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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_52314104_F | Primer3: not found at this Tm | N.d. | 1.00 |
| ontarget_mm0_exon_5730457N03Rik/Evx1_chr6_52314104_R | Primer3: not found at this Tm | N.d. | 1.00 |
| mm4_intergenic_1700019M22Rik|Gm26480_chr12_96160386_F | Primer3: not found at this Tm | N.d. | 0.75 |
| mm4_intergenic_1700019M22Rik|Gm26480_chr12_96160386_R | Primer3: not found at this Tm | N.d. | 0.75 |
| mm4_intergenic_Irf2|Enpp6_chr8_46983581_F | TCGTCGGCAGCGTCGGAGCATCAGCCTTCCTCAG | 60.1 | 0.54 |
| mm4_intergenic_Irf2|Enpp6_chr8_46983581_R | GTCTCGTGGGCTCGGCTAACTGTGCCCTGTGCTCA | 59.9 | 0.54 |
| mm4_exon_Iffo1_chr6_125145296_F | TCGTCGGCAGCGTCCTGCACTGGTCTCCTTCTCC | 59.7 | 0.43 |
| mm4_exon_Iffo1_chr6_125145296_R | GTCTCGTGGGCTCGGCAAAGTGGTCACCTCCCAGA | 59.2 | 0.43 |
| mm4_intergenic_Ly6f|9030619P08Rik_chr15_75311401_F | TCGTCGGCAGCGTCAAAGGGCAAAGGTGGAGGTC | 60.1 | 0.42 |
| mm4_intergenic_Ly6f|9030619P08Rik_chr15_75311401_R | GTCTCGTGGGCTCGGGCGCTACAGAAGTTCCCACT | 60.0 | 0.42 |
| mm3_intron_Wnt7a_chr6_91383113_F | Primer3: not found at this Tm | N.d. | 0.39 |
| mm3_intron_Wnt7a_chr6_91383113_R | Primer3: not found at this Tm | N.d. | 0.39 |
| mm4_intergenic_Gm5611|Chordc1_chr9_18207724_F | Primer3: not found at this Tm | N.d. | 0.36 |
| mm4_intergenic_Gm5611|Chordc1_chr9_18207724_R | Primer3: not found at this Tm | N.d. | 0.36 |
| mm4_intergenic_Gnpnat1|Gm25353_chr14_45388878_F | Primer3: not found at this Tm | N.d. | 0.34 |
| mm4_intergenic_Gnpnat1|Gm25353_chr14_45388878_R | Primer3: not found at this Tm | N.d. | 0.34 |
| mm4_intergenic_Gm10000|Dicer1_chr12_104593761_F | Primer3: not found at this Tm | N.d. | 0.32 |
| mm4_intergenic_Gm10000|Dicer1_chr12_104593761_R | Primer3: not found at this Tm | N.d. | 0.32 |
| mm4_intergenic_Gramd1b|1700110K17Rik_chr9_40321598_F | TCGTCGGCAGCGTCCTGGCCAATGTCCTGCAGTA | 60.0 | 0.26 |
| mm4_intergenic_Gramd1b|1700110K17Rik_chr9_40321598_R | GTCTCGTGGGCTCGGGCCAGCAACTTTCCATTGCA | 59.9 | 0.26 |
| mm4_intergenic_Gm6377/Sh3bgrl|Gm14868_chrX_109228549_F | Primer3: not found at this Tm | N.d. | 0.25 |
| mm4_intergenic_Gm6377/Sh3bgrl|Gm14868_chrX_109228549_R | Primer3: not found at this Tm | N.d. | 0.25 |
| mm4_intron_4732487G21Rik_chr12_86294945_F | TCGTCGGCAGCGTCGGGTTCAGCTGAGGTGTCTC | 60.0 | 0.23 |
| mm4_intron_4732487G21Rik_chr12_86294945_R | GTCTCGTGGGCTCGGGGTTTCGTTAGCACTTCCCC | 58.8 | 0.23 |
| mm4_intron_Zfc3h1_chr10_115404469_F | Primer3: not found at this Tm | N.d. | 0.23 |
| mm4_intron_Zfc3h1_chr10_115404469_R | Primer3: not found at this Tm | N.d. | 0.23 |
| mm4_intergenic_P2ry4|Arr3_chrX_100599971_F | Primer3: not found at this Tm | N.d. | 0.21 |
| mm4_intergenic_P2ry4|Arr3_chrX_100599971_R | Primer3: not found at this Tm | N.d. | 0.21 |
| mm4_intron_A630095N17Rik_chr1_75224791_F | Primer3: not found at this Tm | N.d. | 0.21 |
| mm4_intron_A630095N17Rik_chr1_75224791_R | Primer3: not found at this Tm | N.d. | 0.21 |
| mm4_intron_Fhit_chr14_9588805_F | Primer3: not found at this Tm | N.d. | 0.20 |
| mm4_intron_Fhit_chr14_9588805_R | Primer3: not found at this Tm | N.d. | 0.20 |
| mm4_intergenic_Gm10617|Gm25200_chr8_118102558_F | TCGTCGGCAGCGTCTGGAGTCATGGCCAAATGCT | 59.9 | 0.20 |
| mm4_intergenic_Gm10617|Gm25200_chr8_118102558_R | GTCTCGTGGGCTCGGTGGCTTAGCAGAATGCCCAA | 59.9 | 0.20 |
| mm4_intergenic_Gm25727|F830104G03Rik_chr3_56677569_F | Primer3: not found at this Tm | N.d. | 0.19 |
| mm4_intergenic_Gm25727|F830104G03Rik_chr3_56677569_R | Primer3: not found at this Tm | N.d. | 0.19 |
| mm4_intergenic_Ntf3|Kcna5_chr6_126284263_F | TCGTCGGCAGCGTCGCCCTTCTCAGGAGTGTTCC | 60.0 | 0.19 |
| mm4_intergenic_Ntf3|Kcna5_chr6_126284263_R | GTCTCGTGGGCTCGGTGAGGGAGCAATAAACGGGT | 59.0 | 0.19 |
| mm4_intron_Yy1_chr12_108794183_F | TCGTCGGCAGCGTCATGTGTGTGATGGGCGCC | 60.7 | 0.18 |
| mm4_intron_Yy1_chr12_108794183_R | GTCTCGTGGGCTCGGCGCACAAACTACGCCATTGC | 61.0 | 0.18 |
