nrbf2|Egr2_chr10_67504508_F | TCGTCGGCAGCGTCCCCTCCTGGCTTGTGGAATC | 60.3 | 0.11 |
| mm4_intergenic_Nrbf2|Egr2_chr10_67504508_R | GTCTCGTGGGCTCGGACAGGATAAGCTCTGGGGTCT | 59.9 | 0.11 |
| mm4_intergenic_Gm7488|Tbl1xr1_chr3_21205073_F | Primer3: not found at this Tm | N.d. | 0.11 |
| mm4_intergenic_Gm7488|Tbl1xr1_chr3_21205073_R | Primer3: not found at this Tm | N.d. | 0.11 |
| mm4_intron_Myo18b_chr5_112821415_F | Primer3: not found at this Tm | N.d. | 0.11 |
| mm4_intron_Myo18b_chr5_112821415_R | Primer3: not found at this Tm | N.d. | 0.11 |
| mm4_intergenic_C630043F03Rik|Gm11235_chr4_72259339_F | Primer3: not found at this Tm | N.d. | 0.10 |
| mm4_intergenic_C630043F03Rik|Gm11235_chr4_72259339_R | Primer3: not found at this Tm | N.d. | 0.10 |
| mm4_intron_Trmt44_chr5_35571518_F | Primer3: not found at this Tm | N.d. | 0.10 |
| mm4_intron_Trmt44_chr5_35571518_R | Primer3: not found at this Tm | N.d. | 0.10 |
| mm4_intergenic_n-R5s193|Spsb1_chr4_149888879_F | Primer3: not found at this Tm | N.d. | 0.09 |
| mm4_intergenic_n-R5s193|Spsb1_chr4_149888879_R | Primer3: not found at this Tm | N.d. | 0.09 |
| mm4_intergenic_Mtpap|9430020K01Rik_chr18_4458012_F | Primer3: not found at this Tm | N.d. | 0.09 |
| mm4_intergenic_Mtpap|9430020K01Rik_chr18_4458012_R | Primer3: not found at this Tm | N.d. | 0.09 |
| mm4_exon_Lamp1_chr8_13175015_F | TCGTCGGCAGCGTCGCTGATGGTTAGGCTGCACA | 60.6 | 0.09 |
| mm4_exon_Lamp1_chr8_13175015_R | GTCTCGTGGGCTCGGCAGCCAGATGCCAGAGTTCA | 60.0 | 0.09 |
| mm4_intron_Gphn_chr12_78316818_F | Primer3: not found at this Tm | N.d. | 0.09 |
| mm4_intron_Gphn_chr12_78316818_R | Primer3: not found at this Tm | N.d. | 0.09 |
| mm4_intergenic_Fam227b|Fgf7_chr2_126012629_F | Primer3: not found at this Tm | N.d. | 0.09 |
| mm4_intergenic_Fam227b|Fgf7_chr2_126012629_R | Primer3: not found at this Tm | N.d. | 0.09 |
| mm4_intergenic_Sema5a|Sdc2_chr15_32703053_F | Primer3: not found at this Tm | N.d. | 0.09 |
| mm4_intergenic_Sema5a|Sdc2_chr15_32703053_R | Primer3: not found at this Tm | N.d. | 0.09 |
| mm4_intron_Aldh1l1_chr6_90585821_F | Primer3: not found at this Tm | N.d. | 0.09 |
| mm4_intron_Aldh1l1_chr6_90585821_R | Primer3: not found at this Tm | N.d. | 0.09 |
| mm4_intron_Cant1_chr11_118409630_F | Primer3: not found at this Tm | N.d. | 0.09 |
| mm4_intron_Cant1_chr11_118409630_R | Primer3: not found at this Tm | N.d. | 0.09 |
| mm4_intergenic_Flrt1|Macrod1_chr19_7156856_F | TCGTCGGCAGCGTCGAAGAGGGTCACGGTCCAAC | 60.3 | 0.08 |
| mm4_intergenic_Flrt1|Macrod1_chr19_7156856_R | GTCTCGTGGGCTCGGTCCCGACTGCATGAAGATGG | 59.8 | 0.08 |
| mm4_intergenic_Gm15030|Ppp1r2-ps7_chrX_22455831_F | Primer3: not found at this Tm | N.d. | 0.07 |
| mm4_intergenic_Gm15030|Ppp1r2-ps7_chrX_22455831_R | Primer3: not found at this Tm | N.d. | 0.07 |
