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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_52313731_F | Primer3: not found at this Tm | N.d. | 1.00 |
| ontarget_mm0_exon_5730457N03Rik/Evx1_chr6_52313731_R | Primer3: not found at this Tm | N.d. | 1.00 |
| mm4_intron_Ajap1_chr4_153440133_F | TCGTCGGCAGCGTCGCTGCTACAGAGTCTGAGCA | 59.4 | 0.48 |
| mm4_intron_Ajap1_chr4_153440133_R | GTCTCGTGGGCTCGGGCCGATCCTTTCCCCTTCAA | 60.0 | 0.48 |
| mm4_intron_Atp11a_chr8_12763021_F | TCGTCGGCAGCGTCGTGTCCAGTGGAGAAAGGGG | 59.9 | 0.44 |
| mm4_intron_Atp11a_chr8_12763021_R | GTCTCGTGGGCTCGGCCAGGGTCCTAACAAGGGGA | 60.5 | 0.44 |
| mm4_intergenic_Ctse|5430435G22Rik_chr1_131675664_F | Primer3: not found at this Tm | N.d. | 0.41 |
| mm4_intergenic_Ctse|5430435G22Rik_chr1_131675664_R | Primer3: not found at this Tm | N.d. | 0.41 |
| mm4_intron_Casz1_chr4_148876881_F | TCGTCGGCAGCGTCCTGAGACAGTGGGCATGAGG | 60.1 | 0.39 |
| mm4_intron_Casz1_chr4_148876881_R | GTCTCGTGGGCTCGGTGACCAGTGTCCCAAGGAGA | 60.1 | 0.39 |
| mm4_intron_Col13a1_chr10_61861591_F | Primer3: not found at this Tm | N.d. | 0.39 |
| mm4_intron_Col13a1_chr10_61861591_R | Primer3: not found at this Tm | N.d. | 0.39 |
| mm4_intron_Fbxl13_chr5_21581923_F | TCGTCGGCAGCGTCTCCCCTTAACCCTTTTCTCACT | 58.6 | 0.25 |
| mm4_intron_Fbxl13_chr5_21581923_R | GTCTCGTGGGCTCGGGCTGCGACTTCCGAACAAAA | 59.6 | 0.25 |
| mm4_intron_Dis3l2_chr1_87032500_F | TCGTCGGCAGCGTCTGAGCAGGTGTCAGGTAGGA | 59.8 | 0.25 |
| mm4_intron_Dis3l2_chr1_87032500_R | GTCTCGTGGGCTCGGGACTGCACCAGACACACACA | 60.4 | 0.25 |
| mm4_exon_Sspo_chr6_48457061_F | Primer3: not found at this Tm | N.d. | 0.24 |
| mm4_exon_Sspo_chr6_48457061_R | Primer3: not found at this Tm | N.d. | 0.24 |
| mm4_intergenic_Arrdc3|Gm4211_chr13_80932286_F | TCGTCGGCAGCGTCGGTGGTGTTCATCCCCACAA | 60.1 | 0.23 |
| mm4_intergenic_Arrdc3|Gm4211_chr13_80932286_R | GTCTCGTGGGCTCGGGGGTGGAAATATTTGCAAAGTGC | 59.3 | 0.23 |
| mm4_intergenic_A230028O05Rik|Tprg_chr16_25179877_F | Primer3: not found at this Tm | N.d. | 0.23 |
| mm4_intergenic_A230028O05Rik|Tprg_chr16_25179877_R | Primer3: not found at this Tm | N.d. | 0.23 |
| mm4_intergenic_Mir5133|Gm25603_chr9_62199395_F | TCGTCGGCAGCGTCCCAGAATGTGTACCCCAGCC | 60.3 | 0.21 |
| mm4_intergenic_Mir5133|Gm25603_chr9_62199395_R | GTCTCGTGGGCTCGGGTAGCATCAGTGTTGGCCCT | 60.0 | 0.21 |
| mm4_intergenic_Gm9949|Htr4_chr18_62324124_F | Primer3: not found at this Tm | N.d. | 0.20 |
| mm4_intergenic_Gm9949|Htr4_chr18_62324124_R | Primer3: not found at this Tm | N.d. | 0.20 |
| mm4_intergenic_Zfyve28|Gm15513_chr5_34208085_F | Primer3: not found at this Tm | N.d. | 0.20 |
| mm4_intergenic_Zfyve28|Gm15513_chr5_34208085_R | Primer3: not found at this Tm | N.d. | 0.20 |
| mm4_intergenic_A530020G20Rik|A730020M07Rik_chr3_121575607_F | Primer3: not found at this Tm | N.d. | 0.20 |
| mm4_intergenic_A530020G20Rik|A730020M07Rik_chr3_121575607_R | Primer3: not found at this Tm | N.d. | 0.20 |
| mm4_intergenic_Gm5062/AC087902.1|Cyp2d26_chr15_82789444_F | Primer3: not found at this Tm | N.d. | 0.20 |
| mm4_intergenic_Gm5062/AC087902.1|Cyp2d26_chr15_82789444_R | Primer3: not found at this Tm | N.d. | 0.20 |
| mm4_intron_Elavl3_chr9_22034927_F | TCGTCGGCAGCGTCCCTGTGTTGGCCAGGGTTTA | 60.1 | 0.20 |
| mm4_intron_Elavl3_chr9_22034927_R | GTCTCGTGGGCTCGGAACCTTGGTGTCCTTTGCCT | 59.7 | 0.20 |
| mm4_intron_Plcb4_chr2_135789816_F | TCGTCGGCAGCGTCACTGAACTACTGGCATATTGAGGT | 59.5 | 0.19 |
| mm4_intron_Plcb4_chr2_135789816_R | GTCTCGTGGGCTCGGGAGCCCTGGAAAGCACCTAG | 60.1 | 0.19 |
| mm4_intron_Atxn1_chr13_45576279_F | TCGTCGGCAGCGTCAGGGACATGAGTCTGGACCA | 59.8 | 0.19 |
| mm4_intron_Atxn1_chr13_45576279_R | GTCTCGTGGGCTCGGAATTCCAGAGTGGGCAAGCA | 59.8 | 0.19 |
| mm4_intron_Syt7_chr19_10414790_F | Primer3: not found at this Tm | N.d. | 0.18 |
| mm4_intron_Syt7_chr19_10414790_R | Primer3: not found at this Tm | N.d. | 0.18 |
| mm4_intergenic_Gm11468|Gm14268_chr2_166299280_F | Primer3: not found at this Tm | N.d. | 0.18 |
| mm4_intergenic_Gm11468|Gm14268_chr2_166299280_R | Primer3: not found at this Tm | N.d. | 0.18 |