| mm3_intergenic_Prm2|Prm1_chr16_10794799_F | Primer3: not found at this Tm | N.d. | 0.18 |
| mm3_intergenic_Prm2|Prm1_chr16_10794799_R | Primer3: not found at this Tm | N.d. | 0.18 |
| mm3_intergenic_Prm2|Prm1_chr16_10793679_F | Primer3: not found at this Tm | N.d. | 0.18 |
| mm3_intergenic_Prm2|Prm1_chr16_10793679_R | Primer3: not found at this Tm | N.d. | 0.18 |
| mm4_intron_Lrp1_chr10_127554517_F | TCGTCGGCAGCGTCAAGGAGACAACCATGGCCTG | 59.9 | 0.18 |
| mm4_intron_Lrp1_chr10_127554517_R | GTCTCGTGGGCTCGGACGGCTCCAACTACACACTG | 59.9 | 0.18 |
| mm3_exon_Ppp3cb_chr14_20546428_F | Primer3: not found at this Tm | N.d. | 0.18 |
| mm3_exon_Ppp3cb_chr14_20546428_R | Primer3: not found at this Tm | N.d. | 0.18 |
| mm4_intergenic_Gm12405|Cntfr_chr4_41657091_F | Primer3: not found at this Tm | N.d. | 0.18 |
| mm4_intergenic_Gm12405|Cntfr_chr4_41657091_R | Primer3: not found at this Tm | N.d. | 0.18 |
| mm3_intergenic_Gm22302|Uri1_chr7_37839381_F | Primer3: not found at this Tm | N.d. | 0.17 |
| mm3_intergenic_Gm22302|Uri1_chr7_37839381_R | Primer3: not found at this Tm | N.d. | 0.17 |
| mm3_intergenic_Gm24326|Gm25923_chr12_27945840_F | TCGTCGGCAGCGTCGTGAGGTGCCTGTTCCATCA | 59.9 | 0.16 |
| mm3_intergenic_Gm24326|Gm25923_chr12_27945840_R | GTCTCGTGGGCTCGGGCTCTGTCTGAACCCCACTG | 60.3 | 0.16 |
| mm4_intergenic_Cpeb2|C1qtnf7_chr5_43474710_F | TCGTCGGCAGCGTCACTCCAGCTCCCACAGGTAA | 60.1 | 0.16 |
| mm4_intergenic_Cpeb2|C1qtnf7_chr5_43474710_R | GTCTCGTGGGCTCGGTCTGTCTGTAGTGCTGTGGC | 59.6 | 0.16 |
| mm4_intron_Gdpd5_chr7_99392832_F | Primer3: not found at this Tm | N.d. | 0.16 |
| mm4_intron_Gdpd5_chr7_99392832_R | Primer3: not found at this Tm | N.d. | 0.16 |
| mm4_intron_Tcte2_chr17_13493002_F | TCGTCGGCAGCGTCGGTGAGACCCAGAGGCAAAG | 60.3 | 0.16 |
| mm4_intron_Tcte2_chr17_13493002_R | GTCTCGTGGGCTCGGCCCATGTCTGATCTCGGAGC | 59.9 | 0.16 |
| mm4_intergenic_Unc93a|Smok2a_chr17_13187985_F | Primer3: not found at this Tm | N.d. | 0.16 |
| mm4_intergenic_Unc93a|Smok2a_chr17_13187985_R | Primer3: not found at this Tm | N.d. | 0.16 |
| mm4_exon_Rassf10_chr7_112954644_F | TCGTCGGCAGCGTCGAAGCGTCGCTGCCCAAC | 62.0 | 0.16 |
| mm4_exon_Rassf10_chr7_112954644_R | GTCTCGTGGGCTCGGCTGCTTCTCCTGGGTCAAGG | 60.0 | 0.16 |
| mm4_intergenic_Tekt4|Sstr5_chr17_25480857_F | Primer3: not found at this Tm | N.d. | 0.16 |
| mm4_intergenic_Tekt4|Sstr5_chr17_25480857_R | Primer3: not found at this Tm | N.d. | 0.16 |
| mm3_intergenic_mmu-mir-6393|Zdhhc25_chr15_88444314_F | TCGTCGGCAGCGTCCCGAGCTGGCGTAGTATCC | 59.7 | 0.16 |
| mm3_intergenic_mmu-mir-6393|Zdhhc25_chr15_88444314_R | GTCTCGTGGGCTCGGCTCCGTTTCCCTCTTAGGCC | 59.8 | 0.16 |
| mm4_intron_Blmh_chr11_76960710_F | Primer3: not found at this Tm | N.d. | 0.16 |
| mm4_intron_Blmh_chr11_76960710_R | Primer3: not found at this Tm | N.d. | 0.16 |
| mm3_intron_Nfix_chr8_84714246_F | TCGTCGGCAGCGTCTACCAGTGGAGTCCCCTAGC | 60.0 | 0.15 |
| mm3_intron_Nfix_chr8_84714246_R | GTCTCGTGGGCTCGGCTGGAGAGGAGGCCTGTTTG | 60.0 | 0.15 |
| mm4_intron_Ino80c_chr18_24114952_F | Primer3: not found at this Tm | N.d. | 0.15 |
| mm4_intron_Ino80c_chr18_24114952_R | Primer3: not found at this Tm | N.d. | 0.15 |
| mm4_intergenic_Rpl31-ps16|RP24-68F22.6_chr17_85569951_F | TCGTCGGCAGCGTCCCTGATGGTGCTTGTGAGGT | 59.9 | 0.15 |
| mm4_intergenic_Rpl31-ps16|RP24-68F22.6_chr17_85569951_R | GTCTCGTGGGCTCGGAGGGTCCAATTAAGGCTGCC | 60.0 | 0.15 |
| mm4_intergenic_Colq/Hacl1|Hacl1/Colq_chr14_31553656_F | Primer3: not found at this Tm | N.d. | 0.15 |
| mm4_intergenic_Colq/Hacl1|Hacl1/Colq_chr14_31553656_R | Primer3: not found at this Tm | N.d. | 0.15 |
| mm4_intergenic_Clybl|Gm5089_chr14_122406778_F | TCGTCGGCAGCGTCGGTGTAGCAGTGCTGGGG | 60.0 | 0.15 |
| mm4_intergenic_Clybl|Gm5089_chr14_122406778_R | GTCTCGTGGGCTCGGATCTCGCACCATTACAGCCC | 60.1 | 0.15 |
| mm4_intergenic_Tnfaip8l2|Gm9169_chr3_95144263_F | Primer3: not found at this Tm | N.d. | 0.14 |
