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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_52314223_F | TCGTCGGCAGCGTCACCTAGTAGCTCAGACACCGA | 59.7 | 1.00 |
| ontarget_mm0_exon_5730457N03Rik/Evx1_chr6_52314223_R | GTCTCGTGGGCTCGGACCTTTGCTGTGCTGGTACT | 59.5 | 1.00 |
| mm3_intron_Lrp2_chr2_69430814_F | Primer3: not found at this Tm | N.d. | 0.41 |
| mm3_intron_Lrp2_chr2_69430814_R | Primer3: not found at this Tm | N.d. | 0.41 |
| mm4_intergenic_Clnk|Gm25505_chr5_38941308_F | Primer3: not found at this Tm | N.d. | 0.41 |
| mm4_intergenic_Clnk|Gm25505_chr5_38941308_R | Primer3: not found at this Tm | N.d. | 0.41 |
| mm4_intergenic_Galnt14|Ehd3_chr17_73739940_F | Primer3: not found at this Tm | N.d. | 0.40 |
| mm4_intergenic_Galnt14|Ehd3_chr17_73739940_R | Primer3: not found at this Tm | N.d. | 0.40 |
| mm4_intron_Gm15685_chr6_144495487_F | Primer3: not found at this Tm | N.d. | 0.37 |
| mm4_intron_Gm15685_chr6_144495487_R | Primer3: not found at this Tm | N.d. | 0.37 |
| mm4_intergenic_Gm25041|Gm25853_chr16_53900981_F | Primer3: not found at this Tm | N.d. | 0.32 |
| mm4_intergenic_Gm25041|Gm25853_chr16_53900981_R | Primer3: not found at this Tm | N.d. | 0.32 |
| mm4_exon_Pi4ka_chr16_17282703_F | Primer3: not found at this Tm | N.d. | 0.27 |
| mm4_exon_Pi4ka_chr16_17282703_R | Primer3: not found at this Tm | N.d. | 0.27 |
| mm4_intron_Rbm27_chr18_42330483_F | Primer3: not found at this Tm | N.d. | 0.27 |
| mm4_intron_Rbm27_chr18_42330483_R | Primer3: not found at this Tm | N.d. | 0.27 |
| mm3_intergenic_Ndst2|Camk2g_chr14_20734552_F | Primer3: not found at this Tm | N.d. | 0.25 |
| mm3_intergenic_Ndst2|Camk2g_chr14_20734552_R | Primer3: not found at this Tm | N.d. | 0.25 |
| mm4_intergenic_Arhgef4/Fam168b|Fam168b_chr1_34817472_F | TCGTCGGCAGCGTCCTGCACAGCTCCATCCTCAA | 60.0 | 0.24 |
| mm4_intergenic_Arhgef4/Fam168b|Fam168b_chr1_34817472_R | GTCTCGTGGGCTCGGAGGGTGTTGCTGTAAGGTGG | 59.8 | 0.24 |
| mm4_intergenic_Gm12442|E130309F12Rik_chr4_49039152_F | Primer3: not found at this Tm | N.d. | 0.23 |
| mm4_intergenic_Gm12442|E130309F12Rik_chr4_49039152_R | Primer3: not found at this Tm | N.d. | 0.23 |
| mm4_intergenic_Gria4|Gm24896_chr9_5068265_F | Primer3: not found at this Tm | N.d. | 0.22 |
| mm4_intergenic_Gria4|Gm24896_chr9_5068265_R | Primer3: not found at this Tm | N.d. | 0.22 |
| mm4_intron_Poc1a_chr9_106302709_F | TCGTCGGCAGCGTCGGCCTGCACTTGACAAACAG | 59.9 | 0.19 |
| mm4_intron_Poc1a_chr9_106302709_R | GTCTCGTGGGCTCGGTGTTAGCTTGTCCAGAGCCC | 59.6 | 0.19 |
| mm4_intergenic_Gm5763|Tmem164_chrX_142661969_F | Primer3: not found at this Tm | N.d. | 0.15 |
| mm4_intergenic_Gm5763|Tmem164_chrX_142661969_R | Primer3: not found at this Tm | N.d. | 0.15 |
| mm3_intergenic_Gm22062|Gm15224_chrX_165864396_F | Primer3: not found at this Tm | N.d. | 0.15 |
| mm3_intergenic_Gm22062|Gm15224_chrX_165864396_R | Primer3: not found at this Tm | N.d. | 0.15 |
| mm4_intergenic_Olfr57|2610008E11Rik_chr10_79039130_F | Primer3: not found at this Tm | N.d. | 0.14 |
| mm4_intergenic_Olfr57|2610008E11Rik_chr10_79039130_R | Primer3: not found at this Tm | N.d. | 0.14 |
| mm4_intergenic_Gm22145|Tln2_chr9_67159669_F | TCGTCGGCAGCGTCCTTTGTGTGAGCTGCTCCCA | 60.5 | 0.14 |
| mm4_intergenic_Gm22145|Tln2_chr9_67159669_R | GTCTCGTGGGCTCGGTGATTGATGTTGGCCCCTGG | 60.3 | 0.14 |