| mm4_intergenic_4930564D02Rik|1700095B22Rik_chr3_105301251_F | Primer3: not found at this Tm | N.d. | 0.17 |
| mm4_intergenic_4930564D02Rik|1700095B22Rik_chr3_105301251_R | Primer3: not found at this Tm | N.d. | 0.17 |
| mm4_intergenic_Gm13481|Gm13489_chr2_48599124_F | TCGTCGGCAGCGTCAACCAATGGGCGGGACTTAG | 60.0 | 0.17 |
| mm4_intergenic_Gm13481|Gm13489_chr2_48599124_R | GTCTCGTGGGCTCGGCTCCTGACTGCACTTTGGGT | 59.8 | 0.17 |
| mm4_intergenic_Gm24696|Myc_chr15_61557363_F | Primer3: not found at this Tm | N.d. | 0.17 |
| mm4_intergenic_Gm24696|Myc_chr15_61557363_R | Primer3: not found at this Tm | N.d. | 0.17 |
| mm4_intron_Rab6b_chr9_103146720_F | TCGTCGGCAGCGTCACCACGGGACAGATTGTGAC | 59.9 | 0.16 |
| mm4_intron_Rab6b_chr9_103146720_R | GTCTCGTGGGCTCGGGCTCAGTTAGTGCCCTGGAG | 60.1 | 0.16 |
| mm4_intergenic_Fxyd4|Gm4875_chr6_117961640_F | Primer3: not found at this Tm | N.d. | 0.16 |
| mm4_intergenic_Fxyd4|Gm4875_chr6_117961640_R | Primer3: not found at this Tm | N.d. | 0.16 |
| mm4_intergenic_Gm1815|Zfp353-ps_chr8_41761983_F | Primer3: not found at this Tm | N.d. | 0.16 |
| mm4_intergenic_Gm1815|Zfp353-ps_chr8_41761983_R | Primer3: not found at this Tm | N.d. | 0.16 |
| mm4_intergenic_Uso1|Gm15710_chr5_92138232_F | TCGTCGGCAGCGTCGTGAGATCGGGGCGTCTAC | 59.6 | 0.15 |
| mm4_intergenic_Uso1|Gm15710_chr5_92138232_R | GTCTCGTGGGCTCGGGAAGCCCTCCTGTCACCAC | 60.0 | 0.15 |
| mm4_intron_Srgap3_chr6_112734236_F | Primer3: not found at this Tm | N.d. | 0.15 |
| mm4_intron_Srgap3_chr6_112734236_R | Primer3: not found at this Tm | N.d. | 0.15 |
| mm4_intergenic_2610028E06Rik|Csf3r_chr4_125932618_F | Primer3: not found at this Tm | N.d. | 0.15 |
| mm4_intergenic_2610028E06Rik|Csf3r_chr4_125932618_R | Primer3: not found at this Tm | N.d. | 0.15 |
| mm4_intergenic_Gm25216|Pyroxd2_chr19_42702914_F | Primer3: not found at this Tm | N.d. | 0.14 |
| mm4_intergenic_Gm25216|Pyroxd2_chr19_42702914_R | Primer3: not found at this Tm | N.d. | 0.14 |
| mm4_intron_Gm26691_chr3_134045262_F | Primer3: not found at this Tm | N.d. | 0.14 |
| mm4_intron_Gm26691_chr3_134045262_R | Primer3: not found at this Tm | N.d. | 0.14 |
| mm4_intron_Gm16551_chr9_74857097_F | TCGTCGGCAGCGTCGAGAGCAAAACCCAAACCCG | 59.6 | 0.14 |
| mm4_intron_Gm16551_chr9_74857097_R | GTCTCGTGGGCTCGGTGACCCACAGACACCTAGAAGA | 60.1 | 0.14 |
| mm4_intergenic_Zbtb16|Htr3a_chr9_48854633_F | Primer3: not found at this Tm | N.d. | 0.13 |
| mm4_intergenic_Zbtb16|Htr3a_chr9_48854633_R | Primer3: not found at this Tm | N.d. | 0.13 |
| mm4_intergenic_A930004D18Rik|Gm13330_chr2_18039190_F | TCGTCGGCAGCGTCTTTCTGACACCAGTGGAGGC | 59.8 | 0.13 |
| mm4_intergenic_A930004D18Rik|Gm13330_chr2_18039190_R | GTCTCGTGGGCTCGGCGGCCTTTCCAGGGTCTTAG | 60.1 | 0.13 |
| mm4_intergenic_Gm16087|Gm16086_chr12_107009868_F | Primer3: not found at this Tm | N.d. | 0.13 |
| mm4_intergenic_Gm16087|Gm16086_chr12_107009868_R | Primer3: not found at this Tm | N.d. | 0.13 |
| mm3_intron_Ptprn2_chr12_117055046_F | Primer3: not found at this Tm | N.d. | 0.13 |
| mm3_intron_Ptprn2_chr12_117055046_R | Primer3: not found at this Tm | N.d. | 0.13 |
| mm3_intergenic_Cbx8|Cbx4/Gm26508_chr11_119053465_F | TCGTCGGCAGCGTCGGGAGCGGAGAACAAGGTAT | 59.1 | 0.13 |
| mm3_intergenic_Cbx8|Cbx4/Gm26508_chr11_119053465_R | GTCTCGTGGGCTCGGAATGAGCGTGCACCAGCT | 59.9 | 0.13 |
| mm4_intergenic_Llgl2|Myo15b_chr11_115859771_F | TCGTCGGCAGCGTCGGAGTGTAAGGAGCGCGG | 60.2 | 0.12 |
| mm4_intergenic_Llgl2|Myo15b_chr11_115859771_R | GTCTCGTGGGCTCGGGACCACCGCCAGGGAGAG | 61.7 | 0.12 |
| mm4_intergenic_Gm24839|Tmem132c_chr5_127197586_F | TCGTCGGCAGCGTCTGGGAACACTGGGTCTCTGA | 60.1 | 0.12 |
| mm4_intergenic_Gm24839|Tmem132c_chr5_127197586_R | GTCTCGTGGGCTCGGGGACACTGGACACCCTGTTT | 59.8 | 0.12 |
| mm4_intron_Lpcat3_chr6_124694662_F | Primer3: not found at this Tm | N.d. | 0.12 |
| mm4_intron_Lpcat3_chr6_124694662_R | Primer3: not found at this Tm | N.d. | 0.12 |
| mm4_exon_Cdc25a_chr9_109875783_F | TCGTCGGCAGCGTCGACAGAGAGGGAAGCACCG | 59.7 | 0.12 |
| mm4_exon_Cdc25a_chr9_109875783_R | GTCTCGTGGGCTCGGCAAACACAAACACGACCCCG | 60.2 | 0.12 |
