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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_52313984_F | TCGTCGGCAGCGTCAACCGCCAGAGAAGATGGTG | 60.0 | 1.00 |
| ontarget_mm0_exon_5730457N03Rik/Evx1_chr6_52313984_R | GTCTCGTGGGCTCGGCTGCCTGCTAGTCCATCGAC | 60.2 | 1.00 |
| mm4_intron_Zcchc14_chr8_121648754_F | TCGTCGGCAGCGTCGTTCACACGACTGCCTCAGA | 59.9 | 0.57 |
| mm4_intron_Zcchc14_chr8_121648754_R | GTCTCGTGGGCTCGGGCCAGCAACGTTGAACTTGT | 59.8 | 0.57 |
| mm4_exon_Ahctf1/Gm10518_chr1_179803351_F | Primer3: not found at this Tm | N.d. | 0.33 |
| mm4_exon_Ahctf1/Gm10518_chr1_179803351_R | Primer3: not found at this Tm | N.d. | 0.33 |
| mm4_intron_Stk4_chr2_164110975_F | Primer3: not found at this Tm | N.d. | 0.29 |
| mm4_intron_Stk4_chr2_164110975_R | Primer3: not found at this Tm | N.d. | 0.29 |
| mm4_exon_Gm16065_chr5_119685684_F | TCGTCGGCAGCGTCGGCCTTGACTCAAAGACCCA | 59.8 | 0.27 |
| mm4_exon_Gm16065_chr5_119685684_R | GTCTCGTGGGCTCGGTCAAGAGGTGACAGGGACGT | 60.4 | 0.27 |
| mm4_exon_Acvr2b_chr9_119402496_F | Primer3: not found at this Tm | N.d. | 0.25 |
| mm4_exon_Acvr2b_chr9_119402496_R | Primer3: not found at this Tm | N.d. | 0.25 |
| mm4_intergenic_1700041M05Rik|Grik3_chr4_125288051_F | TCGTCGGCAGCGTCTTGCCTGCGGAAAGATGTCT | 59.9 | 0.23 |
| mm4_intergenic_1700041M05Rik|Grik3_chr4_125288051_R | GTCTCGTGGGCTCGGGAGGGAGCATAGCCACCAAG | 60.1 | 0.23 |
| mm4_exon_Bmp3_chr5_98854949_F | TCGTCGGCAGCGTCCCAGACCTTCCGCCCTCC | 61.7 | 0.22 |
| mm4_exon_Bmp3_chr5_98854949_R | GTCTCGTGGGCTCGGGAGCGGGACACTGAGAGC | 59.8 | 0.22 |
| mm4_intergenic_Hdac4|Ndufa10_chr1_92180156_F | Primer3: not found at this Tm | N.d. | 0.21 |
| mm4_intergenic_Hdac4|Ndufa10_chr1_92180156_R | Primer3: not found at this Tm | N.d. | 0.21 |
| mm4_intergenic_4632428C04Rik|Hes1_chr16_30059158_F | Primer3: not found at this Tm | N.d. | 0.21 |
| mm4_intergenic_4632428C04Rik|Hes1_chr16_30059158_R | Primer3: not found at this Tm | N.d. | 0.21 |
| mm3_intron_Rnf150_chr8_82938239_F | Primer3: not found at this Tm | N.d. | 0.20 |
| mm3_intron_Rnf150_chr8_82938239_R | Primer3: not found at this Tm | N.d. | 0.20 |
| mm4_exon_Kdm6a_chrX_18258612_F | Primer3: not found at this Tm | N.d. | 0.18 |
| mm4_exon_Kdm6a_chrX_18258612_R | Primer3: not found at this Tm | N.d. | 0.18 |
| mm3_intergenic_Ube2g1|Gm24143_chr11_72607914_F | Primer3: not found at this Tm | N.d. | 0.18 |
| mm3_intergenic_Ube2g1|Gm24143_chr11_72607914_R | Primer3: not found at this Tm | N.d. | 0.18 |
| mm3_intergenic_Supt16|Gm26590_chr14_52197401_F | TCGTCGGCAGCGTCTGAAGTCAACAGACCGAGGTG | 59.9 | 0.17 |
| mm3_intergenic_Supt16|Gm26590_chr14_52197401_R | GTCTCGTGGGCTCGGTTTCTGCTCCCCTCCCTCTG | 60.9 | 0.17 |
| mm3_exon_Irx5_chr8_92358045_F | TCGTCGGCAGCGTCCGGGAAGCCAACCAGGAG | 60.0 | 0.17 |
| mm3_exon_Irx5_chr8_92358045_R | GTCTCGTGGGCTCGGCACCTGGCTTCTGGCTGC | 61.0 | 0.17 |
| mm4_intergenic_A530013C23Rik|Gm14321_chr2_167744844_F | Primer3: not found at this Tm | N.d. | 0.17 |
| mm4_intergenic_A530013C23Rik|Gm14321_chr2_167744844_R | Primer3: not found at this Tm | N.d. | 0.17 |
| mm3_exon_Intu_chr3_40540801_F | Primer3: not found at this Tm | N.d. | 0.17 |