| mm3_intergenic_AI846148|Rab11b-ps2_chr19_7392955_F | Primer3: not found at this Tm | N.d. | 0.13 |
| mm3_intergenic_AI846148|Rab11b-ps2_chr19_7392955_R | Primer3: not found at this Tm | N.d. | 0.13 |
| mm4_intergenic_Gm8577|Gm16390_chrX_154788079_F | Primer3: not found at this Tm | N.d. | 0.12 |
| mm4_intergenic_Gm8577|Gm16390_chrX_154788079_R | Primer3: not found at this Tm | N.d. | 0.12 |
| mm4_exon_Zfp92_chrX_73422466_F | Primer3: not found at this Tm | N.d. | 0.12 |
| mm4_exon_Zfp92_chrX_73422466_R | Primer3: not found at this Tm | N.d. | 0.12 |
| mm4_intergenic_St3gal6|Gm813_chr16_58551215_F | Primer3: not found at this Tm | N.d. | 0.11 |
| mm4_intergenic_St3gal6|Gm813_chr16_58551215_R | Primer3: not found at this Tm | N.d. | 0.11 |
| mm4_intergenic_Gm9041|Gm26917_chr17_39746447_F | Primer3: not found at this Tm | N.d. | 0.11 |
| mm4_intergenic_Gm9041|Gm26917_chr17_39746447_R | Primer3: not found at this Tm | N.d. | 0.11 |
| mm4_intergenic_Cbln2|Gm5096_chr18_87505215_F | Primer3: not found at this Tm | N.d. | 0.11 |
| mm4_intergenic_Cbln2|Gm5096_chr18_87505215_R | Primer3: not found at this Tm | N.d. | 0.11 |
| mm4_intron_Nfatc2_chr2_168554510_F | TCGTCGGCAGCGTCAATGCCACCACCAACCAGAA | 60.1 | 0.11 |
| mm4_intron_Nfatc2_chr2_168554510_R | GTCTCGTGGGCTCGGGACAGGATCCCGCATAAGCA | 59.8 | 0.11 |
| mm4_intergenic_Gm11931|Gabrr2_chr4_33055913_F | Primer3: not found at this Tm | N.d. | 0.10 |
| mm4_intergenic_Gm11931|Gabrr2_chr4_33055913_R | Primer3: not found at this Tm | N.d. | 0.10 |
| mm3_exon_Kdm6b_chr11_69405457_F | Primer3: not found at this Tm | N.d. | 0.10 |
| mm3_exon_Kdm6b_chr11_69405457_R | Primer3: not found at this Tm | N.d. | 0.10 |
| mm3_intergenic_Gm12210|Gm11187_chr11_52509407_F | Primer3: not found at this Tm | N.d. | 0.10 |
| mm3_intergenic_Gm12210|Gm11187_chr11_52509407_R | Primer3: not found at this Tm | N.d. | 0.10 |
| mm4_intron_Akap6_chr12_53138961_F | Primer3: not found at this Tm | N.d. | 0.10 |
| mm4_intron_Akap6_chr12_53138961_R | Primer3: not found at this Tm | N.d. | 0.10 |
| mm4_exon_Gm11634_chr11_101595447_F | Primer3: not found at this Tm | N.d. | 0.09 |
| mm4_exon_Gm11634_chr11_101595447_R | Primer3: not found at this Tm | N.d. | 0.09 |
| mm4_intergenic_Ccdc53|Dram1_chr10_88279490_F | Primer3: not found at this Tm | N.d. | 0.09 |
| mm4_intergenic_Ccdc53|Dram1_chr10_88279490_R | Primer3: not found at this Tm | N.d. | 0.09 |
| mm4_intergenic_Cntn5|Gm25365_chr9_12626740_F | Primer3: not found at this Tm | N.d. | 0.09 |
| mm4_intergenic_Cntn5|Gm25365_chr9_12626740_R | Primer3: not found at this Tm | N.d. | 0.09 |
| mm3_intron_Mael_chr1_166212938_F | Primer3: not found at this Tm | N.d. | 0.08 |
| mm3_intron_Mael_chr1_166212938_R | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_intron_Supt3_chr17_44926949_F | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_intron_Supt3_chr17_44926949_R | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_intergenic_Zscan4d|Gm26248_chr7_11238518_F | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_intergenic_Zscan4d|Gm26248_chr7_11238518_R | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_intron_Mastl_chr2_23125593_F | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_intron_Mastl_chr2_23125593_R | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_intron_4930448K12Rik_chr1_61844543_F | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_intron_4930448K12Rik_chr1_61844543_R | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_intergenic_Snx16|Gm22795_chr3_10851669_F | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_intergenic_Snx16|Gm22795_chr3_10851669_R | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_intergenic_Man1a2|Gm23465_chr3_100685980_F | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_intergenic_Man1a2|Gm23465_chr3_100685980_R | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_exon_Coq6_chr12_84370799_F | TCGTCGGCAGCGTCGGCTCTGCTTGAATACGGCT | 60.4 | 0.08 |
| mm4_exon_Coq6_chr12_84370799_R | GTCTCGTGGGCTCGGTCAAACTGCTCAGCCTGTCC | 60.2 | 0.08 |
| mm4_intergenic_Olfr984|Olfr985_chr9_40117660_F | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_intergenic_Olfr984|Olfr985_chr9_40117660_R | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_intergenic_Gm11358|Prl8a2_chr13_27342096_F | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_intergenic_Gm11358|Prl8a2_chr13_27342096_R | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_intergenic_Gm11499|Gm11500_chr11_92643378_F | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_intergenic_Gm11499|Gm11500_chr11_92643378_R | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_exon_Megf11_chr9_64501524_F | TCGTCGGCAGCGTCCCGCAACCGAAGTCTGAGTA | 59.7 | 0.08 |
| mm4_exon_Megf11_chr9_64501524_R | GTCTCGTGGGCTCGGCAGGGTTCAGAGCAAGAGCA | 59.9 | 0.08 |
| mm4_intergenic_Efcab6|Sult4a1_chr15_84074116_F | TCGTCGGCAGCGTCCACCTCTTGGGCTGTGAACA | 60.1 | 0.08 |
| mm4_intergenic_Efcab6|Sult4a1_chr15_84074116_R | GTCTCGTGGGCTCGGGTTCTGCCCATCCCCAAACT | 60.2 | 0.08 |
| mm4_intergenic_4933433F19Rik|Dusp26_chr8_30655209_F | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_intergenic_4933433F19Rik|Dusp26_chr8_30655209_R | Primer3: not found at this Tm | N.d. | 0.08 |
| mm4_intron_Dlg2_chr7_91735386_F | Primer3: not found at this Tm | N.d. | 0.07 |
| mm4_intron_Dlg2_chr7_91735386_R | Primer3: not found at this Tm | N.d. | 0.07 |
| mm4_intergenic_Pcdh18|Slc7a11_chr3_50361819_F | Primer3: not found at this Tm | N.d. | 0.07 |
| mm4_intergenic_Pcdh18|Slc7a11_chr3_50361819_R | Primer3: not found at this Tm | N.d. | 0.07 |
| mm3_intergenic_Nrg3|Gm10713_chr14_39868287_F | Primer3: not found at this Tm | N.d. | 0.07 |
| mm3_intergenic_Nrg3|Gm10713_chr14_39868287_R | Primer3: not found at this Tm | N.d. | 0.07 |
| mm4_intergenic_Ptk2b|1700001G11Rik_chr14_66291773_F | Primer3: not found at this Tm | N.d. | 0.07 |
| mm4_intergenic_Ptk2b|1700001G11Rik_chr14_66291773_R | Primer3: not found at this Tm | N.d. | 0.07 |
| mm4_intron_Lamp3_chr16_19689933_F | Primer3: not found at this Tm | N.d. | 0.07 |
| mm4_intron_Lamp3_chr16_19689933_R | Primer3: not found at this Tm | N.d. | 0.07 |
| mm4_exon_Adnp2_chr18_80129631_F | TCGTCGGCAGCGTCGGGGACAGTCTGGTTTGAGG | 59.9 | 0.07 |
| mm4_exon_Adnp2_chr18_80129631_R | GTCTCGTGGGCTCGGACAGCTCCTTCTCGAGGTCT | 59.9 | 0.07 |
| mm4_intergenic_Irx2|Irx4_chr13_72937830_F | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_intergenic_Irx2|Irx4_chr13_72937830_R | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_intron_Ptch1_chr13_63564603_F | TCGTCGGCAGCGTCTAGCCGAGTGCACAAGGAAG | 60.0 | 0.06 |
| mm4_intron_Ptch1_chr13_63564603_R | GTCTCGTGGGCTCGGGGGGAAGGCAAGCACCTAG | 60.0 | 0.06 |