| mm4_exon_Rnmtl1_chr11_76250492_F | TCGTCGGCAGCGTCCCAGCCCCTCCTCTGCTA | 60.0 | 0.11 |
| mm4_exon_Rnmtl1_chr11_76250492_R | GTCTCGTGGGCTCGGGGAACAGCAGACACTAATAGAAACT | 58.8 | 0.11 |
| mm4_intergenic_Tbc1d22a|Gm23416_chr15_87055288_F | Primer3: not found at this Tm | N.d. | 0.11 |
| mm4_intergenic_Tbc1d22a|Gm23416_chr15_87055288_R | Primer3: not found at this Tm | N.d. | 0.11 |
| mm4_intergenic_Gm13855|Gm14546_chr6_34228493_F | TCGTCGGCAGCGTCTTGCAAGAGTGAGCAGGGTC | 60.2 | 0.11 |
| mm4_intergenic_Gm13855|Gm14546_chr6_34228493_R | GTCTCGTGGGCTCGGTCAAAGGGCGACAGTGGTAC | 59.9 | 0.11 |
| mm4_intron_Jazf1_chr6_52777951_F | TCGTCGGCAGCGTCCCAGCAATCCACAGCTAGGA | 59.4 | 0.11 |
| mm4_intron_Jazf1_chr6_52777951_R | GTCTCGTGGGCTCGGAGGGCTCTGTCATTGTTGTCT | 59.2 | 0.11 |
| mm4_intergenic_Fcrls|Cd5l_chr3_87350456_F | Primer3: not found at this Tm | N.d. | 0.11 |
| mm4_intergenic_Fcrls|Cd5l_chr3_87350456_R | Primer3: not found at this Tm | N.d. | 0.11 |
| mm4_intron_Jph1_chr1_17025470_F | TCGTCGGCAGCGTCAGCAAGTTCTGGATGCAGAGA | 59.3 | 0.10 |
| mm4_intron_Jph1_chr1_17025470_R | GTCTCGTGGGCTCGGAGAACTCAAGCTGCTGACTAGA | 58.8 | 0.10 |
| mm4_intergenic_Rtp4|Gm6640_chr16_23617718_F | Primer3: not found at this Tm | N.d. | 0.10 |
| mm4_intergenic_Rtp4|Gm6640_chr16_23617718_R | Primer3: not found at this Tm | N.d. | 0.10 |
| mm4_intergenic_Gm25574|Ankrd50_chr3_38278798_F | Primer3: not found at this Tm | N.d. | 0.10 |
| mm4_intergenic_Gm25574|Ankrd50_chr3_38278798_R | Primer3: not found at this Tm | N.d. | 0.10 |
| mm4_intergenic_Gm25454|n-R5s165_chr6_112046936_F | Primer3: not found at this Tm | N.d. | 0.10 |
| mm4_intergenic_Gm25454|n-R5s165_chr6_112046936_R | Primer3: not found at this Tm | N.d. | 0.10 |
| mm4_intergenic_Gm11923|Gm11925_chr4_29669703_F | Primer3: not found at this Tm | N.d. | 0.10 |
| mm4_intergenic_Gm11923|Gm11925_chr4_29669703_R | Primer3: not found at this Tm | N.d. | 0.10 |
| mm4_intron_RP23-279M5.3_chr8_86904210_F | Primer3: not found at this Tm | N.d. | 0.10 |
| mm4_intron_RP23-279M5.3_chr8_86904210_R | Primer3: not found at this Tm | N.d. | 0.10 |
| mm4_intron_Gm16976_chr14_44914371_F | Primer3: not found at this Tm | N.d. | 0.09 |
| mm4_intron_Gm16976_chr14_44914371_R | Primer3: not found at this Tm | N.d. | 0.09 |
| mm4_intergenic_Gm13176|Sephs1_chr2_4874940_F | Primer3: not found at this Tm | N.d. | 0.09 |
| mm4_intergenic_Gm13176|Sephs1_chr2_4874940_R | Primer3: not found at this Tm | N.d. | 0.09 |
| mm4_intron_C030017K20Rik_chr4_155457178_F | Primer3: not found at this Tm | N.d. | 0.09 |
| mm4_intron_C030017K20Rik_chr4_155457178_R | Primer3: not found at this Tm | N.d. | 0.09 |
| mm4_intron_Gm21972/Armc9_chr1_86156605_F | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_intron_Gm21972/Armc9_chr1_86156605_R | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_intergenic_Nupr1l|Vkorc1l1_chr5_129938941_F | TCGTCGGCAGCGTCACCACAGACTATGCTTCAGCC | 60.0 | 0.08 |
| mm4_intergenic_Nupr1l|Vkorc1l1_chr5_129938941_R | GTCTCGTGGGCTCGGCACACTGCCTCTCTACAGGT | 58.7 | 0.08 |
| mm4_intergenic_B230217C12Rik|Fbxo47_chr11_97848994_F | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_intergenic_B230217C12Rik|Fbxo47_chr11_97848994_R | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_intergenic_Flt1|Pomp_chr5_147777811_F | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_intergenic_Flt1|Pomp_chr5_147777811_R | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_intergenic_Tet2|Gm23011_chr3_133582811_F | TCGTCGGCAGCGTCGACGTGAAGGCAGAAAGAGGA | 59.9 | 0.07 |
| mm4_intergenic_Tet2|Gm23011_chr3_133582811_R | GTCTCGTGGGCTCGGTTGCTCACCCTTACCTCCCT | 60.1 | 0.07 |
| mm3_intergenic_5S_rRNA|Cops8_chr1_90420687_F | TCGTCGGCAGCGTCGGCCACACCACAAATGACAC | 59.9 | 0.07 |
| mm3_intergenic_5S_rRNA|Cops8_chr1_90420687_R | GTCTCGTGGGCTCGGGGCTTTTGGGGACACAGAGT | 60.1 | 0.07 |
| mm4_intergenic_Gm15985|Gm6116_chr5_74924098_F | TCGTCGGCAGCGTCATGCCTGCCACTTCTGTCTC | 60.0 | 0.07 |
| mm4_intergenic_Gm15985|Gm6116_chr5_74924098_R | GTCTCGTGGGCTCGGTGGAACTTGAGGGAGGAGGT | 59.8 | 0.07 |