| mm4_intergenic_Tnfaip8l2|Gm9169_chr3_95144263_R | Primer3: not found at this Tm | N.d. | 0.14 |
| mm4_intergenic_Gm20696/Eif4e3|Gpr27_chr6_99684730_F | Primer3: not found at this Tm | N.d. | 0.14 |
| mm4_intergenic_Gm20696/Eif4e3|Gpr27_chr6_99684730_R | Primer3: not found at this Tm | N.d. | 0.14 |
| mm4_intergenic_Rpp40|Ppp1r3g_chr13_35938817_F | Primer3: not found at this Tm | N.d. | 0.14 |
| mm4_intergenic_Rpp40|Ppp1r3g_chr13_35938817_R | Primer3: not found at this Tm | N.d. | 0.14 |
| mm4_intron_Lama5_chr2_180195018_F | TCGTCGGCAGCGTCTCTGCTTCACACCCAGTGTC | 59.8 | 0.14 |
| mm4_intron_Lama5_chr2_180195018_R | GTCTCGTGGGCTCGGGGTGGAGTGGATGCAAGACA | 59.9 | 0.14 |
| mm4_exon_Amfr_chr8_94012585_F | Primer3: not found at this Tm | N.d. | 0.13 |
| mm4_exon_Amfr_chr8_94012585_R | Primer3: not found at this Tm | N.d. | 0.13 |
| mm3_intergenic_Gm9855|Foxo3_chr10_42107734_F | TCGTCGGCAGCGTCCCAGTCTGGGCAGAACCAAT | 59.9 | 0.13 |
| mm3_intergenic_Gm9855|Foxo3_chr10_42107734_R | GTCTCGTGGGCTCGGCATCAGTCCCCACCCTTTCC | 60.0 | 0.13 |
| mm4_intron_Ppara_chr15_85754930_F | TCGTCGGCAGCGTCGGTGACTGAGGTGGATCTGG | 59.4 | 0.12 |
| mm4_intron_Ppara_chr15_85754930_R | GTCTCGTGGGCTCGGTCAACCTCCTGGCATCAACC | 59.9 | 0.12 |
| mm4_intergenic_Wnt11/Gm8398|Uvrag_chr7_98856235_F | TCGTCGGCAGCGTCCCCCTAAGTCAGTCAAAGCTC | 58.0 | 0.12 |
| mm4_intergenic_Wnt11/Gm8398|Uvrag_chr7_98856235_R | GTCTCGTGGGCTCGGAGCAGGGCATTAGAGAGAGA | 57.5 | 0.12 |
| mm4_intron_Cyfip1_chr7_55842472_F | Primer3: not found at this Tm | N.d. | 0.12 |
| mm4_intron_Cyfip1_chr7_55842472_R | Primer3: not found at this Tm | N.d. | 0.12 |
| mm3_intergenic_Gm26644|Pax2_chr19_44742301_F | Primer3: not found at this Tm | N.d. | 0.11 |
| mm3_intergenic_Gm26644|Pax2_chr19_44742301_R | Primer3: not found at this Tm | N.d. | 0.11 |
| mm4_intron_Vwa8_chr14_79075026_F | TCGTCGGCAGCGTCTCTGGAGAGGAGGAGGTGTG | 59.9 | 0.11 |
| mm4_intron_Vwa8_chr14_79075026_R | GTCTCGTGGGCTCGGCGAGGTCACCGAGAAATGCT | 60.1 | 0.11 |
| mm4_intron_Grm4_chr17_27466512_F | TCGTCGGCAGCGTCGGCCCAATCCTAGATCTCCC | 59.0 | 0.11 |
| mm4_intron_Grm4_chr17_27466512_R | GTCTCGTGGGCTCGGCTCCAACAGTCAGCAAGCAC | 59.4 | 0.11 |
| mm4_intergenic_Jakmip1|Gm26647_chr5_37033538_F | Primer3: not found at this Tm | N.d. | 0.11 |
| mm4_intergenic_Jakmip1|Gm26647_chr5_37033538_R | Primer3: not found at this Tm | N.d. | 0.11 |
| mm4_intron_Auts2_chr5_131817236_F | TCGTCGGCAGCGTCTCCTTCCAGCAGAGGGAGAA | 59.8 | 0.11 |
| mm4_intron_Auts2_chr5_131817236_R | GTCTCGTGGGCTCGGGGGGAGTTTGGGTGGCTTAA | 59.8 | 0.11 |
| mm4_intergenic_Gm6214|Pdha2_chr3_140917808_F | Primer3: not found at this Tm | N.d. | 0.10 |
| mm4_intergenic_Gm6214|Pdha2_chr3_140917808_R | Primer3: not found at this Tm | N.d. | 0.10 |
| mm4_intron_Ap1b1_chr11_4992675_F | Primer3: not found at this Tm | N.d. | 0.10 |
| mm4_intron_Ap1b1_chr11_4992675_R | Primer3: not found at this Tm | N.d. | 0.10 |
| mm4_intergenic_Gm25247|Tshz3_chr7_36663622_F | TCGTCGGCAGCGTCGCCTGGAGCTGTCAGTCATT | 60.0 | 0.10 |
| mm4_intergenic_Gm25247|Tshz3_chr7_36663622_R | GTCTCGTGGGCTCGGAAGCCAAGCCTAGTGAGAGC | 59.7 | 0.10 |
| mm4_intron_Sh3gl3_chr7_82275158_F | TCGTCGGCAGCGTCCACCTGTCACCCCTTCCTTC | 59.9 | 0.09 |
| mm4_intron_Sh3gl3_chr7_82275158_R | GTCTCGTGGGCTCGGGAAGATGGGTCTTGGTGGGG | 60.0 | 0.09 |
| mm4_intron_Dmd_chrX_84175421_F | TCGTCGGCAGCGTCGAGCCAGGTTGAATTGGTGC | 59.7 | 0.09 |
| mm4_intron_Dmd_chrX_84175421_R | GTCTCGTGGGCTCGGCCCCACCTTTCCTGGAGTTC | 59.9 | 0.09 |
| mm4_intergenic_Prss36|Fus_chr7_127950348_F | Primer3: not found at this Tm | N.d. | 0.09 |
| mm4_intergenic_Prss36|Fus_chr7_127950348_R | Primer3: not found at this Tm | N.d. | 0.09 |
| mm4_exon_Gigyf1_chr5_137524289_F | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_exon_Gigyf1_chr5_137524289_R | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_intron_Myo1d_chr11_80692200_F | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_intron_Myo1d_chr11_80692200_R | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_exon_Bcl11a_chr11_24090322_F | TCGTCGGCAGCGTCTGGCATTTAACTGTGGGGCT | 59.8 | 0.08 |