| mm3_exon_Intu_chr3_40540801_R | Primer3: not found at this Tm | N.d. | 0.17 |
| mm4_exon_Pcdh15_chr10_73099675_F | TCGTCGGCAGCGTCCACAAGCAGATCAGGGACCG | 60.7 | 0.16 |
| mm4_exon_Pcdh15_chr10_73099675_R | GTCTCGTGGGCTCGGACCAAACAAGTTGCAGGTGC | 59.8 | 0.16 |
| mm3_intergenic_Fignl2|Ankrd33_chr15_101077893_F | TCGTCGGCAGCGTCTGGACAAAGACCTGACGGAG | 59.3 | 0.15 |
| mm3_intergenic_Fignl2|Ankrd33_chr15_101077893_R | GTCTCGTGGGCTCGGGGAGCTAGGATTTGCGGGTT | 60.1 | 0.15 |
| mm4_intron_Tfdp2_chr9_96196721_F | TCGTCGGCAGCGTCTCAGGATTTCTCTGCAGCGG | 60.1 | 0.15 |
| mm4_intron_Tfdp2_chr9_96196721_R | GTCTCGTGGGCTCGGAGTGAGAAGCCCAAGTCAGC | 59.9 | 0.15 |
| mm4_intron_Dhx35_chr2_158822537_F | Primer3: not found at this Tm | N.d. | 0.15 |
| mm4_intron_Dhx35_chr2_158822537_R | Primer3: not found at this Tm | N.d. | 0.15 |
| mm4_intron_Uaca_chr9_60847293_F | Primer3: not found at this Tm | N.d. | 0.15 |
| mm4_intron_Uaca_chr9_60847293_R | Primer3: not found at this Tm | N.d. | 0.15 |
| mm3_exon_Cisd2_chr3_135423417_F | Primer3: not found at this Tm | N.d. | 0.14 |
| mm3_exon_Cisd2_chr3_135423417_R | Primer3: not found at this Tm | N.d. | 0.14 |
| mm4_intergenic_Mark1|Rab3gap2_chr1_184999818_F | Primer3: not found at this Tm | N.d. | 0.13 |
| mm4_intergenic_Mark1|Rab3gap2_chr1_184999818_R | Primer3: not found at this Tm | N.d. | 0.13 |
| mm4_intron_Col14a1_chr15_55426301_F | Primer3: not found at this Tm | N.d. | 0.12 |
| mm4_intron_Col14a1_chr15_55426301_R | Primer3: not found at this Tm | N.d. | 0.12 |
| mm4_intron_Kcnd3_chr3_105638926_F | Primer3: not found at this Tm | N.d. | 0.12 |
| mm4_intron_Kcnd3_chr3_105638926_R | Primer3: not found at this Tm | N.d. | 0.12 |
| mm4_intron_Foxa1_chr12_57545347_F | TCGTCGGCAGCGTCGTAAGCGAGCACCGACTCTC | 60.5 | 0.12 |
| mm4_intron_Foxa1_chr12_57545347_R | GTCTCGTGGGCTCGGCGGAAGGGAAGCACTTGTCT | 59.9 | 0.12 |
| mm4_intergenic_Gm20033|Klf3_chr5_64803104_F | TCGTCGGCAGCGTCCAACGCCGCCCTTCCTTC | 61.4 | 0.12 |
| mm4_intergenic_Gm20033|Klf3_chr5_64803104_R | GTCTCGTGGGCTCGGCTCTCCACCCTGGGCCTC | 61.0 | 0.12 |
| mm4_intron_Phf2_chr13_48870255_F | Primer3: not found at this Tm | N.d. | 0.11 |
| mm4_intron_Phf2_chr13_48870255_R | Primer3: not found at this Tm | N.d. | 0.11 |
| mm4_exon_Gbx1_chr5_24526217_F | TCGTCGGCAGCGTCTCAGTCACTTTCTCGCGCG | 60.7 | 0.10 |
| mm4_exon_Gbx1_chr5_24526217_R | GTCTCGTGGGCTCGGGACGCCTACTACGGGCCC | 61.9 | 0.10 |
| mm4_intron_Tulp4_chr17_6106693_F | Primer3: not found at this Tm | N.d. | 0.09 |
| mm4_intron_Tulp4_chr17_6106693_R | Primer3: not found at this Tm | N.d. | 0.09 |
| mm4_intron_Snx3_chr10_42502670_F | TCGTCGGCAGCGTCGCTCTCCGTGGACAGTTTGT | 60.2 | 0.09 |
| mm4_intron_Snx3_chr10_42502670_R | GTCTCGTGGGCTCGGTGTCAAGCCCAGATCAGCTG | 60.0 | 0.09 |
| mm4_intron_Tnfsf14_chr17_57193322_F | Primer3: not found at this Tm | N.d. | 0.09 |
| mm4_intron_Tnfsf14_chr17_57193322_R | Primer3: not found at this Tm | N.d. | 0.09 |
| mm4_intron_Zfand3_chr17_30005316_F | Primer3: not found at this Tm | N.d. | 0.09 |
| mm4_intron_Zfand3_chr17_30005316_R | Primer3: not found at this Tm | N.d. | 0.09 |
| mm4_exon_Frmd5_chr2_121806680_F | TCGTCGGCAGCGTCCAACTTGGCCGAGTCTGGG | 60.6 | 0.08 |