| mm4_intergenic_Gm25718|4930594M17Rik_chr18_81085893_F | TCGTCGGCAGCGTCGCACTGACCAGAGAAGTGGG | 60.3 | 0.06 |
| mm4_intergenic_Gm25718|4930594M17Rik_chr18_81085893_R | GTCTCGTGGGCTCGGCGCAGACTACCCAGAGCAAG | 60.4 | 0.06 |
| mm3_intron_Capn1_chr19_6004512_F | Primer3: not found at this Tm | N.d. | 0.05 |
| mm3_intron_Capn1_chr19_6004512_R | Primer3: not found at this Tm | N.d. | 0.05 |
| mm3_intron_Capn1_chr19_6004217_F | Primer3: not found at this Tm | N.d. | 0.05 |
| mm3_intron_Capn1_chr19_6004217_R | Primer3: not found at this Tm | N.d. | 0.05 |
| mm3_intron_Capn1_chr19_6004109_F | TCGTCGGCAGCGTCATGAGAACACAGGCAGGAGC | 60.0 | 0.05 |
| mm3_intron_Capn1_chr19_6004109_R | GTCTCGTGGGCTCGGCCCTGTGCTGGGCTCCTG | 62.4 | 0.05 |
| mm3_intron_Capn1_chr19_6004083_F | Primer3: not found at this Tm | N.d. | 0.05 |
| mm3_intron_Capn1_chr19_6004083_R | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_intergenic_Kif5b|Rpl27-ps3_chr18_6276124_F | TCGTCGGCAGCGTCTGTTGGGATGAAGCAGCCTT | 59.8 | 0.05 |
| mm4_intergenic_Kif5b|Rpl27-ps3_chr18_6276124_R | GTCTCGTGGGCTCGGGGACTGTTTGCTGCCTTTCC | 59.6 | 0.05 |
| mm3_intron_Capn1_chr19_6004538_F | Primer3: not found at this Tm | N.d. | 0.05 |
| mm3_intron_Capn1_chr19_6004538_R | Primer3: not found at this Tm | N.d. | 0.05 |
| mm3_intron_Capn1_chr19_6004270_F | Primer3: not found at this Tm | N.d. | 0.05 |
| mm3_intron_Capn1_chr19_6004270_R | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_intergenic_Gm8116|Col12a1_chr9_79523472_F | TCGTCGGCAGCGTCTGGGTAGAAGGCATAGGACA | 57.4 | 0.05 |
| mm4_intergenic_Gm8116|Col12a1_chr9_79523472_R | GTCTCGTGGGCTCGGATAGAAGAGGGCCCAGACGC | 61.4 | 0.05 |
| mm3_intron_Thoc2_chrX_41911461_F | Primer3: not found at this Tm | N.d. | 0.05 |
| mm3_intron_Thoc2_chrX_41911461_R | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_intergenic_Gm22174|Gm11454_chr2_163098572_F | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_intergenic_Gm22174|Gm11454_chr2_163098572_R | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_intergenic_Ociad2|Cwh43_chr5_73369257_F | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_intergenic_Ociad2|Cwh43_chr5_73369257_R | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_intergenic_Arsb|Gm25534_chr13_93893457_F | TCGTCGGCAGCGTCCTGAGCCAGTAGAGCATGGG | 59.8 | 0.04 |
| mm4_intergenic_Arsb|Gm25534_chr13_93893457_R | GTCTCGTGGGCTCGGTTTCTCCTTGGACAGGCACC | 59.8 | 0.04 |
| mm4_intron_Ypel2_chr11_86993090_F | TCGTCGGCAGCGTCAACAGAGTTCGTGCCCACC | 60.2 | 0.03 |
| mm4_intron_Ypel2_chr11_86993090_R | GTCTCGTGGGCTCGGCACGTCGCCCTCTAAAGTCC | 60.4 | 0.03 |
| mm4_intron_Fam126b_chr1_58578416_F | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_intron_Fam126b_chr1_58578416_R | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_intergenic_Grik3|2610028E06Rik_chr4_125738239_F | TCGTCGGCAGCGTCGTGTCTGTCACCAGGAAGGG | 59.9 | 0.03 |
| mm4_intergenic_Grik3|2610028E06Rik_chr4_125738239_R | GTCTCGTGGGCTCGGACATCTGCTCTCTGCCCCTA | 60.0 | 0.03 |
| mm4_intergenic_Gm14473|Gm14485_chrX_10991260_F | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_intergenic_Gm14473|Gm14485_chrX_10991260_R | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_intergenic_Memo1|Dpy30_chr17_74295591_F | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_intergenic_Memo1|Dpy30_chr17_74295591_R | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_intron_Syt7_chr19_10419406_F | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_intron_Syt7_chr19_10419406_R | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_intergenic_Gm22463|Npbwr1_chr1_5899811_F | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_intergenic_Gm22463|Npbwr1_chr1_5899811_R | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_intergenic_Rbms3|Gm26614_chr9_117721476_F | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_intergenic_Rbms3|Gm26614_chr9_117721476_R | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_exon_Bhmt_chr13_93621557_F | TCGTCGGCAGCGTCCAGCCTCCAAACCCTCCTTC | 60.3 | 0.02 |
| mm4_exon_Bhmt_chr13_93621557_R | GTCTCGTGGGCTCGGGGTGTCTCCCCACACTAACG | 60.0 | 0.02 |