| mm4_intron_Twf1_chr15_94589720_F | TCGTCGGCAGCGTCCACCCAGAGCAGCTCCAATG | 61.0 | 0.07 |
| mm4_intron_Twf1_chr15_94589720_R | GTCTCGTGGGCTCGGACAGGCATCCAAGGTAACGG | 60.0 | 0.07 |
| mm4_intergenic_Gm16178|Sh3rf1_chr8_61205038_F | TCGTCGGCAGCGTCAGCTATAGAGGACAGCGGGT | 59.8 | 0.06 |
| mm4_intergenic_Gm16178|Sh3rf1_chr8_61205038_R | GTCTCGTGGGCTCGGGCACCAAAAGAACCAGCAGG | 59.9 | 0.06 |
| mm4_exon_Acy3_chr19_3987088_F | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_exon_Acy3_chr19_3987088_R | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_intron_Dscaml1_chr9_45664266_F | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_intron_Dscaml1_chr9_45664266_R | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_intron_Papl_chr7_28630615_F | TCGTCGGCAGCGTCCTTCAGGTGACGGGCTCC | 59.7 | 0.06 |
| mm4_intron_Papl_chr7_28630615_R | GTCTCGTGGGCTCGGTCCCATGCTTTTCTGGGTCC | 59.9 | 0.06 |
| mm4_intergenic_Stim2|Gm24235_chr5_54220027_F | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_intergenic_Stim2|Gm24235_chr5_54220027_R | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_exon_Nphp4_chr4_152488444_F | TCGTCGGCAGCGTCTCGGCTCAGACCCTCCATAT | 59.8 | 0.05 |
| mm4_exon_Nphp4_chr4_152488444_R | GTCTCGTGGGCTCGGCACCAGAGGCAGGTTGTGTC | 60.8 | 0.05 |
| mm4_intergenic_Vmn1r42|Vmn1r43_chr6_89853083_F | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_intergenic_Vmn1r42|Vmn1r43_chr6_89853083_R | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_intergenic_Gm5943|Gm14905_chrX_115167031_F | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_intergenic_Gm5943|Gm14905_chrX_115167031_R | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_intron_Pias1_chr9_62980784_F | TCGTCGGCAGCGTCGCCTACAACTCCAGACTCGG | 59.8 | 0.05 |
| mm4_intron_Pias1_chr9_62980784_R | GTCTCGTGGGCTCGGGCGGAACTAAAGGTAAAGCGC | 60.2 | 0.05 |
| mm4_intron_Ebf1_chr11_44618367_F | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_intron_Ebf1_chr11_44618367_R | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_intron_Ctnna3_chr10_63718353_F | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_intron_Ctnna3_chr10_63718353_R | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_intergenic_PVT1_3|Ndufa4_chr6_11292443_F | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_intergenic_PVT1_3|Ndufa4_chr6_11292443_R | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_intergenic_Gm25460|Gm5263_chr1_146239424_F | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_intergenic_Gm25460|Gm5263_chr1_146239424_R | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_intergenic_Tmprss5|Gm4894_chr9_49146281_F | TCGTCGGCAGCGTCCAAAGGGAGGGATGCCTCTG | 60.1 | 0.05 |
| mm4_intergenic_Tmprss5|Gm4894_chr9_49146281_R | GTCTCGTGGGCTCGGAACACAGCACCACAGGAAGG | 60.4 | 0.05 |
| mm3_intron_Topaz1_chr9_122797550_F | Primer3: not found at this Tm | N.d. | 0.04 |
