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Contents:In the table below, Illumina Nextera Handle sequences have been added and highlighted in bold. Primers for the on-target have been added for convenience. The table below is sorted by the CFD off-target score. Sites with very low CFD scores < 0.02 are unlikely to be cleaved, see our study Haeussler et al. 2016, Figure 2.
In the protocol by Matthew Canver, Harvard, two PCRs are run: one PCR to amplify the potential off-target, then a second PCR to extend the handles with Illumina barcodes. Please click here to download the protocol. Alternatively, you can have a look at Fu et al, 2014.
If a primer was not found, the reason is usually that the region around the off-target is too repetitive. To avoid unspecific primers, all repeats are masked for the primer design (not for off-target search). If you think that we should change the parameters here or should use different primer3 settings, please let us know.
| Name | Primer Sequence | Tm | CFD Score |
|---|---|---|---|
| mm0_exon_Pop5_chr5_115238084_F | Primer3: not found at this Tm | N.d. | 1.00 |
| mm0_exon_Pop5_chr5_115238084_R | Primer3: not found at this Tm | N.d. | 1.00 |
| mm4_intergenic_Zfp91|Lpxn_chr19_12796142_F | TCGTCGGCAGCGTCCGTTGCCGGATGAAAGTCTC | 59.2 | 0.54 |
| mm4_intergenic_Zfp91|Lpxn_chr19_12796142_R | GTCTCGTGGGCTCGGGACTACGTCTCCCAGAGTGC | 59.5 | 0.54 |
| mm4_intergenic_Gm24913|Fgr_chr4_132973943_F | Primer3: not found at this Tm | N.d. | 0.48 |
| mm4_intergenic_Gm24913|Fgr_chr4_132973943_R | Primer3: not found at this Tm | N.d. | 0.48 |
| mm3_intergenic_Dpy19l1|Dpy19l2_chr9_24503222_F | Primer3: not found at this Tm | N.d. | 0.40 |
| mm3_intergenic_Dpy19l1|Dpy19l2_chr9_24503222_R | Primer3: not found at this Tm | N.d. | 0.40 |
| mm4_exon_Dmwd_chr7_19076491_F | Primer3: not found at this Tm | N.d. | 0.36 |
| mm4_exon_Dmwd_chr7_19076491_R | Primer3: not found at this Tm | N.d. | 0.36 |
| mm4_intergenic_Gm26843/Gnao1|Gnao1_chr8_93810428_F | Primer3: not found at this Tm | N.d. | 0.35 |
| mm4_intergenic_Gm26843/Gnao1|Gnao1_chr8_93810428_R | Primer3: not found at this Tm | N.d. | 0.35 |
| mm4_exon_Mapk15_chr15_75998991_F | Primer3: not found at this Tm | N.d. | 0.26 |
| mm4_exon_Mapk15_chr15_75998991_R | Primer3: not found at this Tm | N.d. | 0.26 |
| mm4_intron_Pafah1b2_chr9_45984531_F | TCGTCGGCAGCGTCCTGGCCAGGGTGGAACCAG | 62.5 | 0.26 |
| mm4_intron_Pafah1b2_chr9_45984531_R | GTCTCGTGGGCTCGGGTATTGTGAGGCCCGGCTC | 60.5 | 0.26 |
| mm4_intergenic_Gm25748|Creb1_chr1_64532412_F | TCGTCGGCAGCGTCTTCCCAGCAAAGAACCAGCT | 59.8 | 0.25 |
| mm4_intergenic_Gm25748|Creb1_chr1_64532412_R | GTCTCGTGGGCTCGGCCGCCCGGGAACTTTGAC | 61.0 | 0.25 |
| mm4_intron_Adnp2_chr18_80151324_F | TCGTCGGCAGCGTCGACAGCGCTAGGGACGTC | 59.8 | 0.21 |
| mm4_intron_Adnp2_chr18_80151324_R | GTCTCGTGGGCTCGGGTAGGTACGCCCGCCAGG | 62.2 | 0.21 |
| mm4_exon_Dtx1_chr5_120694845_F | Primer3: not found at this Tm | N.d. | 0.20 |
| mm4_exon_Dtx1_chr5_120694845_R | Primer3: not found at this Tm | N.d. | 0.20 |
| mm4_exon_2410012M07Rik_chr9_98865019_F | TCGTCGGCAGCGTCCCACAGAGCCGTCCATCATG | 60.8 | 0.20 |
| mm4_exon_2410012M07Rik_chr9_98865019_R | GTCTCGTGGGCTCGGCTGGTGTCTGCGGTGACC | 60.3 | 0.20 |
| mm4_intergenic_Gm12904|1700121C08Rik_chr4_123842071_F | Primer3: not found at this Tm | N.d. | 0.20 |
| mm4_intergenic_Gm12904|1700121C08Rik_chr4_123842071_R | Primer3: not found at this Tm | N.d. | 0.20 |