| mm4_intergenic_Gm13026|Arhgef10l_chr4_140467395_F | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_intergenic_Gm13026|Arhgef10l_chr4_140467395_R | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_intergenic_Pcsk1|Gm4149/Mir682_chr13_75507562_F | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_intergenic_Pcsk1|Gm4149/Mir682_chr13_75507562_R | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_intron_1700092E19Rik_chr13_26309596_F | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_intron_1700092E19Rik_chr13_26309596_R | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_intergenic_n-R5s61|Gm15571_chr12_69025356_F | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_intergenic_n-R5s61|Gm15571_chr12_69025356_R | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_intergenic_Olfr1305|Olfr1306_chr2_111883406_F | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_intergenic_Olfr1305|Olfr1306_chr2_111883406_R | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_intergenic_Gm25670|Gm26255_chr14_110638136_F | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_intergenic_Gm25670|Gm26255_chr14_110638136_R | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_intergenic_Gm23892|Gm25382_chr10_15930692_F | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_intergenic_Gm23892|Gm25382_chr10_15930692_R | Primer3: not found at this Tm | N.d. | 0.06 |
| mm4_intergenic_Mirlet7b|Ppara_chr15_85709449_F | TCGTCGGCAGCGTCGGGTGGAGTCAGGATTCAAGG | 60.0 | 0.05 |
| mm4_intergenic_Mirlet7b|Ppara_chr15_85709449_R | GTCTCGTGGGCTCGGACAACCCCAGGAGTCACTTC | 59.2 | 0.05 |
| mm4_intergenic_Bri3|Nptx2_chr5_144480005_F | TCGTCGGCAGCGTCGCGCCGGAACAAAGTGAAAT | 60.0 | 0.05 |
| mm4_intergenic_Bri3|Nptx2_chr5_144480005_R | GTCTCGTGGGCTCGGCACTTGAAGTCACAGCCCCT | 59.8 | 0.05 |
| mm4_intron_Hrh1_chr6_114410664_F | TCGTCGGCAGCGTCGGGTGTATGCCCTTCAGAGG | 59.8 | 0.05 |
| mm4_intron_Hrh1_chr6_114410664_R | GTCTCGTGGGCTCGGCCTATCACAGCCGCACTCAT | 59.8 | 0.05 |
| mm4_intergenic_Arg1|Gm22566_chr10_25001015_F | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_intergenic_Arg1|Gm22566_chr10_25001015_R | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_intergenic_Gm25153|Bcar3_chr3_122473817_F | Primer3: not found at this Tm | N.d. | 0.05 |
| mm4_intergenic_Gm25153|Bcar3_chr3_122473817_R | Primer3: not found at this Tm | N.d. | 0.05 |
| mm3_intergenic_Gm1043|Crmp1_chr5_37194271_F | TCGTCGGCAGCGTCAGTGTCCTCCAAAGCCTGTG | 59.8 | 0.04 |
| mm3_intergenic_Gm1043|Crmp1_chr5_37194271_R | GTCTCGTGGGCTCGGTGAGGTGAAGGCATGTGCTT | 59.8 | 0.04 |
| mm4_intergenic_Zscan4c|Zscan4d_chr7_11090780_F | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_intergenic_Zscan4c|Zscan4d_chr7_11090780_R | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_intergenic_Vmn1r71|Zscan4b_chr7_10822179_F | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_intergenic_Vmn1r71|Zscan4b_chr7_10822179_R | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_intergenic_Cln3|Apobr_chr7_126584800_F | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_intergenic_Cln3|Apobr_chr7_126584800_R | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_intergenic_Gm22469|Gm23909_chr14_37266686_F | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_intergenic_Gm22469|Gm23909_chr14_37266686_R | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_exon_Pou4f1_chr14_104465690_F | TCGTCGGCAGCGTCAGGAACTCCCCAAATGCAGG | 59.9 | 0.04 |