| mm3_intron_Topaz1_chr9_122797550_R | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_intergenic_Mthfr-ps1|Gm25756_chr5_78607549_F | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_intergenic_Mthfr-ps1|Gm25756_chr5_78607549_R | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_intergenic_Gm12983|Gm12984_chr4_135298177_F | TCGTCGGCAGCGTCGTCTGCTCCCACACTTACCC | 60.0 | 0.03 |
| mm4_intergenic_Gm12983|Gm12984_chr4_135298177_R | GTCTCGTGGGCTCGGGGGGAAGTAGTGGTGGCAG | 59.7 | 0.03 |
| mm3_exon_Foxa1_chr12_57542524_F | TCGTCGGCAGCGTCCTAGCCTTTCCGTGCACACC | 61.2 | 0.03 |
| mm3_exon_Foxa1_chr12_57542524_R | GTCTCGTGGGCTCGGGCCCAGAAAGTCGCAAGGA | 60.3 | 0.03 |
| mm4_intron_Ntn1_chr11_68244020_F | TCGTCGGCAGCGTCTTCCTCACACAGCACAGCTC | 60.2 | 0.03 |
| mm4_intron_Ntn1_chr11_68244020_R | GTCTCGTGGGCTCGGCCTGTTCATCCATCCCAGGG | 59.8 | 0.03 |
| mm4_intergenic_Gm23176|Nt5e_chr9_88163288_F | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_intergenic_Gm23176|Nt5e_chr9_88163288_R | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_intergenic_Gm5621|Pik3r4_chr9_105594361_F | TCGTCGGCAGCGTCAAGTGGTTCTGTTAGCAGCT | 57.0 | 0.03 |
| mm4_intergenic_Gm5621|Pik3r4_chr9_105594361_R | GTCTCGTGGGCTCGGTCTGAAACCACGCTAACGCT | 59.9 | 0.03 |
| mm4_intergenic_Zfp664|Fam101a_chr5_124954378_F | TCGTCGGCAGCGTCCAGCCTAGGGATGCAGTGAC | 60.1 | 0.03 |
| mm4_intergenic_Zfp664|Fam101a_chr5_124954378_R | GTCTCGTGGGCTCGGAGCAGAAAACCTACAGGCCC | 59.9 | 0.03 |
| mm4_intergenic_Ppapdc1a|Wdr11_chr7_129553351_F | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_intergenic_Ppapdc1a|Wdr11_chr7_129553351_R | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_intron_Nav1_chr1_135513583_F | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_intron_Nav1_chr1_135513583_R | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_intergenic_F2rl1|F2r_chr13_95581709_F | TCGTCGGCAGCGTCCCAGAGCACAGGATTCCTTCC | 60.4 | 0.03 |
| mm4_intergenic_F2rl1|F2r_chr13_95581709_R | GTCTCGTGGGCTCGGTCAAATCAGACTCCACATGGCT | 59.6 | 0.03 |
| mm4_exon_Trp73_chr4_154140132_F | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_exon_Trp73_chr4_154140132_R | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_intergenic_Rbm15|Gm24383_chr3_107393727_F | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_intergenic_Rbm15|Gm24383_chr3_107393727_R | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_intron_Slc7a9_chr7_35456948_F | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_intron_Slc7a9_chr7_35456948_R | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_intergenic_Gm14688|Gm4910_chrX_68292263_F | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_intergenic_Gm14688|Gm4910_chrX_68292263_R | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_intergenic_Gm15083|Slc6a11_chr6_114060496_F | TCGTCGGCAGCGTCGCACACTGCAGTCAACTGTG | 59.9 | 0.02 |