| mm4_exon_Frmd5_chr2_121806680_R | GTCTCGTGGGCTCGGGACGACAGCGAGTACACCTG | 60.4 | 0.08 |
| mm4_exon_Dlg5_chr14_24245623_F | TCGTCGGCAGCGTCGACGATCGGGCAGCTCTC | 59.9 | 0.07 |
| mm4_exon_Dlg5_chr14_24245623_R | GTCTCGTGGGCTCGGCCGCCGTAGCCAACATGG | 61.2 | 0.07 |
| mm4_exon_Wsb1_chr11_79254462_F | TCGTCGGCAGCGTCATTCCGGGAACTCGATTCGG | 59.8 | 0.07 |
| mm4_exon_Wsb1_chr11_79254462_R | GTCTCGTGGGCTCGGGCTCTCTCTGCAGTCTCCAC | 59.8 | 0.07 |
| mm4_exon_BC022687_chr12_112809082_F | TCGTCGGCAGCGTCCTCTGGGAGCTCGGGACC | 61.1 | 0.07 |
| mm4_exon_BC022687_chr12_112809082_R | GTCTCGTGGGCTCGGTGGTGGATGAGCTGCAGAAC | 60.3 | 0.07 |
| mm4_exon_Snf8_chr11_96034984_F | Primer3: not found at this Tm | N.d. | 0.07 |
| mm4_exon_Snf8_chr11_96034984_R | Primer3: not found at this Tm | N.d. | 0.07 |
| mm4_intergenic_5730460C07Rik|Gm25757_chr3_153813393_F | Primer3: not found at this Tm | N.d. | 0.07 |
| mm4_intergenic_5730460C07Rik|Gm25757_chr3_153813393_R | Primer3: not found at this Tm | N.d. | 0.07 |
| mm4_intergenic_Gm26228|Gdf10_chr14_33662242_F | TCGTCGGCAGCGTCACATCCATCTGCTGCGAGTC | 60.1 | 0.06 |
| mm4_intergenic_Gm26228|Gdf10_chr14_33662242_R | GTCTCGTGGGCTCGGTGAGTAGCCCTGTTCCCCAT | 60.2 | 0.06 |
| mm4_intron_Npepl1_chr2_174110847_F | TCGTCGGCAGCGTCCTCGAGACCCGCTTCCATG | 60.2 | 0.06 |
| mm4_intron_Npepl1_chr2_174110847_R | GTCTCGTGGGCTCGGGGGACCCTCTGCTTCAAACA | 59.8 | 0.06 |
| mm4_intron_Nedd1_chr10_92722150_F | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_intron_Nedd1_chr10_92722150_R | Primer3: not found at this Tm | N.d. | 0.06 |
| mm2_intergenic_Gm12296|Shisa6_chr11_66369319_F | Primer3: not found at this Tm | N.d. | 0.05 |
| mm2_intergenic_Gm12296|Shisa6_chr11_66369319_R | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_exon_Pomt2/Gstz1_chr12_87147544_F | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_exon_Pomt2/Gstz1_chr12_87147544_R | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_intergenic_Suclg1|Gm24370_chr6_73327598_F | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_intergenic_Suclg1|Gm24370_chr6_73327598_R | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_exon_Plekhg1_chr10_3740437_F | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_exon_Plekhg1_chr10_3740437_R | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_exon_Smarca2_chr19_26607438_F | TCGTCGGCAGCGTCCGAGGGAGGAAGAGGAGGT | 59.6 | 0.05 |
| mm4_exon_Smarca2_chr19_26607438_R | GTCTCGTGGGCTCGGGCTCCTTACCTGGGCGAC | 59.8 | 0.05 |
| mm4_intergenic_Rnd2/Vat1|Rnd2_chr11_101468144_F | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_intergenic_Rnd2/Vat1|Rnd2_chr11_101468144_R | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_intergenic_Gm26748|Tpt1-ps3_chr6_99739702_F | TCGTCGGCAGCGTCCCATTCACAGCCCTGAACCT | 59.9 | 0.05 |
| mm4_intergenic_Gm26748|Tpt1-ps3_chr6_99739702_R | GTCTCGTGGGCTCGGAAAACAGAAAGACAGCGGCG | 59.6 | 0.05 |