| mm3_intergenic_Prr14|Fbrs_chr7_127479113_F | Primer3: not found at this Tm | N.d. | 0.19 |
| mm3_intergenic_Prr14|Fbrs_chr7_127479113_R | Primer3: not found at this Tm | N.d. | 0.19 |
| mm4_exon_Timp2_chr11_118355209_F | TCGTCGGCAGCGTCCGCGCAAACTTTCTGTCCTC | 60.1 | 0.18 |
| mm4_exon_Timp2_chr11_118355209_R | GTCTCGTGGGCTCGGCATAGAAGGCAGCGGAGGAG | 59.9 | 0.18 |
| mm4_exon_Cpeb2/Gm7854_chr5_43234704_F | Primer3: not found at this Tm | N.d. | 0.16 |
| mm4_exon_Cpeb2/Gm7854_chr5_43234704_R | Primer3: not found at this Tm | N.d. | 0.16 |
| mm3_intron_Usp9x_chrX_13072731_F | Primer3: not found at this Tm | N.d. | 0.16 |
| mm3_intron_Usp9x_chrX_13072731_R | Primer3: not found at this Tm | N.d. | 0.16 |
| mm4_exon_Pmepa1_chr2_173276216_F | Primer3: not found at this Tm | N.d. | 0.16 |
| mm4_exon_Pmepa1_chr2_173276216_R | Primer3: not found at this Tm | N.d. | 0.16 |
| mm3_exon_Zfp523_chr17_28177446_F | TCGTCGGCAGCGTCCCCTGGAACCTGGATATCGC | 59.9 | 0.15 |
| mm3_exon_Zfp523_chr17_28177446_R | GTCTCGTGGGCTCGGACAGACCACCATGCACCG | 59.9 | 0.15 |
| mm3_intron_Psmd11_chr11_80428764_F | TCGTCGGCAGCGTCCGACATCCTCCACTCCATCG | 59.9 | 0.14 |
| mm3_intron_Psmd11_chr11_80428764_R | GTCTCGTGGGCTCGGTGAGTCAGCAGCACCATAGC | 60.1 | 0.14 |
| mm3_intergenic_Gm9755|Nat3_chr8_67523120_F | TCGTCGGCAGCGTCAGCACGCAGATTCCAGACAA | 59.9 | 0.14 |
| mm3_intergenic_Gm9755|Nat3_chr8_67523120_R | GTCTCGTGGGCTCGGCTTTTGAGCTGTTTCCTCCCC | 59.1 | 0.14 |
| mm4_intron_Snx6_chr12_54795579_F | TCGTCGGCAGCGTCAAGAGAGACATTAGCGCCCA | 58.8 | 0.14 |
| mm4_intron_Snx6_chr12_54795579_R | GTCTCGTGGGCTCGGGGACTCGAAGCAGCCATGAT | 60.1 | 0.14 |
| mm4_intron_Dpp9_chr17_56218676_F | Primer3: not found at this Tm | N.d. | 0.13 |
| mm4_intron_Dpp9_chr17_56218676_R | Primer3: not found at this Tm | N.d. | 0.13 |
| mm4_intergenic_Gm20204|Cmip_chr8_117256794_F | Primer3: not found at this Tm | N.d. | 0.12 |
| mm4_intergenic_Gm20204|Cmip_chr8_117256794_R | Primer3: not found at this Tm | N.d. | 0.12 |
| mm4_exon_Nrxn2_chr19_6498310_F | Primer3: not found at this Tm | N.d. | 0.12 |
| mm4_exon_Nrxn2_chr19_6498310_R | Primer3: not found at this Tm | N.d. | 0.12 |
| mm3_exon_Ift57_chr16_49699391_F | TCGTCGGCAGCGTCGCTTGGACGATGGGGTGTC | 60.7 | 0.12 |
| mm3_exon_Ift57_chr16_49699391_R | GTCTCGTGGGCTCGGAACATGTGGTAGGCCGCTC | 60.0 | 0.12 |
| mm3_intergenic_1700128E19Rik|Arhgef7_chr8_11727861_F | TCGTCGGCAGCGTCCCGCCCTACCCACAAAGG | 60.0 | 0.11 |
| mm3_intergenic_1700128E19Rik|Arhgef7_chr8_11727861_R | GTCTCGTGGGCTCGGTCACCGGAGAAGAAAGACGC | 60.0 | 0.11 |
| mm4_intergenic_Vapa|Txndc2_chr17_65613726_F | Primer3: not found at this Tm | N.d. | 0.11 |
| mm4_intergenic_Vapa|Txndc2_chr17_65613726_R | Primer3: not found at this Tm | N.d. | 0.11 |
| mm4_intron_Gata4_chr14_63255790_F | Primer3: not found at this Tm | N.d. | 0.11 |
| mm4_intron_Gata4_chr14_63255790_R | Primer3: not found at this Tm | N.d. | 0.11 |
| mm4_exon_Baz2a_chr10_128092811_F | Primer3: not found at this Tm | N.d. | 0.10 |
| mm4_exon_Baz2a_chr10_128092811_R | Primer3: not found at this Tm | N.d. | 0.10 |
| mm4_exon_Insm2_chr12_55599655_F | Primer3: not found at this Tm | N.d. | 0.10 |
| mm4_exon_Insm2_chr12_55599655_R | Primer3: not found at this Tm | N.d. | 0.10 |
| mm3_intron_Mdm1_chr10_118141982_F | Primer3: not found at this Tm | N.d. | 0.10 |
| mm3_intron_Mdm1_chr10_118141982_R | Primer3: not found at this Tm | N.d. | 0.10 |
| mm4_intron_Slc2a1_chr4_119109248_F | TCGTCGGCAGCGTCGCTAAAAGAGCCGAGCCCC | 60.8 | 0.09 |