| mm2_intergenic_Gm11412|n-R5s187_chr4_81901007_F | Primer3: not found at this Tm | N.d. | 0.02 |
| mm2_intergenic_Gm11412|n-R5s187_chr4_81901007_R | Primer3: not found at this Tm | N.d. | 0.02 |
| mm3_intron_Chst15_chr7_132315918_F | TCGTCGGCAGCGTCCCACGGACTAGCACGCTATC | 60.3 | 0.02 |
| mm3_intron_Chst15_chr7_132315918_R | GTCTCGTGGGCTCGGCAGAACGAGGCAGCTCTGAG | 60.4 | 0.02 |
| mm4_intron_Slc9a7_chrX_20188485_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intron_Slc9a7_chrX_20188485_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Fshr|Gm10184_chr17_89650546_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Fshr|Gm10184_chr17_89650546_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Gm6133|Gm26430_chr18_78515708_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Gm6133|Gm26430_chr18_78515708_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Gm26844|Gm4812_chr13_69279078_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Gm26844|Gm4812_chr13_69279078_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Erg|Ets2_chr16_95692826_F | TCGTCGGCAGCGTCTTCAAAGGTGGGATGGAGCC | 59.9 | 0.01 |
| mm4_intergenic_Erg|Ets2_chr16_95692826_R | GTCTCGTGGGCTCGGGGCCTCTCGATTGCTCTCTC | 59.9 | 0.01 |
| mm4_exon_Ddx49/Homer3_chr8_70293191_F | TCGTCGGCAGCGTCACCCTAGTCTGCCATGGAGT | 59.9 | 0.01 |
| mm4_exon_Ddx49/Homer3_chr8_70293191_R | GTCTCGTGGGCTCGGAACCTGGGTAGAAGCACTGC | 59.9 | 0.01 |
| mm4_intron_Tmem132b_chr5_125762656_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intron_Tmem132b_chr5_125762656_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm3_intron_6330403A02Rik_chr1_180481693_F | TCGTCGGCAGCGTCGCTCTCCTGCCCACCTAATT | 59.4 | 0.01 |
| mm3_intron_6330403A02Rik_chr1_180481693_R | GTCTCGTGGGCTCGGACCTGTCTGTCTCCCTGAGA | 59.2 | 0.01 |
| mm4_exon_Plcb4_chr2_135741997_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_exon_Plcb4_chr2_135741997_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Gm22978|Gm20540_chr17_49341334_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Gm22978|Gm20540_chr17_49341334_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Gm23296|Akap6_chr12_52640336_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intergenic_Gm23296|Akap6_chr12_52640336_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intergenic_Tnnt3|Mrpl23_chr7_142528853_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intergenic_Tnnt3|Mrpl23_chr7_142528853_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intergenic_Gm23094|Whsc1l1_chr8_25679750_F | TCGTCGGCAGCGTCCGACAACATCCCTGGGTTGA | 59.9 | 0.00 |
| mm4_intergenic_Gm23094|Whsc1l1_chr8_25679750_R | GTCTCGTGGGCTCGGAGGTCCCCGACATAATGCAA | 59.0 | 0.00 |
| mm4_intron_Adora2a_chr10_75325215_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intron_Adora2a_chr10_75325215_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intron_Tnik_chr3_28548081_F | TCGTCGGCAGCGTCTGCTTCCTGTGTACTAAGCCC | 59.7 | 0.00 |
| mm4_intron_Tnik_chr3_28548081_R | GTCTCGTGGGCTCGGGGAGACAATCCCACCTGGTG | 60.0 | 0.00 |
| mm4_intron_Tbx5_chr5_119839793_F | TCGTCGGCAGCGTCGAAGGCGGTGGGTCTGTTTA | 59.9 | 0.00 |
| mm4_intron_Tbx5_chr5_119839793_R | GTCTCGTGGGCTCGGCAGAGACAGTGCAGGCCTTT | 60.2 | 0.00 |
| mm4_intron_Slc14a2_chr18_78163492_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intron_Slc14a2_chr18_78163492_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intron_Nol9_chr4_152050049_F | TCGTCGGCAGCGTCGGTTTGGCAGGGACACAGAA | 60.4 | 0.00 |
| mm4_intron_Nol9_chr4_152050049_R | GTCTCGTGGGCTCGGCAGCACTGCCAAGCAAAAGT | 59.8 | 0.00 |
| mm4_intergenic_Card10|Cdc42ep1_chr15_78827006_F | TCGTCGGCAGCGTCGGTCTGGAACCTGTGACTGT | 59.2 | 0.00 |
| mm4_intergenic_Card10|Cdc42ep1_chr15_78827006_R | GTCTCGTGGGCTCGGGCCCCAAAGACTCCAAGAGG | 60.3 | 0.00 |
| mm4_exon_Efcab10_chr12_33395045_F | TCGTCGGCAGCGTCGTACCTGGGAGGGAAGAGGA | 59.6 | 0.00 |
| mm4_exon_Efcab10_chr12_33395045_R | GTCTCGTGGGCTCGGCCACAGGCTCCATGTTTCCT | 59.9 | 0.00 |
These only list off-targets that have primers in the table above. Primers underlined, off-targets in bold.