| mm4_intergenic_Gm15083|Slc6a11_chr6_114060496_R | GTCTCGTGGGCTCGGGACAGCAGGGCACATACAGT | 60.0 | 0.02 |
| mm4_intron_Fam35a_chr14_34242149_F | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_intron_Fam35a_chr14_34242149_R | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_exon_Nek11/Aste1_chr9_105395290_F | TCGTCGGCAGCGTCGGAGGGCGTGGTTGTTTAAC | 59.4 | 0.02 |
| mm4_exon_Nek11/Aste1_chr9_105395290_R | GTCTCGTGGGCTCGGCTTCCGTTGGATTGGACGCC | 61.6 | 0.02 |
| mm4_intron_Tns3_chr11_8664296_F | TCGTCGGCAGCGTCCTCAGTCCTGGATCCCAAGC | 59.8 | 0.02 |
| mm4_intron_Tns3_chr11_8664296_R | GTCTCGTGGGCTCGGGGTCTTGGAACTGGGTTGCA | 60.4 | 0.02 |
| mm4_intron_Anp32b_chr4_46452371_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intron_Anp32b_chr4_46452371_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intron_Abcc1_chr16_14361662_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intron_Abcc1_chr16_14361662_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intron_Glb1l2_chr9_26782876_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intron_Glb1l2_chr9_26782876_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intron_Ofcc1_chr13_40091798_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intron_Ofcc1_chr13_40091798_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Pax5|Mir5120_chr4_44575493_F | TCGTCGGCAGCGTCTTTGCTGTGTTGGCCTCTGA | 60.1 | 0.01 |
| mm4_intergenic_Pax5|Mir5120_chr4_44575493_R | GTCTCGTGGGCTCGGTTCTCACTGGGTGTGGTTCG | 59.8 | 0.01 |
| mm4_exon_Plekha8/Fkbp14_chr6_54595317_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_exon_Plekha8/Fkbp14_chr6_54595317_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Foxi3|Gm23485_chr6_70963674_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Foxi3|Gm23485_chr6_70963674_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intron_Rgl1_chr1_152599999_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intron_Rgl1_chr1_152599999_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intergenic_Tmem156|Klhl5_chr5_65103888_F | TCGTCGGCAGCGTCGGGGTCTTAAGCCATGCTGT | 60.0 | 0.00 |
| mm4_intergenic_Tmem156|Klhl5_chr5_65103888_R | GTCTCGTGGGCTCGGTCCCTTCTTCGAGACCACAC | 59.0 | 0.00 |
| mm4_intergenic_F630040K05Rik|Vegfa_chr17_45864764_F | TCGTCGGCAGCGTCGTGGGGTGAAGACTGACAGG | 59.9 | 0.00 |
| mm4_intergenic_F630040K05Rik|Vegfa_chr17_45864764_R | GTCTCGTGGGCTCGGGGAACAACTGAACACTGGGC | 59.3 | 0.00 |
| mm4_exon_Cdk13_chr13_17804613_F | TCGTCGGCAGCGTCCTCCAACTTCTTCTCGGCCC | 60.3 | 0.00 |
| mm4_exon_Cdk13_chr13_17804613_R | GTCTCGTGGGCTCGGGACATGGCCAGGGTCTGAC | 60.0 | 0.00 |
These only list off-targets that have primers in the table above. Primers underlined, off-targets in bold.
| ontarget_mm0_exon_5730457N03Rik/Evx1_chr6_52313713 |