| mm4_exon_Bcl11a_chr11_24090322_R | GTCTCGTGGGCTCGGCGCCTCTCCCTGAACTGAAG | 60.1 | 0.08 |
| mm4_intron_Mad1l1_chr5_140027913_F | TCGTCGGCAGCGTCACAAAGCACGTTCTAGGCAA | 58.0 | 0.08 |
| mm4_intron_Mad1l1_chr5_140027913_R | GTCTCGTGGGCTCGGCCCTCAGGCTTACATGGCTT | 59.7 | 0.08 |
| mm4_intron_Tet2_chr3_133534875_F | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_intron_Tet2_chr3_133534875_R | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_intron_Stap2_chr17_55999877_F | TCGTCGGCAGCGTCAAGCCTGAAACAGAGAGGGC | 59.9 | 0.07 |
| mm4_intron_Stap2_chr17_55999877_R | GTCTCGTGGGCTCGGGAAGGTTCTAGGTGTGTGCGA | 59.9 | 0.07 |
| mm4_intergenic_Gm8910|Gm22547_chr3_11044345_F | TCGTCGGCAGCGTCTTCTTGGGCTGTTTCAGGGG | 60.1 | 0.07 |
| mm4_intergenic_Gm8910|Gm22547_chr3_11044345_R | GTCTCGTGGGCTCGGGGATCAGGGTCTGGTGAAGG | 59.4 | 0.07 |
| mm4_intron_Anapc10_chr8_79731041_F | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_intron_Anapc10_chr8_79731041_R | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_exon_1110004F10Rik_chr7_116093357_F | TCGTCGGCAGCGTCGTGACGACTGTAGCGGTGAA | 60.0 | 0.06 |
| mm4_exon_1110004F10Rik_chr7_116093357_R | GTCTCGTGGGCTCGGCCTGACGGGGATATGCCAAA | 59.8 | 0.06 |
| mm4_intergenic_Gm24434|Arl4a_chr12_39884741_F | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_intergenic_Gm24434|Arl4a_chr12_39884741_R | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_intergenic_Lrp6|Mansc1_chr6_134573008_F | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_intergenic_Lrp6|Mansc1_chr6_134573008_R | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_intron_Naa25_chr5_121404257_F | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_intron_Naa25_chr5_121404257_R | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_exon_Bicd2_chr13_49379624_F | TCGTCGGCAGCGTCCCTCTACCACCATGTGTGCA | 59.6 | 0.06 |
| mm4_exon_Bicd2_chr13_49379624_R | GTCTCGTGGGCTCGGCTTGGGCAAGAGGACAGGTG | 60.6 | 0.06 |
| mm4_intron_Ptpn7_chr1_135132862_F | TCGTCGGCAGCGTCCAGACATCCTATGGCCCTGG | 59.6 | 0.06 |
| mm4_intron_Ptpn7_chr1_135132862_R | GTCTCGTGGGCTCGGCTTAGCCCTCCAGTCACAGG | 59.4 | 0.06 |
| mm3_intron_Bcas3_chr11_85501742_F | Primer3: not found at this Tm | N.d. | 0.05 |
| mm3_intron_Bcas3_chr11_85501742_R | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_intergenic_Pkdcc|Gm24240_chr17_83226037_F | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_intergenic_Pkdcc|Gm24240_chr17_83226037_R | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_intron_Gtf2i_chr5_134244656_F | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_intron_Gtf2i_chr5_134244656_R | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_intron_Txlnb_chr10_17809308_F | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_intron_Txlnb_chr10_17809308_R | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_intron_Trabd2b_chr4_114555828_F | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_intron_Trabd2b_chr4_114555828_R | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_intron_Tnk2_chr16_32679295_F | TCGTCGGCAGCGTCTGAGGCCTGAAGTTCTGCAG | 59.9 | 0.04 |
| mm4_intron_Tnk2_chr16_32679295_R | GTCTCGTGGGCTCGGACTGTCAACTCCCCTAGCCA | 60.1 | 0.04 |
| mm4_exon_4930596M17Rik_chr9_121602923_F | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_exon_4930596M17Rik_chr9_121602923_R | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_intron_Nfatc2_chr2_168584444_F | TCGTCGGCAGCGTCGTTCAGACATCTGGGCCCTC | 60.1 | 0.04 |
| mm4_intron_Nfatc2_chr2_168584444_R | GTCTCGTGGGCTCGGGTAGCTGCAGCCTCCAGTAG | 59.8 | 0.04 |
| mm4_intron_Fer_chr17_63917126_F | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_intron_Fer_chr17_63917126_R | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_intron_Sez6l_chr5_112550336_F | TCGTCGGCAGCGTCAGGAGCCTGGTCCCTGATAG | 60.1 | 0.03 |