| mm4_intron_Ajap1_chr4_153440133 |
GCTGCTACAGAGTCTGAGCAATAGCAACATGGCAGGCGCCAGGCTCGGCGACTCTCTCACCTCACTCGGTTATACCGAGA AGAGGAAGTGCTGTTGTTACTCTCATCTTGAAGGGGAAAGGATCGGC |
| mm4_intron_Atp11a_chr8_12763021 |
GTGTCCAGTGGAGAAAGGGGGCAGTGTGAAGGCTGTGGGGGCCTGAGCGTCTGATGCCTGGTGCCTGCCTTGTTGCTTGC CATCACCCTTAGGTGCCTTGTGAACTCTTCTCCCCTTGTTAGGACCCTGG |
| mm4_intron_Casz1_chr4_148876881 |
CTGAGACAGTGGGCATGAGGGCGTGGCCAGGTGTCTGCCTTGTAGCCTGTCTAGCTGAGTCTCCAATCTCCTTGGGACAC TGGTCA |
| mm4_intron_Fbxl13_chr5_21581923 |
TCCCCTTAACCCTTTTCTCACTTTGGATACAAGAGAACAAGGCAGGCCCCTGGGGCAAGCATACTTACTGACAGCTTTCA AGGTTTTTGTTCGGAAGTCGCAGC |
| mm4_intron_Dis3l2_chr1_87032500 |
TGAGCAGGTGTCAGGTAGGAGCCTGTATTTTGACATGGAGAGGACAAGGCAGGTGCCTGGGTGCTGCCAGGTGGAAAGGG CAAACGGCCTGTGTGTGTGTCTGGTGCAGTC |
| mm4_intergenic_Arrdc3|Gm4211_chr13_80932286 |
GGTGGTGTTCATCCCCACAATGTAATTCCTGGTGCCTGCCCTGTGGTCTTCTGTGGTTTCTCTGATGATCTCTAGCACTT TGCAAATATTTCCACCC |
| mm4_intergenic_Mir5133|Gm25603_chr9_62199395 |
CCAGAATGTGTACCCCAGCCTGAGCAGCGTAGACTGCAGAAGGAAACAGGGCAGGCTCCTGGGAAGGCAGCTGAAGCAAG AAGGTGAACGGGAACCTGGAGGGCCAACACTGATGCTAC |
| mm4_intron_Elavl3_chr9_22034927 |
CCTGTGTTGGCCAGGGTTTAACCTTAAGAGTCATTAGGAGCTGCCCACCTGTGAGGGTAGAATGCCAGGGGTCTGCCTCG TCACCTTCTGTACTAAGTTACAGGCAAAGGACACCAAGGTT |
| mm4_intron_Plcb4_chr2_135789816 |
ACTGAACTACTGGCATATTGAGGTAATGTGACAAGACAGGCTCCAGGAATCCGAGGAAAATTGGTTAGGTTCCCATAGGA ACATCAGTAATGCCTAGGTGCTTTCCAGGGCTC |
| mm4_intron_Atxn1_chr13_45576279 |
AGGGACATGAGTCTGGACCAGGATGGAGGGGACAAGGCAGGCATCTGGCTTGAGACATCTGTAGAAGCTGCTCACATGGG GAATGTGGCTGCAGCTCAGTGTGGCCAGTGTCCCCTGGCTGCTTGCCCACTCTGGAATT |
| mm4_intergenic_Gm13481|Gm13489_chr2_48599124 |
AACCAATGGGCGGGACTTAGAACACACTGAGAGAAGAACTACCAGGTGCCTAGCTTGTGGCCTTGGGTCACTGAGCCAAC CCAAAGTGCAGTCAGGAG |
| mm4_intron_Rab6b_chr9_103146720 |
ACCACGGGACAGATTGTGACCTTGAAAAGCCAGGTGCCTGCCCTGTGACCTTGGGAGCCAGCATCTCCTCCTCCAGGGCA CTAACTGAGC |
| mm4_intergenic_Uso1|Gm15710_chr5_92138232 |
GTGAGATCGGGGCGTCTACGCCGCTCCCGTCGCCTGCCTTCTTTCCTTCCCCCTGCTCGGACGCGCGAGCTCCCCACGCG GCGGTGCAGCCCGGGCCGTGGTGACAGGAGGGCTTC |
| mm4_intron_Gm16551_chr9_74857097 |
GAGAGCAAAACCCAAACCCGGCAGAGAAGGCTGAGGAGGGGAGAGCAGGCAACAGGGCAGGCGCTCGGAACACCTTGCGT TTTTATTTTTAAATCTTCTAGGTGTCTGTGGGTCA |
| mm4_intergenic_A930004D18Rik|Gm13330_chr2_18039190 |
TTTCTGACACCAGTGGAGGCTCAAGAAGAAATCTGCTTTTTTCTAGCTGCAGTGTCAGAGGGAAAGGTTGCAAGGCAGGC GTCAGGCTGCTTTTCCCTTGGACCCACCAGGTCCTAAGACCCTGGAAAGGCCG |
| mm3_intergenic_Cbx8|Cbx4/Gm26508_chr11_119053465 |