| mm4_intron_Slc2a1_chr4_119109248_R | GTCTCGTGGGCTCGGGAAGTGCCTTCTCCTCCTGG | 59.7 | 0.09 |
| mm4_exon_Gtpbp3_chr8_71489250_F | TCGTCGGCAGCGTCGGTCCAGCTAGCGGGCTC | 62.2 | 0.09 |
| mm4_exon_Gtpbp3_chr8_71489250_R | GTCTCGTGGGCTCGGGAACCAGAGGACGAGTGAGC | 60.1 | 0.09 |
| mm4_intergenic_Tac2|Zbtb39_chr10_127739501_F | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_intergenic_Tac2|Zbtb39_chr10_127739501_R | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_exon_Itgb4_chr11_115974880_F | Primer3: not found at this Tm | N.d. | 0.07 |
| mm4_exon_Itgb4_chr11_115974880_R | Primer3: not found at this Tm | N.d. | 0.07 |
| mm4_intergenic_Efna2|Mum1_chr10_80219449_F | Primer3: not found at this Tm | N.d. | 0.07 |
| mm4_intergenic_Efna2|Mum1_chr10_80219449_R | Primer3: not found at this Tm | N.d. | 0.07 |
| mm4_intergenic_Pde7a|Gm22282_chr3_19311445_F | Primer3: not found at this Tm | N.d. | 0.07 |
| mm4_intergenic_Pde7a|Gm22282_chr3_19311445_R | Primer3: not found at this Tm | N.d. | 0.07 |
| mm4_exon_Nfatc2_chr2_168590141_F | Primer3: not found at this Tm | N.d. | 0.07 |
| mm4_exon_Nfatc2_chr2_168590141_R | Primer3: not found at this Tm | N.d. | 0.07 |
| mm4_exon_Npnt_chr3_132950052_F | TCGTCGGCAGCGTCCTGCAGGTAGAGCGAGGAC | 59.5 | 0.06 |
| mm4_exon_Npnt_chr3_132950052_R | GTCTCGTGGGCTCGGGAAGGCGGCCGGGAGATC | 62.6 | 0.06 |
| mm4_intergenic_Slc23a2|Gm14051_chr2_132145187_F | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_intergenic_Slc23a2|Gm14051_chr2_132145187_R | Primer3: not found at this Tm | N.d. | 0.06 |
| mm3_intergenic_Chd6|Gm14243_chr2_161109342_F | TCGTCGGCAGCGTCCTAGATCTCCCCGCCTTGC | 59.6 | 0.05 |
| mm3_intergenic_Chd6|Gm14243_chr2_161109342_R | GTCTCGTGGGCTCGGGCTTGCAAAACAGAGCGCAG | 61.2 | 0.05 |
| mm3_intron_Sctr_chr1_120007339_F | Primer3: not found at this Tm | N.d. | 0.05 |
| mm3_intron_Sctr_chr1_120007339_R | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_exon_Chpt1_chr10_88503973_F | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_exon_Chpt1_chr10_88503973_R | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_intron_Zzz3_chr3_152396156_F | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_intron_Zzz3_chr3_152396156_R | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_exon_Csnk1a1_chr18_61555448_F | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_exon_Csnk1a1_chr18_61555448_R | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_exon_Map2k7_chr8_4240713_F | TCGTCGGCAGCGTCTGTGATCACTCTAAGCCCTGC | 59.7 | 0.04 |
| mm4_exon_Map2k7_chr8_4240713_R | GTCTCGTGGGCTCGGAGCGGTTAGGTCAATGTGCA | 59.9 | 0.04 |
| mm4_exon_Gm1673_chr5_33983854_F | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_exon_Gm1673_chr5_33983854_R | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_exon_Gnas/Gm20721_chr2_174330246_F | TCGTCGGCAGCGTCCTTGCCTTAGTCCGAGCCG | 60.5 | 0.04 |
| mm4_exon_Gnas/Gm20721_chr2_174330246_R | GTCTCGTGGGCTCGGCGGTCTTACTGTTGCCGAGG | 60.7 | 0.04 |
| mm4_intergenic_4933405D12Rik|1810037I17Rik_chr3_122924314_F | TCGTCGGCAGCGTCCTAGAAAGGGAGGACGCCTG | 59.5 | 0.03 |
| mm4_intergenic_4933405D12Rik|1810037I17Rik_chr3_122924314_R | GTCTCGTGGGCTCGGCGCCCAGTCTAGCAACCAAT | 60.3 | 0.03 |
| mm4_exon_Btbd2_chr10_80656426_F | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_exon_Btbd2_chr10_80656426_R | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_exon_Aspscr1_chr11_120673356_F | TCGTCGGCAGCGTCGTCCGCCCCATCCTCTAGAT | 60.5 | 0.03 |