| mm4_intron_Sez6l_chr5_112550336_R | GTCTCGTGGGCTCGGCTGCTGACTGTCCTGATGGG | 60.1 | 0.03 |
| mm4_intergenic_Rbm19|Gm26474_chr5_120279591_F | TCGTCGGCAGCGTCGAGCTCAGTTGCCTCCTGTT | 59.9 | 0.03 |
| mm4_intergenic_Rbm19|Gm26474_chr5_120279591_R | GTCTCGTGGGCTCGGTCCTGGGAGCAAACATCCAC | 59.9 | 0.03 |
| mm4_intergenic_Tmbim4|Llph_chr10_120226856_F | TCGTCGGCAGCGTCCCTTTCTCGTGAGGCTGTCA | 59.6 | 0.03 |
| mm4_intergenic_Tmbim4|Llph_chr10_120226856_R | GTCTCGTGGGCTCGGTTGGCTGACCCCTACACCTA | 59.8 | 0.03 |
| mm4_intergenic_Ppapdc3|Prrc2b_chr2_32131551_F | TCGTCGGCAGCGTCTAGGGACCAGTGTCAGCAAC | 59.3 | 0.03 |
| mm4_intergenic_Ppapdc3|Prrc2b_chr2_32131551_R | GTCTCGTGGGCTCGGGGAGGTCTGTGCATTGTGGA | 59.9 | 0.03 |
| mm4_intergenic_Gm24248|Rybp_chr6_100173714_F | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_intergenic_Gm24248|Rybp_chr6_100173714_R | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_intergenic_Gm24601|Gm26501_chr6_94887904_F | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_intergenic_Gm24601|Gm26501_chr6_94887904_R | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_exon_Pde4a_chr9_21181797_F | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_exon_Pde4a_chr9_21181797_R | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_intergenic_Mad1l1|Gm16121_chr5_140096291_F | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_intergenic_Mad1l1|Gm16121_chr5_140096291_R | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_intergenic_Antxrl|Anxa8_chr14_34079227_F | TCGTCGGCAGCGTCACCCACCTTTCACGACATCC | 59.9 | 0.02 |
| mm4_intergenic_Antxrl|Anxa8_chr14_34079227_R | GTCTCGTGGGCTCGGGCACACAAGACCCCTTCTGT | 60.1 | 0.02 |
| mm4_intron_Mov10_chr3_104795298_F | TCGTCGGCAGCGTCTTGGTTATCCTGCCGGCTTC | 60.3 | 0.02 |
| mm4_intron_Mov10_chr3_104795298_R | GTCTCGTGGGCTCGGACTCAGCCCCTCTACCTCAG | 60.0 | 0.02 |
| mm4_intergenic_Fam161b|Coq6/Fam161b_chr12_84359162_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Fam161b|Coq6/Fam161b_chr12_84359162_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Cdh26|Gm14314_chr2_178918931_F | TCGTCGGCAGCGTCCTGCTCCTCCGTTCATCCAG | 60.1 | 0.01 |
| mm4_intergenic_Cdh26|Gm14314_chr2_178918931_R | GTCTCGTGGGCTCGGCCCCAAGGTTAATGCACACA | 58.3 | 0.01 |
| mm4_intergenic_Gm7656|Gm24880_chr7_70496363_F | TCGTCGGCAGCGTCGCAAACGTGAGGAAAGCTGG | 60.0 | 0.01 |
| mm4_intergenic_Gm7656|Gm24880_chr7_70496363_R | GTCTCGTGGGCTCGGGCTCCTTGACAGACCTAGGG | 59.1 | 0.01 |
| mm4_intergenic_Gm5294|Pdgfa_chr5_138898462_F | TCGTCGGCAGCGTCGATGGGCCCCAATTCCTCTG | 60.4 | 0.01 |
| mm4_intergenic_Gm5294|Pdgfa_chr5_138898462_R | GTCTCGTGGGCTCGGAGACCTGGTATGCAGGAGGT | 59.9 | 0.01 |
| mm4_intron_Tspan9_chr6_128072695_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intron_Tspan9_chr6_128072695_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_exon_Nsmf_chr2_25054450_F | TCGTCGGCAGCGTCCTCTCCTACAGTGGCTGGAC | 59.1 | 0.01 |
| mm4_exon_Nsmf_chr2_25054450_R | GTCTCGTGGGCTCGGCTAGGTCTCAGCCTCAGGGT | 60.0 | 0.01 |
| mm4_intron_Slc24a2_chr4_87008622_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intron_Slc24a2_chr4_87008622_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intergenic_Dusp16|Crebl2_chr6_134825105_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intergenic_Dusp16|Crebl2_chr6_134825105_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intron_Tbl1xr1_chr3_22092895_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intron_Tbl1xr1_chr3_22092895_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intron_Gm9999_chr7_46986712_F | TCGTCGGCAGCGTCGGGGTAGCTCCTTTTCCAACT | 59.6 | 0.00 |
| mm4_intron_Gm9999_chr7_46986712_R | GTCTCGTGGGCTCGGAGAGGCCAGACTCAGACACT | 59.8 | 0.00 |
| mm4_intergenic_Gm5615|RP23-265F16.2_chr9_36537082_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intergenic_Gm5615|RP23-265F16.2_chr9_36537082_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.