GGGAGCGGAGAACAAGGTATAGCCTGTATTTAGGTTCCAGTCCTTATATGGCGATGCGCACGAGCGCCAGCCGAGCGGCC GCACCATATAAGGACACACGGCAGGCGCCGGGCTGAGCTGGTGCACGCTCATT |
| mm4_intergenic_Llgl2|Myo15b_chr11_115859771 |
GGAGTGTAAGGAGCGCGGCCGCGAGAGGGCGCTCGAGGCGCGGGGCAGGGTGCCCGGGCCACGGCGCTGGTTGGCCTTGC GCCTGGCCTGTCGCCTGGTGGGGCTCCGGGGAACGCCGCGAGCTCTCCCTGGCGGTGGTC |
| mm4_intergenic_Gm24839|Tmem132c_chr5_127197586 |
TGGGAACACTGGGTCTCTGATATGGAAGATCAGAGAATGGCAGGATGAAGACTAAGGGCTGGGTCCTGACACCTGCCTTG TGGCCTGTGTTCATACATGATCCATTCCTGAGACAAAACAGGGTGTCCAGTGTCC |
| mm4_exon_Cdc25a_chr9_109875783 |
GACAGAGAGGGAAGCACCGGTGCTTGTGCCTGGCGCCTGCCGAGTCCCCTACGCTCGCCGGTCCGCGCCGCTGCCCGTGG CGGCCGCGTCTCTGAACCGCGGGGTCGTGTTTGTGTTTG |
| mm4_exon_Rnmtl1_chr11_76250492 |
CCAGCCCCTCCTCTGCTAGGAGGCTGGCCAAGGTGACAACACAGGAGCCAGGGGGTAGGCACTGCCACCATTGTGTGGTA CTTAAAAAAAAAGAGTTTCTATTAGTGTCTGCTGTTCC |
| mm4_intergenic_Gm13855|Gm14546_chr6_34228493 |
TTGCAAGAGTGAGCAGGGTCTGTTGCCACTGTGAATTTGTTTTCTCCCACCCAGCCCCTGCCTGCTTTTTGGCTTCCTGA CCCAAGGGCCTGCCATGTCGTCTTCCTGTACCACTGTCGCCCTTTGA |
| mm4_intron_Jazf1_chr6_52777951 |
CCAGCAATCCACAGCTAGGAACTAGTGAAGCAAGGATTTCGTTCTGGGATAAGATTATAGTTAGGACTGCCCATGGCTGC AAAGCGACCAGGAAGGCTCCAGGGGTCCAAGCACAAATAGACAACAATGACAGAGCCCT |
| mm4_intron_Jph1_chr1_17025470 |
AGCAAGTTCTGGATGCAGAGACCTGGTGCCTGACTTGCCTCCTTTCTTGGAGTAGCCAGAACTTTTACATGCTACGTATT CACAATCAGAGTAATTATAAACTTGTTTTCTAGTCAGCAGCTTGAGTTCT |
| mm4_intergenic_Nupr1l|Vkorc1l1_chr5_129938941 |
ACCACAGACTATGCTTCAGCCCCGGTCTCCTGCCTTGTCTCTTTGGTTGTCTCTTCCTGCTTTTGGAAATAGCTCTTTCT TCTTCCTTTGAGGGACTGATTGGTCCTTTATAGAATTTAACCTGTAGAGAGGCAGTGTG |
| mm4_intergenic_Tet2|Gm23011_chr3_133582811 |
GACGTGAAGGCAGAAAGAGGACTATTTAGGGAGAAGGGGACAATGTAGGAGCCAGGGGACAGTGGAGCAGAGGGAGGTAA GGGTGAGCAA |
| mm3_intergenic_5S_rRNA|Cops8_chr1_90420687 |
GGCCACACCACAAATGACACTATGCAATTGTTTTCCTGTTGAAAATATTTTCATGCTATAGTGATGAGCGGGAGAAAGGT CTAAAGGGGACAAGGCAGACGGCAGGGTGAGACTCTGTGTCCCCAAAAGCC |
| mm4_intergenic_Gm15985|Gm6116_chr5_74924098 |
ATGCCTGCCACTTCTGTCTCAAATCCTCTCCCGGTGCGTGCCCTGCCGCCTTGTCACCACTGGACCTCCTCCCTCAAGTT CCA |
| mm4_intergenic_Gm25718|4930594M17Rik_chr18_81085893 |
GCACTGACCAGAGAAGTGGGGGTCGGGGGTGGGACAAGCCGAGAATGCAGGCCCCGGGCGGTCTGCAGCCTTCGGGAGGG AGGGGTGGCTGGCCTGAGGATGCATGCTTGCTCTGGGTAGTCTGCG |
| mm3_intron_Capn1_chr19_6004109 |
ATGAGAACACAGGCAGGAGCCCAGCACAGGGGGACACAGGCAGGAGTCCAGCACAGGGGGACAAGGCAGGAGCCCAGCAC AGGGGGACAAGGCAGGAGCCCAGCACAGGGGGGGACAAGGCAGGAGCCCAGCACAGGG |
| mm4_intergenic_Kif5b|Rpl27-ps3_chr18_6276124 |
TGTTGGGATGAAGCAGCCTTGAAGTGGACAAGCCAGGAGCCAGGACTGTGAAGGTCAAAGTCTGTGCTCAGATGTTTAAA CCAAGTGAGAAGAGGAAAGGCAGCAAACAGTCC |