| mm4_exon_Uri1_chr7_38019295_F | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_exon_Uri1_chr7_38019295_R | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_intergenic_Gm14544|4930525M21Rik/4930525M21RIK_chrX_37953429_F | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_intergenic_Gm14544|4930525M21Rik/4930525M21RIK_chrX_37953429_R | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_exon_Zc3hav1l_chr6_38299007_F | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_exon_Zc3hav1l_chr6_38299007_R | Primer3: not found at this Tm | N.d. | 0.04 |
| mm3_intergenic_Gm26296|Col14a1_chr15_55271173_F | TCGTCGGCAGCGTCCAAGACCTGGGCAGCAGAAG | 60.9 | 0.04 |
| mm3_intergenic_Gm26296|Col14a1_chr15_55271173_R | GTCTCGTGGGCTCGGCTACCCTCCCTTTCCCTGGA | 59.9 | 0.04 |
| mm4_intergenic_Larp4b|Gm23553_chr13_9094622_F | TCGTCGGCAGCGTCTATGCAGCCCGAGGAGAATG | 59.6 | 0.03 |
| mm4_intergenic_Larp4b|Gm23553_chr13_9094622_R | GTCTCGTGGGCTCGGGCTGTCTGGCCGGTCTCC | 62.4 | 0.03 |
| mm4_intergenic_Plag1|Chchd7_chr4_3938502_F | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_intergenic_Plag1|Chchd7_chr4_3938502_R | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_exon_Stk11/Dos_chr10_80131796_F | TCGTCGGCAGCGTCAAAGAGCGTCCGTCTTCTCG | 60.1 | 0.02 |
| mm4_exon_Stk11/Dos_chr10_80131796_R | GTCTCGTGGGCTCGGTCAGAACTTCCTGCTCCAGC | 59.6 | 0.02 |
| mm4_intron_Ttc25_chr11_100562923_F | TCGTCGGCAGCGTCCTATTCAGTGGGGTGGGTGG | 59.7 | 0.02 |
| mm4_intron_Ttc25_chr11_100562923_R | GTCTCGTGGGCTCGGCTCTCCAGAAAGGGTGGCTG | 60.0 | 0.02 |
| mm4_intron_Nbea_chr3_55787979_F | TCGTCGGCAGCGTCTGTTTATTGGAGGGTCCGCG | 60.3 | 0.02 |
| mm4_intron_Nbea_chr3_55787979_R | GTCTCGTGGGCTCGGTTAAGGGAGCGGTTCGAACC | 60.0 | 0.02 |
| mm4_intergenic_Rbfox3|Enpp7_chr11_118962108_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Rbfox3|Enpp7_chr11_118962108_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intron_Ebf3_chr7_137310039_F | TCGTCGGCAGCGTCGCAGGAAGCTGTGCACGG | 61.7 | 0.01 |
| mm4_intron_Ebf3_chr7_137310039_R | GTCTCGTGGGCTCGGTCTAAATATCATCGGGCGAGAAG | 57.9 | 0.01 |
| mm4_exon_Sppl2b_chr10_80868644_F | TCGTCGGCAGCGTCGGGTGTCCAAGCAGTCCTTT | 60.1 | 0.01 |
| mm4_exon_Sppl2b_chr10_80868644_R | GTCTCGTGGGCTCGGACAGGAGGCCACTGTGAGTA | 60.1 | 0.01 |
| mm4_intron_Ptdss2_chr7_141123343_F | TCGTCGGCAGCGTCAGACCAATCCCAGACGATGC | 59.8 | 0.01 |
| mm4_intron_Ptdss2_chr7_141123343_R | GTCTCGTGGGCTCGGTCGCCCAGACAAAGCTGAAT | 59.9 | 0.01 |
| mm4_exon_Sorbs3_chr14_70201496_F | TCGTCGGCAGCGTCTGCTGTCCTTGGTCCATGTG | 60.2 | 0.01 |
| mm4_exon_Sorbs3_chr14_70201496_R | GTCTCGTGGGCTCGGCTCTCACAGACCCAGCATGG | 60.1 | 0.01 |
| mm4_intergenic_Syt1|Gm22097_chr10_109012035_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Syt1|Gm22097_chr10_109012035_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intron_Smyd3_chr1_179343678_F | TCGTCGGCAGCGTCCCGTGACATGTAGCGCACTA | 60.1 | 0.01 |
| mm4_intron_Smyd3_chr1_179343678_R | GTCTCGTGGGCTCGGACTGATGAGTTGGCTGTGCA | 59.8 | 0.01 |
| mm4_intron_Rcor3_chr1_192137612_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intron_Rcor3_chr1_192137612_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intron_Dynll2_chr11_87986957_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intron_Dynll2_chr11_87986957_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_exon_A930035D04Rik/Cul1_chr6_47454319_F | TCGTCGGCAGCGTCGAGAGGGCGGAGGTTGCG | 62.8 | 0.00 |