| mm4_intergenic_Irf2|Enpp6_chr8_46983581 |
GGAGCATCAGCCTTCCTCAGTGCCCCTGGCCAAGCATGTCTGCACCTCATGGCCACCAATTTCCCTGAGCACAGGGCACA GTTAG |
| mm4_exon_Iffo1_chr6_125145296 |
CTGCACTGGTCTCCTTCTCCCGGCAGAAGGCGCAGCCATGAATCCGTTATTTGGTCCCAACCTCTTCCTCCTACAGCAGG AGCAGCAAGGCTTGGCCGGGCCGCTGGGGGACCCTCTGGGAGGTGACCACTTTG |
| mm4_intergenic_Ly6f|9030619P08Rik_chr15_75311401 |
AAAGGGCAAAGGTGGAGGTCAATGGAAGGATCATCACAGCAATGTCTGCAGTTGGACTGAAACCAGGCTGAACATGGCCA CTCCATGTGATGGTCCAGGTGCTGCCACAAGTGGGAACTTCTGTAGCGC |
| mm4_intergenic_Gramd1b|1700110K17Rik_chr9_40321598 | CTGGCCAATGTCCTGCAGTAACCCCAGGCCTAGCCTGGCCTCACCAGCAGATGTTTCCTGCAATGGAAAGTTGCTGGC |
| mm4_intron_4732487G21Rik_chr12_86294945 |
GGGTTCAGCTGAGGTGTCTCACAAAGCCAGCTCCTGGCCAAGCATGACATCTACAAGTGTGGGGGAAGTGCTAACGAAAC C |
| mm4_intergenic_Gm10617|Gm25200_chr8_118102558 |
TGGAGTCATGGCCAAATGCTGTTCTTGGTGAGAAGTTCACAAGAGCTATGCTGACCATCCTGGTCAAGCCTGGACTCTCC AGGTACACCGAGGAGGAGGCAGGAGTGTGTATTTTCTTTTGGGCATTCTGCTAAGCCA |
| mm4_intergenic_Ntf3|Kcna5_chr6_126284263 |
GCCCTTCTCAGGAGTGTTCCTTCCCTGGCCAAGCATGCGCCCTCCTTATCCATACTGGTACATAGGACCTCCTCTCCCCC ATCTTCTCTTCTTCCTTTACCCGTTTATTGCTCCCTCA |
| mm4_intron_Yy1_chr12_108794183 |
ATGTGTGTGATGGGCGCCGCCATCTTCTCCGCCCGGGCAAGTATGGCGGCCCCAAAAGATGGCGGGGGCGGCGGGCCGCG AAGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTAGGCCGCAATGGCGTAGTTTGTGCG |
| mm4_intron_Lrp1_chr10_127554517 |
AAGGAGACAACCATGGCCTGGCGGTGGGAAGAACTGGGGAGGCCATACTGGGCCCGGGCAGTCAACAACGGGTGTAAAGA AGGCTTGGTTTTGGCACCTGCTTAAGCAGTGTGTAGTTGGAGCCGT |
| mm3_intergenic_Gm24326|Gm25923_chr12_27945840 |
GTGAGGTGCCTGTTCCATCAGTGTGCTTTGGAGAGGCCATGCCTGTCCTGGCGATTCCTTGATTTATAGCTATGCCAGTG GGGTTCAGACAGAGC |
| mm4_intergenic_Cpeb2|C1qtnf7_chr5_43474710 |
ACTCCAGCTCCCACAGGTAATCCTTGCTGTACAGATGGAGTCTCCTGGCCAAGAGTGGCCTCACCATCAGTTTCTATCTT GTCTTTTCTCATTGTTAGATGCCACAGCACTACAGACAGA |
| mm4_intron_Tcte2_chr17_13493002 |
GGTGAGACCCAGAGGCAAAGATTCAGGCTGCCTGGCCAAGCATGGCTCCTGCGGCACTGCCTGACCCTCCTGTTCAATCT CCACTGAAATAGAGCTCTCTGTCTGCCCAGCTCTGCTCCGAGATCAGACATGGG |
| mm4_exon_Rassf10_chr7_112954644 |
GAAGCGTCGCTGCCCAACGCCGGACCGCGCAGCGCCGAGGCGCGGGTAGTGCTCAGCCGCGAGCGCCCCTGCTTGGCCCG GGGCGCCCCAGCACGGCCCAGCCTGGCCTTGACCCAGGAGAAGCAG |
| mm3_intergenic_mmu-mir-6393|Zdhhc25_chr15_88444314 |
CCGAGCTGGCGTAGTATCCAGTTTTCTGTGAAGGATGTGACAGGAGCATCCATGCTTGGCCAAGACAAAAAGAACACAAG GCTGTGAGCAACAGGAAAAAAATCAAAATACAAAGGCCTAAGAGGGAAACGGAG |
| mm3_intron_Nfix_chr8_84714246 |
TACCAGTGGAGTCCCCTAGCTTTTCTACTTGTAGAAGGGCCGTGCAAAGGTGGGAGCTGGGCAGCCTGGAGCAGCCTGGC TTGGCCGGGCAATGGCCCTCTCAAACAGGCCTCCTCTCCAG |
| mm4_intergenic_Rpl31-ps16|RP24-68F22.6_chr17_85569951 |