| mm4_intergenic_Gm8116|Col12a1_chr9_79523472 |
TGGGTAGAAGGCATAGGACATATTCTTCTTTCAAAAGAATGAGACCAGCCTGGCACCTGCATTGTCTCATTAAATGTTGG CGTCTGGGCCCTCTTCTAT |
| mm4_intergenic_Arsb|Gm25534_chr13_93893457 |
CTGAGCCAGTAGAGCATGGGCGCAGGTTCCAGAGCATTGCAGGAGCTTAGGCCCAGAGCCTGCCGTGTCCCCTTCAGACT GAAGCCTTGCTGCAGGGGTGCCTGTCCAAGGAGAAA |
| mm4_intron_Ypel2_chr11_86993090 |
AACAGAGTTCGTGCCCACCCCTTGGCAAGGCCGCAGGGGAGGCGCCGGGAAGCGTCCAGGCAGGAACTCGCTGTGGTTCC CTTGGCTTGGGGCTGCCGAAGCGCTCCGGGGACTTTAGAGGGCGACGTG |
| mm4_intergenic_Grik3|2610028E06Rik_chr4_125738239 | GTGTCTGTCACCAGGAAGGGAAAGGAGACAAGGGAAGTGCCAGGATATAGGGGCAGAGAGCAGATGT |
| mm4_exon_Bhmt_chr13_93621557 |
CAGCCTCCAAACCCTCCTTCATGAGCTTCACAGTCTGTAAGCTGACGCTGGGGTCGAAGTGGCAGTTCACGCCGACAATG GAGGCGCCTGGAAGTGAGGGGGCGCGTTAGTGTGGGGAGACACC |
| mm3_intron_Chst15_chr7_132315918 |
CCACGGACTAGCACGCTATCAACATCCTCAGCGTCGCTCCTCGCGTCCGGGCCCCTGCCTTCTCGGCTTCCACCATCACC ACCCGCCACCGCCGCCCCCACGGCTTAGCTCAGAGCTGCCTCGTTCTG |
| mm4_intergenic_Erg|Ets2_chr16_95692826 |
TTCAAAGGTGGGATGGAGCCAACCTGATTCAGAGAGCAACAAGGGCACCAGGCAGGGGCCAGGTCTGAGTGGAAGGAAGG AAACAAAGGCAGTGGCCTCCTCCAGAAGCCAGAGAGAGCAATCGAGAGGCC |
| mm4_exon_Ddx49/Homer3_chr8_70293191 |
ACCCTAGTCTGCCATGGAGTGTCTGCGGCCTCAAGGCGCCCTGGCAGGGGCCAGGGGACCCCAGCTGTCTCTGAGCTTTG CACTGTGTAGAGTTTTCTAGAATCCTTGGGCAGTGCTTCTACCCAGGTT |
| mm3_intron_6330403A02Rik_chr1_180481693 |
GCTCTCCTGCCCACCTAATTCTTTGTTTCCTCAAAGCCTATGTCAGGATGTTGTTATTTCAACACTTATAATTCTAACAG CATGCACCCCGCGCGCGTGCCTTGTGGCCTTGATATTCTCAGGGAGACAGACAGGT |
| mm4_intergenic_Gm23094|Whsc1l1_chr8_25679750 |
CGACAACATCCCTGGGTTGAAGGAAGGAAGGAAGACGAGAAGGCAGGCGGGCGGTGATGAGATGAACTTCAGTTGGTTTC CTTGGGTTTTGCATTATGTCGGGGACCT |
| mm4_intron_Tnik_chr3_28548081 |
TGCTTCCTGTGTACTAAGCCCTATACATAGGTCCTTCTGAATTTGCTCAGACAGAAGACGACAATGCAGTCACCAGGTAG TGCCACCAGGTGGGATTGTCTCC |
| mm4_intron_Tbx5_chr5_119839793 |
GAAGGCGGTGGGTCTGTTTATATCAGACATCTGAGGTTCCCTTTCCCATCCTGCCCAGGAGGGAAAGTCCCAGCCGGCTG CCTTGTCGTCCTCGCTGGAGCCGAGAGGATTTAACTATAAAAGGCCTGCACTGTCTCTG |
| mm4_intron_Nol9_chr4_152050049 | GGTTTGGCAGGGACACAGAATCCTGGCCACTGCCTTGTGGCCATGACACAGCTACTTTTGCTTGGCAGTGCTG |
| mm4_intergenic_Card10|Cdc42ep1_chr15_78827006 |
GGTCTGGAACCTGTGACTGTGACTTTAGCATCTGGATACCTCACATGTCCTTAGAACAAGAGAAGACCCAGGGAAGGCCA CAAGGAAGCAGCCTGGAGACAGGGGAGAATCAATCCTCTTGGAGTCTTTGGGGC |
| mm4_exon_Efcab10_chr12_33395045 |
GTACCTGGGAGGGAAGAGGAGTGGGGCTGGGGAAGGTGAGGTGTTTCACGTGAATGAGCACGAAAGGGGCGGAGTTGGGC CCCCTGGAGGCTGCCTGGTCGCCTAGCAACGGCTCAGCTAGGAAACATGGAGCCTGTGG |