CGCATCACAAGGTGACCCTAGCTCCCCACTGCCATCTCCGCGGTCGCCGTCGACACGGCGCTGGGGCTACCCGGCGCCTG CCTTGTCGCCTTAGCTCCTCTTCTCAGCCAAGATCCCAGGGAGCCTGGGATTAGGAG |
| mm2_intergenic_E130006D01Rik|Miat/MIAT_exon5_3/MIAT_exon5_2/Gm26953/MIAT_exon5_1_chr5_111870160 |
ATTCGTGGGACCTGTGGAACCCAGAGCTGACCCAGACAGTCCTTGGAATGTGTCTGACCTCAGGACACGGGGCTGGGGCC ACCTGGCTGCTAATGTGCCCTTGGAACG |
| mm4_intron_Arid1b_chr17_5225423 |
GCAGAGTCACCCTCAACCTCCAGTTCAAAAGAAGGGGTCACAGTTTTCTTCTACTGAGACCTGGTTGCCCCAGGGTTGTG TCTGCCCAGAGGACCTCCTTGTCCAAGGCTCATCATGGC |
| mm4_intron_Kat6b_chr14_21558695 |
GCCAGAACCCTTGTCTGGAAGTATTGCAAGGCGTTTTATAACCCTCCCTCACCACACCCCAGCACTGTGAGCTCCTGGAA TCCCCAGCTCAGTGTCTCCTCTTTCTTTTCCCAGCTCACCGCCATGCCCTAAGATCCAG |
| mm4_intergenic_B230206L02Rik|Tob1_chr11_94172602 | AGGGGATGCAAAGTTAGCCCAAGGGGGCTCCGTGTAGCCCCAGTGTAGTGTCCAGGGGCAAACATGGAGAAGG |
| mm4_intron_Wfs1_chr5_36982676 |
CACAGAGGCTTAGGCTGGTCCTAAGCTCAATGGGCTGTTTCCTTAGAAAGAGACACAGCCCAGGGGCTACAGGGAGATGG ACCAGAGGCTGAAGTAAGACAGACAACTGCAGGAGAACAAACACCAAGGACTGACAGCC |
| mm4_intergenic_Gm24248|Rybp_chr6_99898251 |
AACAAGAGCAGGTACCAGGCTGCCATGAGGCCGCAATGACATTGCACTGGGGCCACCTGGCAGGAAGCCTAAATGCTGTC TGGCAC |
| mm4_exon_Ddx54/Ccdc42b_chr5_120627299 |
CCAGGAAGGGCAAGATGAGGAAAAGGATGTGAGGAGCCAGACGCAGCCCTGGGGCTTCCTGGTAGCCCCGGGTGTGGACG TCAGGGACTATGTCC |
| mm4_intron_Tshz1_chr18_84026506 |
AGCCTGGGACCCACTATGAAAGAATCCAGCAGGTTCCAACCTGGTTGCCCCAGCTCCCTGCCCCAGAGCAGGGTAACGTG TACCTGTGGCAACCCTCTGACAGGAAGCACTCGGAGGAAG |
| mm4_intergenic_Gm26883|Gm26883/Tshz2_chr2_169815159 |
TTCTCCACTTATGCTCCCGGGGCCTGTGTGCCCTGCCTCGCAGAGGGACCCGGGTTGCCCCAGCCCAGTGTGGAGAACAG GGGTTTTTGTTAGCCCAGGCAACTCTG |
| mm4_intergenic_Plch2|Pex10_chr4_155066885 |
CCTGTCATTACCCGCCACTTCACTGTGCCGCTTCACCCTCCAAGCACAGACCACACCCCTCCCCGGGTAGCCCCACCCCT ATGTCGTGGACACGCCCACTACTCCGCCTCCACAGAT |
| mm4_intron_Drd2_chr9_49392725 |
GGTGTTGCAGGACCATGACTCTTGTCTGATGTAAGAACAGGTGGTAGAGAGGGGGAAAAGGGGAAGACAGGGCGCTGGGG ATAAAGGGAGGGAACATAGGAAGCTGAGGATCATGGGAGGGGA |
| mm4_intron_Ralgds_chr2_28548638 |
ATCACTGTTGCCTGGTGACAGCTGCGTATCCAGGCTCCAGCTTGGGGGCTACCCCGATTGGGAGCCCCAGCTTGGCTCCT GGTAGCCTCACAGCCATGTCTACCTTAGCTACACCCTGTCGTGTGAGCTGGAG |
| mm4_intergenic_Nrbf2|Egr2_chr10_67504508 |
CCCTCCTGGCTTGTGGAATCTGTCTTAAAGGAAAAGCAGTGAGTTCCTAGTATCCCCAGGGCCGTGACATTTCCCTCAAG CTCTGCAAATAGTGTCAGATCCTAAGACCCCAGAGCTTATCCTGT |
| mm4_exon_Lamp1_chr8_13175015 |
GCTGATGGTTAGGCTGCACACTTAAGAAGCAAACGGGAGCAGGGAAGGCTTGCCACACAGGCACGCACAGGGTCAACCTC TGGACACTTGGCTTGGGCTACCTGGCCTGGGGGGGCTGAACTCTGGCATCTGGCTG |
| mm4_intergenic_Flrt1|Macrod1_chr19_7156856 |
GAAGAGGGTCACGGTCCAACCCCTCCTCCAGTCCCTCTCCACCCACCATGCCTGGCAGCCCCAGGGCACTGTCACACCTA GTCCGGGGGACACTTTGAGCTGGATCTAGCCATCTTCATGCAGTCGGGA |
| mm4_intron_Twf1_chr15_94589720 |
CACCCAGAGCAGCTCCAATGCCGTGCGCGCCTCCAGCGTTCCGGCCCGCAGCCTCCCGGGAGCCCCTGCCCCGTGGCGCC GTTACCTTGGATGCCTGT |
| mm4_intergenic_Gm16178|Sh3rf1_chr8_61205038 |