CCTGATGGTGCTTGTGAGGTAGTGAGGATGCTCTCACAGTGGAGGGTAAAACCTTTGGCAAACCGCTTTCCCTGCCAAGC ATGGCCCCACCCTGCACGTGGCAGCCTTAATTGGACCCT |
| mm4_intergenic_Clybl|Gm5089_chr14_122406778 |
GGTGTAGCAGTGCTGGGGCGCAGCGGCCAGGCTAGGCCGGGGCCGCAGTGGGGGGATCCCCGTGGCCCAGTGGCCAGGAC TGCGGGCCTCCCGGACCCCGTGAGCCTGTCGCGCAGCCGGGCTGTAATGGTGCGAGAT |
| mm4_intron_Lama5_chr2_180195018 |
TCTGCTTCACACCCAGTGTCCATTGGGGACAGCCACAGCCACTCCAGGCCGTGCACGGCAGCTCCATCATCTTACAACCT TGTCTTGCATCCACTCCACC |
| mm3_intergenic_Gm9855|Foxo3_chr10_42107734 |
CCAGTCTGGGCAGAACCAATTGAATGAGGACGTGATCAGAAAGTATGGGGTCACAGCTTCAAGAGAGGGTATGAACCACA GGAGCTGTGCAGCAGCCATGCTGGGCCTGGCAGGGGAAAGGGTGGGGACTGATG |
| mm4_intron_Ppara_chr15_85754930 |
GGTGACTGAGGTGGATCTGGTAACGTAAAATGGGGGCAGGTATAGTGGAAAGAGCAAGCTTAGTTTGGGATAGCAGGGTC AGGCCCATTGTGGGGCAGCCATGAATGGCCTGGGGAGAAGGTTGATGCCAGGAGGTTGA |
| mm4_intergenic_Wnt11/Gm8398|Uvrag_chr7_98856235 |
CCCCTAAGTCAGTCAAAGCTCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGTATCTCTCTCTAATGCCCTGCT |
| mm4_intron_Vwa8_chr14_79075026 |
TCTGGAGAGGAGGAGGTGTGTTAGGAAGTCCCGGCCAAAAATAGCAGCTCCACCCAATCTTCCCATCTTGCGAATCCAGA TGACAGCATTTCTCGGTGACCTCG |
| mm4_intron_Grm4_chr17_27466512 |
GGCCCAATCCTAGATCTCCCAAAGGAAGCTCTTTCCTGGCCTGGCCTGGCCTCTCCATCCTGCAAGCACTCGTGTGCGTG NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCGTGCTTGCTGACTGTTGGAG |
| mm4_intron_Auts2_chr5_131817236 |
TCCTTCCAGCAGAGGGAGAAGAGTGATTCCAAGAGAAGACAGAGGTCAATGCCATGCCTAGAACTGGAGAGGCCAGGCTG GACCAGGTCACTGCTTAAGCCACCCAAACTCCCC |
| mm4_intergenic_Gm25247|Tshz3_chr7_36663622 |
GCCTGGAGCTGTCAGTCATTGTGCTGGACTTGGTCCATCCTTTTTTTAAGCCAAGGGATAAGAACAATTCTGAGCCCTGC CCTAGCATGGCCTCTCCCCCAACCCGATCTTCTGCCTAGCTCTCACTAGGCTTGGCTT |
| mm4_intron_Sh3gl3_chr7_82275158 |
CACCTGTCACCCCTTCCTTCCATCCCAGGAAAAGCATGCCCACTCCACACTGGGCCCAGGTCCATCCCTCTCACCCCACC AAGACCCATCTTC |
| mm4_intron_Dmd_chrX_84175421 |
GAGCCAGGTTGAATTGGTGCCACCTGGAGCGTTCATGATTGGCAAGGCACCCCTTACAACACTTGACTAGAACTCCAGGA AAGGTGGGG |
| mm4_exon_Bcl11a_chr11_24090322 |
TGGCATTTAACTGTGGGGCTGTCCAGGGGCTAGAAAATGCAGCTGGATGTGGAACTGCCAGGCTGGGCCAGGGCAGGCAC CTTCAGTTCAGGGAGAGGCG |
| mm4_intron_Mad1l1_chr5_140027913 |
ACAAAGCACGTTCTAGGCAAATGCCAGGCCAGGCATCGCCATTCCAGTGTGAGCATCCTACAGAGAACTTTCAGCCACAT AACCAAGCCATGTAAGCCTGAGGG |
| mm4_intron_Stap2_chr17_55999877 |
AAGCCTGAAACAGAGAGGGCGGGCAGCCTGGAGGCAGCGTGGAGGCCCGGAGCTAGCCCCCCGAGAGAGTATCCCTGTCC AAGCCTGGCAGCCCCACATCGCACACACCTAGAACCTTC |
| mm4_intergenic_Gm8910|Gm22547_chr3_11044345 |
TTCTTGGGCTGTTTCAGGGGCTTCTTTTTGCCACCTTCCTGGCCCAACATGGCACCTCCAGCTCCTTCACCAGACCCTGA TCC |
| mm4_exon_1110004F10Rik_chr7_116093357 |