| mm4_exon_A930035D04Rik/Cul1_chr6_47454319_R | GTCTCGTGGGCTCGGCCCGCTCCTCCTCCTCCT | 62.1 | 0.00 |
| mm4_exon_Ncor2_chr5_125025493_F | TCGTCGGCAGCGTCAGTCTGGAGGAGTGGGCTAG | 60.0 | 0.00 |
| mm4_exon_Ncor2_chr5_125025493_R | GTCTCGTGGGCTCGGCCTTAGGCCCCATGAAGCTC | 60.1 | 0.00 |
| mm4_intron_Coq10b_chr1_55053238_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intron_Coq10b_chr1_55053238_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intron_Tle4_chr19_14597051_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intron_Tle4_chr19_14597051_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intron_Tbx5_chr5_119867334_F | TCGTCGGCAGCGTCCGATGGACGGAGGGATTGAA | 59.5 | 0.00 |
| mm4_intron_Tbx5_chr5_119867334_R | GTCTCGTGGGCTCGGACTCACGAATGAAGGGGCTG | 60.0 | 0.00 |
| mm4_intron_Dnajc11_chr4_151933855_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intron_Dnajc11_chr4_151933855_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intergenic_Rhpn1|Mafa_chr15_75746747_F | TCGTCGGCAGCGTCTAGGTACCTGGAGCTGGGG | 59.6 | 0.00 |
| mm4_intergenic_Rhpn1|Mafa_chr15_75746747_R | GTCTCGTGGGCTCGGGACAAGTTTGCGCAGGCC | 60.0 | 0.00 |
| mm4_intergenic_Phf10|Gm3417_chr17_14961591_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intergenic_Phf10|Gm3417_chr17_14961591_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intergenic_Lhx5|Sdsl_chr5_120457324_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intergenic_Lhx5|Sdsl_chr5_120457324_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intergenic_Gm3435|Tcte3_chr17_15024542_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intergenic_Gm3435|Tcte3_chr17_15024542_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intergenic_Gm26669/Zfp36l1|2310015A10Rik_chr12_80115394_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intergenic_Gm26669/Zfp36l1|2310015A10Rik_chr12_80115394_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intergenic_Barx1|Phf2_chr13_48737703_F | TCGTCGGCAGCGTCCTCCTCCGCCAACAGTCTAC | 59.8 | 0.00 |
| mm4_intergenic_Barx1|Phf2_chr13_48737703_R | GTCTCGTGGGCTCGGTCCATCCTGAGTGGGACCAT | 59.9 | 0.00 |
| mm4_intergenic_Atp6v0a1|mmu-mir-6928_chr11_101029427_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intergenic_Atp6v0a1|mmu-mir-6928_chr11_101029427_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intergenic_Ahrr|Pdcd6_chr13_74292347_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intergenic_Ahrr|Pdcd6_chr13_74292347_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intergenic_9030025P20Rik|Gm3448_chr17_14993174_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intergenic_9030025P20Rik|Gm3448_chr17_14993174_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_exon_Sim2_chr16_94125767_F | TCGTCGGCAGCGTCAACTACCACCGCGTGCTG | 60.3 | 0.00 |
| mm4_exon_Sim2_chr16_94125767_R | GTCTCGTGGGCTCGGAGGTAATGCGGTCGGGGC | 62.1 | 0.00 |
| mm4_exon_Ptk2_chr15_73423134_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_exon_Ptk2_chr15_73423134_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_exon_Myoz3_chr18_60579510_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_exon_Myoz3_chr18_60579510_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.