AGCTATAGAGGACAGCGGGTTAAATTCTAATTCAGAAAAGAGATTGATAATTCTTTCCTTATGTCTTTCCTGCATAATCT GTTTTACCTGGCAGCCCCAGAGCCGACTCAGCTTTCCCTGCTGGTTCTTTTGGTGC |
| mm4_intron_Papl_chr7_28630615 |
CTTCAGGTGACGGGCTCCCCAGACAGCCCGAGCCCCGTGTCCCACAGGTCCGGCCGGTCCCTGGCGCCCCACGCCCACCC TCACGCCCCCCTCAGGGTGGGGCGCAGAAAGAGGGGACCCAGAAAAGCATGGGA |
| mm4_exon_Nphp4_chr4_152488444 |
TCGGCTCAGACCCTCCATATCTTGGTTCCATCTGCTAATGGGATGGCTGCCAGTCAGCCCCAGGCCCGTGTCATGCGGAC ACAACCTGCCTCTGGTG |
| mm4_intron_Pias1_chr9_62980784 |
GCCTACAACTCCAGACTCGGGTGGAGCCCGGCCCGAGCGGGCCCCCCAGGGTCCGACCCATCCCCCCGGCAGCCGCGGCG CCGTCTCCGCGGCCGAATATTAGAAGTGAATTCGAGCTGCGCTTTACCTTTAGTTCCGC |
| mm4_intergenic_Tmprss5|Gm4894_chr9_49146281 |
CAAAGGGAGGGATGCCTCTGAGTGAGGGTGGATGGGGGCAGCTGTGAGCTGTCTCAGGCCAGGCAGCCACAGTGCAGTGT CTAGCTCCTCTTTCACCTCCTTCCTGTGGTGCTGTGTT |
| mm4_intergenic_Gm12983|Gm12984_chr4_135298177 |
GTCTGCTCCCACACTTACCCTTGCTGGGCGCCAGGGAGCCCAAGCTCCGTGGCCCCAGCTGTGGGGTGGCCACCCCCACA TCAGGCTGTGCTGTGCTGAGGGCTGCCACCACTACTTCCCC |
| mm3_exon_Foxa1_chr12_57542524 |
CTAGCCTTTCCGTGCACACCCCGGTGAAGGGGTGACTCGGCGCTGGGGTTCCCCGGGCCTGAGGGGTCCTTGCGACTTTC TGGGC |
| mm4_intron_Ntn1_chr11_68244020 |
TTCCTCACACAGCACAGCTCGAAGGGTCCCTGGGAGCCACAGTGCTGTGTCTACTCAGCTCTGTTACCCAGCACCCTGGG ATGGATGAACAGG |
| mm4_intergenic_Gm5621|Pik3r4_chr9_105594361 |
AAGTGGTTCTGTTAGCAGCTAAGTGATCCAGGTGCCCCCAGCGCCGACTCCTACGTTAGCATTAGCGTTAGCGTGGTTTC AGA |
| mm4_intergenic_Zfp664|Fam101a_chr5_124954378 |
CAGCCTAGGGATGCAGTGACAGACAGGGAGCTGGGGCTCTCTGGGGACATCAACTTGGAAGAAAGGAAGGGACAAGGCAG GAATAGCTGTGGACTGCTACCCTCTGGGGCCTGTAGGTTTTCTGCT |
| mm4_intergenic_F2rl1|F2r_chr13_95581709 | CCAGAGCACAGGATTCCTTCCTAAGCCAGACACGGCACTGTGGTTTCCTGGAAGCCATGTGGAGTCTGATTTGA |
| mm4_intergenic_Gm15083|Slc6a11_chr6_114060496 |
GCACACTGCAGTCAACTGTGGAAATCAGGAAGAAATGCTGAAATCACAGTGTATGTGACCCGACAGCACAGTCGCCTGTC ACCCTCAGCGCCGTGTCTGATGTCACTGTATGTGCCCTGCTGTC |
| mm4_exon_Nek11/Aste1_chr9_105395290 |
GGAGGGCGTGGTTGTTTAACATCGTCGCCACGGAGACGGCGCGGGGGCTGCTGGGAAGTCGACGTTCCGGCGTCCAATCC AACGGAAG |
| mm4_intron_Tns3_chr11_8664296 |
CTCAGTCCTGGATCCCAAGCGCCCTTCCCGGGTGCCCCCGCGCCTTGTCCCTACACCCTCAACTGTCTCCGCGCCCAGGT TTGGTGTCTGCTCGGCTGCAACCCAGTTCCAAGACC |
| mm4_intergenic_Pax5|Mir5120_chr4_44575493 |
TTTGCTGTGTTGGCCTCTGAGGACTCTCCTGACCCGGAGCTGTGGCTCCCGGGACCCTCCCTGAGAGCAGTGGGTATTTC CGCTGCCTGGTGCCTTCTCCATCACTCTCCTCAGTGAGCACGAACCACACCCAGTGAGAA |
| mm4_intergenic_Tmem156|Klhl5_chr5_65103888 |
GGGGTCTTAAGCCATGCTGTGGTGAAACATAAAAACAGCAGTCAACAGGGTCGGGTAGCCCCACCTCCAAGTCAGAAAGT GTGGTCTCGAAGAAGGGA |
| mm4_intergenic_F630040K05Rik|Vegfa_chr17_45864764 |
GTGGGGTGAAGACTGACAGGAAAGAGGGGACACGGCCCTGTGGCTCGCCGGCCATTTAAGAAGCCCAGTGTTCAGTTGTT CC |
| mm4_exon_Cdk13_chr13_17804613 |
CTCCAACTTCTTCTCGGCCCAGCTCAGGCCCCCGCCTCCCCCCAGCGCCGTGTCCGAGCTACTCGGCATCGCCTAGAGCC CGCCGCAGAGTGCGGCGCGGGTGCGGCCTCCTCCGGGGTCAGACCCTGGCCATGTC |