GTGACGACTGTAGCGGTGAAGGGCCGGAGGGGGCTCTGCGTTCTGGAGTGGCGCTGCTTGGTCCGGCGGCTGGGTGAGGG CTGCTGGTGTCGCGTTTGAGGAGAACTGCGAGTGTGTTTGGCATATCCCCGTCAGG |
| mm4_exon_Bicd2_chr13_49379624 |
CCTCTACCACCATGTGTGCATGTGCAACAACGAGACGCCCAACCGTGTCATGCTCGACTATTATCGTGAGGGCCAGGGCA AGGCTGGCCGCACCAGCCCAGAGGGCCGCGGGCGCCGGTCACCTGTCCTCTTGCCCAAG |
| mm4_intron_Ptpn7_chr1_135132862 |
CAGACATCCTATGGCCCTGGGGTGGGATGGGGGGCTCCAAGGATGGGTTGAAGAAGCATTGAGTTTGGGGCTCCCATGCC TGGCCAGGGCATGAGAAGTGACATATCTGGTGTCCCTGTGACTGGAGGGCTAAG |
| mm4_intron_Tnk2_chr16_32679295 |
TGAGGCCTGAAGTTCTGCAGAGAAGGTTCTGTCCTGTTTGAGTAAGGTCAGGTGTGCTCTGGGCAGCAGGGCTACCTGGA GGGGCCTTGCATGGCACGGTTGGGGTGGGGGGCACTTGGCTAGGGGAGTTGACAGT |
| mm4_intron_Nfatc2_chr2_168584444 |
GTTCAGACATCTGGGCCCTCCCATCCCACCTGGTCACACACAGGAGCTGCCATGCATGGGCGGGCCCGTCGGATGCCTAC TGGAGGCTGCAGCTAC |
| mm4_intron_Sez6l_chr5_112550336 |
AGGAGCCTGGTCCCTGATAGCTTGGAGCCGCCTTGCTGGGTCAGGACTGTCCACACTGGCACCGCAGAGCAACCCACCGC CACCTCAAGTACACTAGAGATCTATTGACCTTCCCATCAGGACAGTCAGCAG |
| mm4_intergenic_Rbm19|Gm26474_chr5_120279591 |
GAGCTCAGTTGCCTCCTGTTGATGGGGAGGCTCTCTGCCTCGCAGACATGCCAGGCCAGGGCTGGCAGCTCCAGTTGTGG ATGTTTGCTCCCAGGA |
| mm4_intergenic_Tmbim4|Llph_chr10_120226856 |
CCTTTCTCGTGAGGCTGTCACAGACAGGGCCCCCGGCCAGGCTTGGCCCATCCAAGGCTTTGAGATGCTTTGATTTATAA TTTGCCACTCCCGACAGGAAATTCCTTAAACTTTCTCCTGTAGGTGTAGGGGTCAGCCAA |
| mm4_intergenic_Ppapdc3|Prrc2b_chr2_32131551 |
TAGGGACCAGTGTCAGCAACTCCCGTCCAAGCCTGGCCCATCCACTACTACCTTTGTGTCCTGAAGCTAACCTCAGTCTT TCCCATCTGCAACATTAGCCAGGGCTAACCCCCAGCCTGTCCACAATGCACAGACCTCC |
| mm4_intergenic_Antxrl|Anxa8_chr14_34079227 |
ACCCACCTTTCACGACATCCCTGGGAAGCTGTGAGCTGTGCTGGCGGAAGAGAGCCCATCACCATGTCCCCACCCAAGCA TGGCCTCCCCAGCAGAGTCCCACACCCGCCTCCAGCCTACAGAAGGGGTCTTGTGTGC |
| mm4_intron_Mov10_chr3_104795298 |
TTGGTTATCCTGCCGGCTTCCCACACTTCACCTCCCTGGCCCAGCAGGGCCCATCCATACCTGAGGTAGAGGGGCTGAGT |
| mm4_intergenic_Cdh26|Gm14314_chr2_178918931 |
CTGCTCCTCCGTTCATCCAGTCCCATGGAAGGCATGGCCGCTCCAGTCCTGTCCTCATCCAACATTTTGGTCCCCAGTCA AACTCTTCAAATGTGTGCATTAACCTTGGGG |
| mm4_intergenic_Gm7656|Gm24880_chr7_70496363 |
GCAAACGTGAGGAAAGCTGGAAGACTATCTATGGAGTGGCCATCTGTGGCCAGGTGGCTGATTAATGAAACCCTAGGTCT GTCAAGGAGC |
| mm4_intergenic_Gm5294|Pdgfa_chr5_138898462 |
GATGGGCCCCAATTCCTCTGTGGAGTGGCCATCCCTGGGCGGGCAGGAACCGGCCCAGCCTGGGGCTCCTCTCACCTCCT GCATACCAGGTCT |
| mm4_exon_Nsmf_chr2_25054450 |
CTCTCCTACAGTGGCTGGACGCGCTGGGCGCTGGGTGCGGCCATGCGGGGCCTGGGCCTAAGTCTGACCCTGACCCTGAG GCTGAGACCTAG |
| mm4_intron_Gm9999_chr7_46986712 |
GGGGTAGCTCCTTTTCCAACTTTCTTTCATCCAAACAAACCTAACATCCTGGCCAGCCTTGGCCGCTCTAACCCTTGAGC CCCCCAACTCCCCATGTCATAGGAACTGATGTCACAATTAGTGTCTGAGTCTGGCCTCT |