| mm4_exon_Aspscr1_chr11_120673356_R | GTCTCGTGGGCTCGGGACAAGCGCCGAAGATTCTG | 59.6 | 0.03 |
| mm4_exon_Ttc39a_chr4_109407069_F | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_exon_Ttc39a_chr4_109407069_R | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_exon_Rela_chr19_5637808_F | TCGTCGGCAGCGTCCTTTACTTTAGCGCGCCGTG | 60.2 | 0.02 |
| mm4_exon_Rela_chr19_5637808_R | GTCTCGTGGGCTCGGGAGCTCTAGGGCAGCCATC | 59.6 | 0.02 |
| mm4_intron_Brwd1_chr16_96081931_F | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_intron_Brwd1_chr16_96081931_R | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_exon_Brd2_chr17_34119838_F | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_exon_Brd2_chr17_34119838_R | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_exon_Ppp2r3d_chr9_124422716_F | TCGTCGGCAGCGTCCCCACATACCTTGGCAACCA | 60.2 | 0.02 |
| mm4_exon_Ppp2r3d_chr9_124422716_R | GTCTCGTGGGCTCGGCTACTTCCCTTGCGGTCGAC | 60.4 | 0.02 |
| mm3_intron_Akap9_chr5_3928556_F | Primer3: not found at this Tm | N.d. | 0.02 |
| mm3_intron_Akap9_chr5_3928556_R | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_exon_Csnk2a2_chr8_95488634_F | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_exon_Csnk2a2_chr8_95488634_R | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_exon_Sept9_chr11_117266364_F | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_exon_Sept9_chr11_117266364_R | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_exon_Rest_chr5_77266293_F | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_exon_Rest_chr5_77266293_R | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_intron_Vrk1_chr12_106010517_F | TCGTCGGCAGCGTCGGAAGCCCGGTTCTAGAAGG | 59.8 | 0.02 |
| mm4_intron_Vrk1_chr12_106010517_R | GTCTCGTGGGCTCGGCCAGTGCTAAGGAAGTGGCA | 59.9 | 0.02 |
| mm4_intergenic_Ptch1|Ercc6l2_chr13_63573369_F | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_intergenic_Ptch1|Ercc6l2_chr13_63573369_R | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_intron_Hrasls_chr16_29209999_F | TCGTCGGCAGCGTCGCAAGGAGAATCCGGGGATC | 60.2 | 0.02 |
| mm4_intron_Hrasls_chr16_29209999_R | GTCTCGTGGGCTCGGTACCCCTGGTCTTTGGAGCT | 60.1 | 0.02 |
| mm4_exon_Fbxl3_chr14_103099195_F | TCGTCGGCAGCGTCGAACCTCCGCCGTACCTG | 59.8 | 0.02 |
| mm4_exon_Fbxl3_chr14_103099195_R | GTCTCGTGGGCTCGGGGGAGGCCTCATGTGAGAG | 59.1 | 0.02 |
| mm4_intergenic_Ctnnbip1|Gm25191_chr4_149518427_F | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_intergenic_Ctnnbip1|Gm25191_chr4_149518427_R | Primer3: not found at this Tm | N.d. | 0.02 |
| mm3_exon_Slc7a5_chr8_121907490_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm3_exon_Slc7a5_chr8_121907490_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_exon_Tlk1_chr2_70825521_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_exon_Tlk1_chr2_70825521_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Gm14983|Diap2_chrX_129614489_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Gm14983|Diap2_chrX_129614489_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_exon_Dbp_chr7_45706907_F | TCGTCGGCAGCGTCGGACCTGGACGCCTTCTTG | 60.3 | 0.01 |
| mm4_exon_Dbp_chr7_45706907_R | GTCTCGTGGGCTCGGGGGAAGAGGAGCTGCAAGAG | 60.1 | 0.01 |
| mm4_exon_Gm10657/Cd276_chr9_58555037_F | TCGTCGGCAGCGTCACAAAGGTGGACCCAGCAG | 59.8 | 0.01 |
| mm4_exon_Gm10657/Cd276_chr9_58555037_R | GTCTCGTGGGCTCGGCAACAGTGGCGGCGATTG | 59.8 | 0.01 |