| ontarget_mm0_exon_5730457N03Rik/Evx1_chr6_52313984 |
AACCGCCAGAGAAGATGGTGCCCCACGGTTGCCTGAGCCCGCGAGCCGGCCCTCCGACTTCCCGGGAGCGTGGCGGGGGA GGCCAGGAGGAGGAGCCGGTCGATGGACTAGCAGGCAG |
| mm4_intron_Zcchc14_chr8_121648754 |
GTTCACACGACTGCCTCAGAGAGGACAAACTCACAGACAGACATTTGGCCGTGTCTCTTGGGGGCTGGGTGGGAGAATGC AGGGACGGCTCACAGGCTCGGGTATCTGAACAAGTTCAACGTTGCTGGC |
| mm4_exon_Gm16065_chr5_119685684 |
GGCCTTGACTCAAAGACCCAGCTGGAGCCCGCCAGGCGGCTGACTTGCCCCCAACCCCCATCCCGGAGCCCGCCAGCCGG GCCCAACGTCCCTGTCACCTCTTGA |
| mm4_intergenic_1700041M05Rik|Grik3_chr4_125288051 |
TTGCCTGCGGAAAGATGTCTGGATCTAACCATGCTCTCAGGAAGAGAGCCGGCCCCCAGGCTCTGGCCCTACTTGTCCTT CCCATGTAGTCTGAACTTTACAGGAAGGTCTTTCTTGGTGGCTATGCTCCCTC |
| mm4_exon_Bmp3_chr5_98854949 |
CCAGACCTTCCGCCCTCCGGCTGGCCGGCGAGAGGAGCTGAGCGGGCGCGGCTGCCACCCAGAGCCCACCTGCCGACCCT CGCGGCCTCGCTCCAGCTGTGCCCGGCTCTCAGTGTCCCGCTC |
| mm3_intergenic_Supt16|Gm26590_chr14_52197401 |
TGAAGTCAACAGACCGAGGTGCAGCGCGGGCTCGCGGGCTCTGGAAGCTCTCTCCGGCGCCAGAGGCTCCCGTCACGTGA CCCGCCCACTTTCCGAGCTCCGGGCGCTCTGGGCGGCGGGCAGAGGGAGGGGAGCAGAAA |
| mm3_exon_Irx5_chr8_92358045 |
CGGGAAGCCAACCAGGAGGCGCCGCGGGCCGGAGCCCGGGAGCCGGGGCTCGAAGAGCTGCGGCCCGGGGCAGCCAGAAG CCAGGTG |
| mm4_exon_Pcdh15_chr10_73099675 |
CACAAGCAGATCAGGGACCGCGAGGTGCGCCCGCGGTCGCCCGCGGAGCAGAGAGCTGTCTCCCGGGCTCGGGCGCCGGG TGATTTTTCTCCCAGCTGGGGAAGGCGCCTCGGTGAACCCGCACCTGCAACTTGTTTGGT |
| mm3_intergenic_Fignl2|Ankrd33_chr15_101077893 |
TGGACAAAGACCTGACGGAGTGGGAGGGGCCTGCGGGCCGGCCCTCGGGCTCAGGCCGCCGGACCCTTCTGGGACCCGAA CCCGCAAATCCTAGCTCC |
| mm4_intron_Tfdp2_chr9_96196721 |
TCAGGATTTCTCTGCAGCGGGGCCAAGCAACCCTGGAATACCTGATGAGGCTCCGGAGCCCGCGGGCTCGCCATCACCCG GGATCAGGAAGGGCAAGGGCTGACTTGGGCTTCTCACT |
| mm4_intron_Foxa1_chr12_57545347 |
GTAAGCGAGCACCGACTCTCTCAGTTATTCTTTACTCAAGCCAGAGCCCGCCTGCCCGCCCGCGGCTCCCGGGGCTGGGC TCCAGCCCCGGCTCTCTAGCGGGCAAAGACAAGTGCTTCCCTTCCG |
| mm4_intergenic_Gm20033|Klf3_chr5_64803104 |
CAACGCCGCCCTTCCTTCCCCCCGGGGCTCGGGCCGCAGCGAGGAGGCCAGGACAGCTAGGGCGGGGCCGCGGGCTCAGG GCGCCGGGCGGAGCGCTCAGGCGGGGTGGAGGCCCAGGGTGGAGAG |
| mm4_exon_Gbx1_chr5_24526217 |