| mm4_exon_Smad6_chr9_64020813_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_exon_Smad6_chr9_64020813_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_exon_Zer1_chr2_30124393_F | TCGTCGGCAGCGTCAGGAGGTCGGATCCGGTC | 60.1 | 0.01 |
| mm4_exon_Zer1_chr2_30124393_R | GTCTCGTGGGCTCGGCCGAGGGCAAGGGAACGG | 62.7 | 0.01 |
| mm4_exon_Tmem127_chr2_127248584_F | TCGTCGGCAGCGTCCATGTATGCCCCTGGAGGTG | 60.1 | 0.01 |
| mm4_exon_Tmem127_chr2_127248584_R | GTCTCGTGGGCTCGGCTTGGGAAGAGCGCTGCTTC | 61.6 | 0.01 |
| mm4_intron_Brd4_chr17_32250538_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intron_Brd4_chr17_32250538_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Gm20646|Pou3f3_chr1_42696928_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Gm20646|Pou3f3_chr1_42696928_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Zfp609|Trip4_chr9_65827692_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Zfp609|Trip4_chr9_65827692_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm3_exon_Necab2_chr8_119446956_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm3_exon_Necab2_chr8_119446956_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Gm11746|Slc24a3_chr2_145167691_F | TCGTCGGCAGCGTCTCCTCTCGCCGGTCCTTC | 60.7 | 0.01 |
| mm4_intergenic_Gm11746|Slc24a3_chr2_145167691_R | GTCTCGTGGGCTCGGGGGGTCCCTCTCCTGCTC | 60.7 | 0.01 |
| mm4_exon_Homer3_chr8_70283049_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_exon_Homer3_chr8_70283049_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_exon_Kdm5b_chr1_134560325_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_exon_Kdm5b_chr1_134560325_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Nr1d1|Msl1_chr11_98795432_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Nr1d1|Msl1_chr11_98795432_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_exon_Tbc1d4_chr14_101608149_F | TCGTCGGCAGCGTCTGCTCGAAGATGAACACCCC | 60.0 | 0.00 |
| mm4_exon_Tbc1d4_chr14_101608149_R | GTCTCGTGGGCTCGGGAGGTGATCCTGGTGCTCAG | 59.8 | 0.00 |
| mm4_exon_Hipk2_chr6_38876020_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_exon_Hipk2_chr6_38876020_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intergenic_Zfp853|E130309D02Rik_chr5_143293438_F | TCGTCGGCAGCGTCCCGGCACAGGAAGTCCCC | 62.4 | 0.00 |
| mm4_intergenic_Zfp853|E130309D02Rik_chr5_143293438_R | GTCTCGTGGGCTCGGCGCGGCCTAGAGAGACTATG | 59.4 | 0.00 |
| mm4_exon_Tsc22d1_chr14_76415295_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_exon_Tsc22d1_chr14_76415295_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_exon_Gm8770_chrX_78785864_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_exon_Gm8770_chrX_78785864_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_exon_Cdc34_chr10_79682266_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_exon_Cdc34_chr10_79682266_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intron_Eif5a2_chr3_28781427_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intron_Eif5a2_chr3_28781427_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intron_Wdr20a_chr12_110738493_F | TCGTCGGCAGCGTCGGGGCTTCGGGAGTGAGG | 61.7 | 0.00 |
| mm4_intron_Wdr20a_chr12_110738493_R | GTCTCGTGGGCTCGGGATCGGAACCTGACAGACCC | 59.8 | 0.00 |
| mm4_intergenic_Ccny|Gm22765_chr18_9450166_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intergenic_Ccny|Gm22765_chr18_9450166_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_exon_Pcsk1n_chrX_7919802_F | TCGTCGGCAGCGTCACAGTAGGAGACAGTGGGGC | 60.9 | 0.00 |