TCAGTCACTTTCTCGCGCGCGGGCAGCAGCTCCTCAGCGTCCAGCGCTCCGTCAGTGCGCCGGGCCGCGGGCTCCGGGTT GCTTCGCGAGGCGGTGGAGGCGGCGGCGGCGGCGAGCTCCGGGGGCCCGTAGTAGGCGTC |
| mm4_intron_Snx3_chr10_42502670 |
GCTCTCCGTGGACAGTTTGTATGGGGACCAGCTCGCTGGCTCCGGTAGAAGGTGCTGGAAGACGAGGGCGTGGGTTGAGC TCTGCTAGCCGAGATCTCAGGCAGCTGATCTGGGCTTGACA |
| mm4_exon_Frmd5_chr2_121806680 |
CAACTTGGCCGAGTCTGGGGAGCCGGATCCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNCGCGGCGCTGACCTGGATGGT GCAGGTGTACTCGCTGTCGTC |
| mm4_exon_Dlg5_chr14_24245623 | GACGATCGGGCAGCTCTCAACGGCCGCCTCCCGGGCTCCGGGGCGCAGCCATGTTGGCTACGGCGG |
| mm4_exon_Wsb1_chr11_79254462 |
ATTCCGGGAACTCGATTCGGACGCGACAACAGAGAAGGGACTCAGCGGGGGCTGAGGGGCGTGACGCGGGCTCAGGCTCT CCCGGGTGTGGAGACTGCAGAGAGAGC |
| mm4_exon_BC022687_chr12_112809082 |
CTCTGGGAGCTCGGGACCCCCTCCGTCTGCGCCTGGGACCTGGTCCCGGAGCCCGCGAGACTCCCGTCTGGGACGCGATC CCCGAGCTCCCTGCCCTCAGCCTCCGGCCTCGCAGACCGGGTTCTGCAGCTCATCCACCA |
| mm4_intergenic_Gm26228|Gdf10_chr14_33662242 |
ACATCCATCTGCTGCGAGTCCAGGAAGTGGGGTCTGGCTCGAGGGCTCCGGAAGAGGAGGAAGATTGGGAACAGCTGCTG AGGGCTATGCTGGGGAAGGCAGGCAGCAGGGGATGGGGAACAGGGCTACTCA |
| mm4_intron_Npepl1_chr2_174110847 | CTCGAGACCCGCTTCCATGGCCACTAGCCAGGGCCCAGGAGCCGGGCCTCCAAGTGTTTGAAGCAGAGGGTCCC |
| mm4_exon_Smarca2_chr19_26607438 |
CGAGGGAGGAAGAGGAGGTNNNNNNNNNNNNNNNNNNNNNNNNNNNNTAAGCCGCGCTGTGCACACCGCTCCCTCGCAGC CCCGGGCGGCGCCAGCTCGAGAGCCCTGGCCGTTCAGCGTCGCCCAGGTAAGGAGC |
| mm4_intergenic_Gm26748|Tpt1-ps3_chr6_99739702 |
CCATTCACAGCCCTGAACCTGACCTGGATTCACAGCAGGGTGGGACCCACCTGAGCCAGCCAGCCGGGCCTAGGCTTCCC AGCTTCTGCTAGGATGAGTCTTCGTCGCCGCTGTCTTTCTGTTTT |
| mm3_intergenic_Gm26296|Col14a1_chr15_55271173 |
CAAGACCTGGGCAGCAGAAGGCTGTGCAGAGGGCAGGCTCACGGGCTGGGGATCAACCTGAACTGGACATTCAGCCAAAC TGTCTAGACCAGTGGAAAATGCTTTCCAGGGAAAGGGAGGGTAG |
| mm4_intergenic_Larp4b|Gm23553_chr13_9094622 |
TATGCAGCCCGAGGAGAATGGGCTGGGGTCGCAGGCCACCATCGCCCCGAGGGCANNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNTCGGTCCCGCCGGAGACCGGCCAGACAGC |
| mm4_exon_Stk11/Dos_chr10_80131796 |
AAAGAGCGTCCGTCTTCTCGTCGATGCTGTAATCGCGGCGCGGCCTGCGTGGCCAGGCTCGCGGGCTGCGGGGAGGACTG CGGGCTGGAGCAGGAAGTTCTGA |
| mm4_intron_Ttc25_chr11_100562923 |