| mm4_exon_Pcsk1n_chrX_7919802_R | GTCTCGTGGGCTCGGGGGTATTAGGCACAGCAGCA | 60.1 | 0.00 |
| mm4_intergenic_BC052040|Meis2_chr2_115859177_F | TCGTCGGCAGCGTCAGCAAATGCATTCACAGGCA | 59.0 | 0.00 |
| mm4_intergenic_BC052040|Meis2_chr2_115859177_R | GTCTCGTGGGCTCGGTCCCCTCCTCTATCCACCAA | 58.9 | 0.00 |
| mm4_exon_Cdk4_chr10_127063539_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_exon_Cdk4_chr10_127063539_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_exon_Inhbb_chr1_119420949_F | TCGTCGGCAGCGTCGCACGACGTACAGGTGTCC | 60.7 | 0.00 |
| mm4_exon_Inhbb_chr1_119420949_R | GTCTCGTGGGCTCGGCTGCCTTCTGCTCCTGGTG | 60.3 | 0.00 |
| mm3_intron_Sh3bp4_chr1_89070772_F | TCGTCGGCAGCGTCTTCCCTGCCCTCTGTGGT | 60.1 | 0.00 |
| mm3_intron_Sh3bp4_chr1_89070772_R | GTCTCGTGGGCTCGGCGCTCTCTTCGCTCCTTCTC | 60.2 | 0.00 |
| mm4_intron_Rab31_chr17_65729984_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intron_Rab31_chr17_65729984_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intron_Rcc2_chr4_140701920_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intron_Rcc2_chr4_140701920_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intron_Rala_chr13_17943813_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intron_Rala_chr13_17943813_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intron_1810013L24Rik_chr16_8830747_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intron_1810013L24Rik_chr16_8830747_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intergenic_Usp15|Usp15/AC158802.1_chr10_123196795_F | TCGTCGGCAGCGTCGACCTGTCCGCACCTGTC | 60.0 | 0.00 |
| mm4_intergenic_Usp15|Usp15/AC158802.1_chr10_123196795_R | GTCTCGTGGGCTCGGTCAAAACCTCGCTCCGGAAA | 59.8 | 0.00 |
| mm4_intergenic_Nfkbiz|Nxpe3_chr16_55838909_F | TCGTCGGCAGCGTCAAAAGACACCGACCCGAGTC | 59.9 | 0.00 |
| mm4_intergenic_Nfkbiz|Nxpe3_chr16_55838909_R | GTCTCGTGGGCTCGGATCCCCTAGATTCCCGGGAC | 60.1 | 0.00 |
| mm4_intergenic_Hdac5|Hdac5/mmu-mir-8101_chr11_102229900_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intergenic_Hdac5|Hdac5/mmu-mir-8101_chr11_102229900_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intergenic_Gsc2|Slc25a1_chr16_17915158_F | TCGTCGGCAGCGTCCGCCAGTCCTCAGAGAGCTA | 60.7 | 0.00 |
| mm4_intergenic_Gsc2|Slc25a1_chr16_17915158_R | GTCTCGTGGGCTCGGCAGCTCTAGACGTGGCAGAG | 59.9 | 0.00 |
| mm4_intergenic_Gm8935|Gm2464_chr3_13471605_F | TCGTCGGCAGCGTCCCGCAGCATCAGCACCAG | 61.5 | 0.00 |
| mm4_intergenic_Gm8935|Gm2464_chr3_13471605_R | GTCTCGTGGGCTCGGCACACGCACACGCAGACG | 62.3 | 0.00 |
| mm4_exon_Speg_chr1_75421992_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_exon_Speg_chr1_75421992_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_exon_Macrod2_chr2_140395402_F | TCGTCGGCAGCGTCCCCTGAGGCTGAAGTAGGGG | 61.3 | 0.00 |
| mm4_exon_Macrod2_chr2_140395402_R | GTCTCGTGGGCTCGGGCCTCGCGCTAACCTAACA | 60.1 | 0.00 |
| mm4_exon_Brd3_chr2_27475363_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_exon_Brd3_chr2_27475363_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_exon_Bag5_chr12_111713156_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_exon_Bag5_chr12_111713156_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm3_intron_Il17d_chr14_57525158_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm3_intron_Il17d_chr14_57525158_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm3_intron_Ephx4_chr5_107403457_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm3_intron_Ephx4_chr5_107403457_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_Zfp91|Lpxn_chr19_12796142 |