CTATTCAGTGGGGTGGGTGGGCACAGCCCTAGGGAGCCTCAGAGACAGCCCAGACCCCGAGAGCCAGCCTTCTTGAGTGC AGCCACCCTTTCTGGAGAG |
| mm4_intron_Nbea_chr3_55787979 |
TGTTTATTGGAGGGTCCGCGCTAGCCGGCGCCTCCAGCCTCCCGGGCCCTCCTTGGATCTCCCGNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNGGGGTTCGAACCGCTCCCTTAA |
| mm4_intron_Ebf3_chr7_137310039 |
GCAGGAAGCTGTGCACGGCGGTCGCACGTGCTCGTGCCACGCCAGGGAGCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNACGTGCTTCTCGCCCGATGATATTTAGA |
| mm4_exon_Sppl2b_chr10_80868644 |
GGGTGTCCAAGCAGTCCTTTCACCTCTTGGGTAGTCGGAGGTGCTCCGCGAGGTCCCGCTCGAGGGCCCTGGCTTTAGGT TGTCAGGGGATTAAACAGCTTTTCATACTCACAGTGGCCTCCTGT |
| mm4_intron_Ptdss2_chr7_141123343 |
AGACCAATCCCAGACGATGCCCCCAAGCCAGCGAGCCACCCCTCGCAGAAGCAGTCTCGAGTTGAAGTTACTGCATTCAG CTTTGTCTGGGCGA |
| mm4_exon_Sorbs3_chr14_70201496 |
TGCTGTCCTTGGTCCATGTGGCTGACCAGTTCTGGGCATGCTGGGAAGCAGGTGGCTTCGGGCTCATAGAGGGCCGGCTC CCAGGGCCTGGCCAGGTCTGATACCATGCTGGGTCTGTGAGAG |
| mm4_intron_Smyd3_chr1_179343678 |
CCGTGACATGTAGCGCACTAATTCAGTTTGACGGGGGCGATGCAGTTCTACTGCGCTGCAGCACATAAGGCCCCCAGCCT GAGAGCCGGCCTTCTGCACAGCCAACTCATCAGT |
| mm4_exon_A930035D04Rik/Cul1_chr6_47454319 |
GAGAGGGCGGAGGTTGCGTGGTGCANNNNNNNNNNNNNNNNNNNNGAGGAGGAGGGCCGGCAGGCGGGCAGGGGAGGAGG AGGAGGAGCGGG |
| mm4_exon_Ncor2_chr5_125025493 |
AGTCTGGAGGAGTGGGCTAGATGAGGGCTGGCTCTCGGGCAGTGGCCGCAGATGTGGGAGATGGGCAGCCTCCGCGCTGA GCTTCATGGGGCCTAAGG |
| mm4_intron_Tbx5_chr5_119867334 |
CGATGGACGGAGGGATTGAAGGTAAAAGCAGCAGACTGTTGGAGCAGTGCGCCTTGTCCAGTGCCCCCGACCCTGCCCTC TTGTAGCCAATCCACAGTTCTGTCTTTTCAGCCCAGCCCCTTCATTCGTGAGT |
| mm4_intergenic_Rhpn1|Mafa_chr15_75746747 |
TAGGTACCTGGAGCTGGGGCTTGGCGGCGGGGTGCGCAGGGCGGACAGGAGGACCCCGGCAGCTGCGGCTGCACCGCCGG AGCGCGCGTCCCGGGCCTCAGAGTCTGAACCGAGACCGGGGCGGCCTGCGCAAACTTGTC |
| mm4_intergenic_Barx1|Phf2_chr13_48737703 |
CTCCTCCGCCAACAGTCTACCTATCTATCCCCCAACCACGAGAGCCGGCCCTCTGTCTGGTAGATGTCAGACTGCATAAT GGTCCCGGGATCACAATGGTCCCACTCAGGATGGA |
| mm4_exon_Sim2_chr16_94125767 |
AACTACCACCGCGTGCTGGCGCGCCGCGGGCCTCTGGGGAGCGCTGCGCCCGGAGCCCCCGAGGCGGCCGGCTCGCTGAG GCCCCGACACCCAGGCCCCGTCGCCGCCTCTGCGCCCGGCGCGCCCCGACCGCATTACCT |