CGTTGCCGGATGAAAGTCTCTGAAAAAATGGCGGCGATAGGATAGAGGCGGGGCCGAGGGGACAGCGCGGGATAGTCGTG AGGCGCACGCGCAGGGCCAACTTCGCCGAGGGCACTCTGGGAGACGTAGTC |
| mm4_intron_Pafah1b2_chr9_45984531 |
CTGGCCAGGGTGGAACCAGGGCGCCGCAGGGCAGCGGCGACGGCGCGGGGCCCCGGAGGCCCTGCAGGGCGACANNNNNN NNNNNNNNNNNNNNNNNNNNNNNTGGGGGAGGGGAGCCGGGCCTCACAATAC |
| mm4_intergenic_Gm25748|Creb1_chr1_64532412 |
TTCCCAGCAAAGAACCAGCTCCGGCCCGGCAGACTCCCCTGGCCGGTAGCCGGCGTCTCCAACCTTCCAGCGCCGTCCGC GCGGCTCTGGGCCCTCGCGGCGCGTCAAAGTTCCCGGGCGG |
| mm4_intron_Adnp2_chr18_80151324 |
GACAGCGCTAGGGACGTCGGGGCGGACCCAGGAGTGGACGGCGGGTGGGTCGCGGGGAGGGTCGGGGGGTCGGCGCAGGC CTGGCGGGCGTACCTAC |
| mm4_exon_2410012M07Rik_chr9_98865019 |
CCACAGAGCCGTCCATCATGCTGCGCACCAGGCCCCGCAGCCCCAGCGCCGACCCCGCGCCCTGCTGGTCACCGCAGACA CCAG |
| mm4_exon_Timp2_chr11_118355209 |
CGCGCAAACTTTCTGTCCTCTTTGTCAAGGGGCGCAGCGGCGAGGGGACGGCGCAGGGCAGTGCACCCGGCGGAGAAGAA AGAGGCTGGGGGGCGGCGAGCGAGCGCAGCCCGGCTCGGCTCCTCCGCTGCCTTCTATG |
| mm3_exon_Zfp523_chr17_28177446 |
CCCTGGAACCTGGATATCGCGCGAGGCAAGCCGCGCGCGGGCGGGCTATGGCGCAGGCGGGTTGCGGGGCCGGCGCTGGT GGCAGGGCCCGGTGCATGGTGGTCTGT |
| mm3_intron_Psmd11_chr11_80428764 |
CGACATCCTCCACTCCATCGGTAAAGGGCCTGGCGCCGTCCCCGCGGCTCCGCCGTCCCGGCGCGGCCTGTGTGGGTCGG AGGCGGCGGAGAGGGGCCGGGCTAGCCGGCTATGGTGCTGCTGACTCA |
| mm3_intergenic_Gm9755|Nat3_chr8_67523120 |
AGCACGCAGATTCCAGACAACTCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNGTGGGGGAGGAAACAGCTCAAAAG |
| mm4_intron_Snx6_chr12_54795579 |
AAGAGAGACATTAGCGCCCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGTTCGGCGCCGCCGTG AACACCCACCATCATGGCTGCTTCGAGTCC |
| mm3_exon_Ift57_chr16_49699391 |
GCTTGGACGATGGGGTGTCTCGGGCTCGCGGGGAAGGCGCAGGGGAGGCTGTGGTGGAGCGCGGGCCAGGAGCGGCCTAC CACATGTT |
| mm3_intergenic_1700128E19Rik|Arhgef7_chr8_11727861 |
CCGCCCTACCCACAAAGGCGCGCAGCCCCGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCGCGTCTTTCTTCTCCGGTGA |
| mm4_intron_Slc2a1_chr4_119109248 |
GCTAAAAGAGCCGAGCCCCCGGCCGGGCCCCGGCTAGGAGCGGAGGAGGCGGGACCCGCCCGGAGCCCGCGCCGCGCCCG GAACCCGGGCCATGGGGGTGGCCAGGAGGAGAAGGCACTTC |
| mm4_exon_Gtpbp3_chr8_71489250 |
GGTCCAGCTAGCGGGCTCGCGCTCCGCAGCCTCACGGCGCTCCAGGAGCCGCCTCCTGCCCGCAGAGCCTGCCTGCGCCT TCTCCGCCACCCGTGCTCCGGGGAGCCACTGGACCGCTCACTCGTCCTCTGGTTC |
| mm4_exon_Npnt_chr3_132950052 |
CTGCAGGTAGAGCGAGGACGCGAGCACCGCCGCTAGGAGCACAGCCATGCCGGAGGACCGGGACGCGGGGACGCTGAAGG TTGCGGGGAGCTGCGCGTCCCGGGATCTCCCGGCCGCCTTC |
| mm3_intergenic_Chd6|Gm14243_chr2_161109342 |
CTAGATCTCCCCGCCTTGCAGACAGCGCAGCTCCCGGCCCGCCCCCCCGGAATGAAGCGGCCGGGCCGCGNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTGCGCTCTGTTTTGCAAGC |
| mm4_exon_Map2k7_chr8_4240713 |
TGTGATCACTCTAAGCCCTGCTCCTGCCCCGTCCCAGCGAGCAGGTACCAGCCTTTTTATCATTGCTGCTTGCATATCTG CACATTGACCTAACCGCT |
| mm4_exon_Gnas/Gm20721_chr2_174330246 |
CTTGCCTTAGTCCGAGCCGCCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGGGCTGCCTCGGCAACAGTAAGACCG |
| mm4_intergenic_4933405D12Rik|1810037I17Rik_chr3_122924314 |
CTAGAAAGGGAGGACGCCTGCGCAGTCCGGAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCGC CTAGTCGATTGGCGGGGTTACCCGGAATTGGTTGCTAGACTGGGCG |
| mm4_exon_Aspscr1_chr11_120673356 |
GTCCGCCCCATCCTCTAGATCTGGGTCCCGGGGGCGGGGCGGGATACTTGGAGGCGCGTTTGCTGAGCACGGTGGGGTGG ACCCCACTAACAGGGTCGAGCCTTGCGAGCCCCAGAATCTTCGGCGCTTGTC |
| mm4_exon_Rela_chr19_5637808 |
CTTTACTTTAGCGCGCCGTGGGCTCAGCTGCGACCCCGGCCCCGCCCCCGGGACCCTGACCATGGACGGTGAGGCTGCCC TCTGGCTCGGGGGATGGCTGCCCTAGAGCTC |
| mm4_exon_Ppp2r3d_chr9_124422716 |
CCCACATACCTTGGCAACCACGGCCATGTCGCCCAGACCCGCCCTCCCACGAGGCAGCCCCTCGAACGCGCACTCCACGA GGGCGATGGCATCCTCCGTGTCCTGGGGACGGGGCGGGGGTCGACCGCAAGGGAAGTAG |
| mm4_intron_Vrk1_chr12_106010517 |
GGAAGCCCGGTTCTAGAAGGCCGCCCGAAGCCTAGCCGGGACCAGGGTGGNNNNNNNNNNNNNNNNNNNNNNNNNCTGGA CCGGCCGAGCCTGCCACTTCCTTAGCACTGG |
| mm4_intron_Hrasls_chr16_29209999 |
GCAAGGAGAATCCGGGGATCCCATGCCTGAGGCGTGCTTGGAGGATTTGGGTGGCGGGGAGGGCGCGGGTCTGGGCCGAG CTCCAAAGACCAGGGGTA |
| mm4_exon_Fbxl3_chr14_103099195 |
GAACCTCCGCCGTACCTGCTGCCGGGGGCGGCTTCCCCCACACAGCACCCCGGGCCGCGCGGANNNNNNNNNNNNNNNNN NNNNNNNNTCCCGCGCCTCTCACATGAGGCCTCCC |
| mm4_exon_Dbp_chr7_45706907 |
GGACCTGGACGCCTTCTTGCTGGAGCACGGGCTACCGCCGANNNNNNNNNNNNNNNNNNNNNTGTCGCCGGCACCCTCTC CAGCGCGCACTCCCGCGCCCTCCCCCGGGCCCGGCTCTTGCAGCTCCTCTTCCC |
| mm4_exon_Gm10657/Cd276_chr9_58555037 |
ACAAAGGTGGACCCAGCAGCCCACGCCGCCCCGCGCCACGCAAGCACTCACCGCGCCGCGCCGACTCCCGGGACTCGGGG ACGCGGCGGGGCGCAGCCCAATCGCCGCCACTGTTG |
| mm4_exon_Zer1_chr2_30124393 |
AGGAGGTCGGATCCGGTCCGGGTCCGGGTCNNNNNNNNNNNNNNNNNNNNNNNNNNAATGCTGCGACCGGAGCCCCGGAC GGAGGCCGTTCCCTTGCCCTCGG |
| mm4_exon_Tmem127_chr2_127248584 | CATGTATGCCCCTGGAGGTGCCGGGCTGCCGGGAGGGCGCCGGCGGAGAAGCCCGGGAAGCAGCGCTCTTCCCAAG |
| mm4_intergenic_Gm11746|Slc24a3_chr2_145167691 |
TCCTCTCGCCGGTCCTTCCCCGCTCCTCCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNC CAGGCCGAACGCGGGCGCGGAGCGTGGGAGCCATGGCGCGCGAGCAGGAGAGGGACCCC |
| mm4_exon_Tbc1d4_chr14_101608149 |
TGCTCGAAGATGAACACCCCGGTGTTGGGCTGCACAGCCCCGGAGCCTGCGCCCCCGCCGACCCCGGCACCCGGCGCAGG GACACAACGCAGAAAGGGGGCGCTGAGCACCAGGATCACCTC |
| mm4_intergenic_Zfp853|E130309D02Rik_chr5_143293438 |
CCGGCACAGGAAGTCCCCCCGGCATCCGCATCCTGTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNTAAGCCATAGTCTCTCTAGGCCGCG |
| mm4_intron_Wdr20a_chr12_110738493 |
GGGGCTTCGGGAGTGAGGCGCCGGCGGCAGCGCTGCCTCCTAGGGGAGGAGGGGGCTCTGGAGCCGGGTCGCGGAGATGC CCCGGGAGTAGCCGGTCGCCTCCTCCCCCGGCGGGGTCTGTCAGGTTCCGATC |
| mm4_exon_Pcsk1n_chrX_7919802 |
ACAGTAGGAGACAGTGGGGCGGGAGTGGGGGGGACGGGGACGCGGGGAGGGGGCAGGCTCCTGGATGTGCGCAGCCGCAG AGCGCTGCTGCTGTGCCTAATACCC |
| mm4_intergenic_BC052040|Meis2_chr2_115859177 |
AGCAAATGCATTCACAGGCAAAATTGCATCCTCTGTGAACGAAACAAACCTAGGTCTATTTTGTTACTTTATTCCCGGGT CTTGGGGAGGGGGCGGGGTGTACAGAATCCATTGGTGGATAGAGGAGGGGA |
| mm4_exon_Inhbb_chr1_119420949 |
GCACGACGTACAGGTGTCCTGCGAGCCACCCGGAGCTCCGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNAGAGCCCCAGGCCTCGGGTCCCAACCAGCCGGCCACCAGGAGCAGAAGGCAG |
| mm3_intron_Sh3bp4_chr1_89070772 |
TTCCCTGCCCTCTGTGGTCACAGCCCGACCTGGGCTGCGGATCGTGGTCGCTANNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNTTCTGAGAAGGAGCGAAGAGAGCG |
| mm4_intergenic_Usp15|Usp15/AC158802.1_chr10_123196795 |
GACCTGTCCGCACCTGTCACCAGCCGGCGACACCAGCCCACCGCTCCCGCCCAGCTCTCCGCCAGCCTNNNNNNNNNNNN NNNNNNNNNACCCCGTTCCCTACCAGGTGTCCCCTTTCCGGAGCGAGGTTTTGA |
| mm4_intergenic_Nfkbiz|Nxpe3_chr16_55838909 |
AAAAGACACCGACCCGAGTCCCGGACATTCCCCGCCAGGGCGGTCCCCAAGACCCGGACTGGAGCCGCGCGGAGGACTGA GGCCCCGCAGAGCTGTTTTCAGGACTCCTGTCCCAGTGTCCCGGGAATCTAGGGGAT |
| mm4_intergenic_Gsc2|Slc25a1_chr16_17915158 |
CGCCAGTCCTCAGAGAGCTAATCCCCGGCCATGGAGGAGGGCAAGCCCCTTCGTCTGGGTACCGGGGACTGCGCTGGGAG CAGGGAGTCCTGCACTCTGCCACGTCTAGAGCTG |
| mm4_intergenic_Gm8935|Gm2464_chr3_13471605 |
CCGCAGCATCAGCACCAGCGGCAGTACCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCGCCTC CGGCCCGCCCCGCGCGGTCCCCGCTAGCCCGCGCCCTGCCCGTCTGCGTGTGCGTGTG |
| mm4_exon_Macrod2_chr2_140395402 |
CCCTGAGGCTGAAGTAGGGGCGCGCCTTGGCTAGAGCCGGGAGAGCGGCGGGCGGAGCAGCCAATGGGCGGCGGCGCTGC CTGGCTGCCGGGAGGCGGGGCCTGCGCGGGTGTTAGGTTAGCGCGAGGC |