| mm4_exon_Pou4f1_chr14_104465690_R | GTCTCGTGGGCTCGGTGCCACTTACTGAGGAGGGT | 60.1 | 0.04 |
| mm4_intergenic_Gm12053|Gm12054_chr11_22633214_F | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_intergenic_Gm12053|Gm12054_chr11_22633214_R | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_intron_Sept6_chrX_36976648_F | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_intron_Sept6_chrX_36976648_R | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_exon_Aebp1_chr11_5869519_F | TCGTCGGCAGCGTCTATGCCAGGAGTACCGCGAT | 60.8 | 0.04 |
| mm4_exon_Aebp1_chr11_5869519_R | GTCTCGTGGGCTCGGATAGCCATCAGGGTTCAGCG | 59.8 | 0.04 |
| mm3_intron_Spsb1_chr4_149921838_F | Primer3: not found at this Tm | N.d. | 0.04 |
| mm3_intron_Spsb1_chr4_149921838_R | Primer3: not found at this Tm | N.d. | 0.04 |
| mm4_intergenic_Gm15461|Mapre3_chr5_30850355_F | TCGTCGGCAGCGTCCCTGTGCAGTCTAATGGCCA | 60.0 | 0.03 |
| mm4_intergenic_Gm15461|Mapre3_chr5_30850355_R | GTCTCGTGGGCTCGGTGCCAACAAAGGAGAGGAGG | 59.5 | 0.03 |
| mm4_intron_Pdxk_chr10_78444766_F | TCGTCGGCAGCGTCGGGTGGGTGAGTCTGCTTAT | 59.0 | 0.03 |
| mm4_intron_Pdxk_chr10_78444766_R | GTCTCGTGGGCTCGGCCCCAGGAGAGTCAGACAGA | 59.9 | 0.03 |
| mm4_intron_Trpc7_chr13_56806042_F | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_intron_Trpc7_chr13_56806042_R | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_intergenic_Gm23891|1700018B24Rik_chr3_47764128_F | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_intergenic_Gm23891|1700018B24Rik_chr3_47764128_R | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_intron_Zfp219_chr14_52014197_F | TCGTCGGCAGCGTCCACCTCCACTGTGCTCACG | 60.6 | 0.03 |
| mm4_intron_Zfp219_chr14_52014197_R | GTCTCGTGGGCTCGGGGCTTTGTAGGGACCGTGAG | 60.3 | 0.03 |
| mm4_exon_Repin1_chr6_48597490_F | TCGTCGGCAGCGTCGTGGCAAGAACTTCGGCAAG | 60.0 | 0.03 |
| mm4_exon_Repin1_chr6_48597490_R | GTCTCGTGGGCTCGGTGGCTGCCCTGTGAGAAAC | 60.2 | 0.03 |
| mm4_intron_Fam170b_chr14_32834514_F | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_intron_Fam170b_chr14_32834514_R | Primer3: not found at this Tm | N.d. | 0.03 |
| mm4_intergenic_Anxa9|Gm10691_chr3_95307592_F | TCGTCGGCAGCGTCAATGCAGGTCAGACAGGCTC | 60.0 | 0.03 |
| mm4_intergenic_Anxa9|Gm10691_chr3_95307592_R | GTCTCGTGGGCTCGGTCACTGGAGCTTATGGGCCA | 60.9 | 0.03 |
| mm4_intergenic_Gm11493|Akap1_chr11_88804416_F | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_intergenic_Gm11493|Akap1_chr11_88804416_R | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_intergenic_Gm22492|Pdcd6ip_chr9_113646371_F | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_intergenic_Gm22492|Pdcd6ip_chr9_113646371_R | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_intergenic_Samd5|Stxbp5_chr10_9675344_F | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_intergenic_Samd5|Stxbp5_chr10_9675344_R | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_intron_Lgr6_chr1_135057322_F | TCGTCGGCAGCGTCCTCCTGTCAGCTCTCCCTCT | 60.0 | 0.02 |
| mm4_intron_Lgr6_chr1_135057322_R | GTCTCGTGGGCTCGGGGAAGCAAACAGAGAGGGGA | 59.3 | 0.02 |
| mm4_intergenic_Dsg3|Dsg2_chr18_20553297_F | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_intergenic_Dsg3|Dsg2_chr18_20553297_R | Primer3: not found at this Tm | N.d. | 0.02 |
| mm4_exon_Ccdc151_chr9_21995248_F | TCGTCGGCAGCGTCTTGCTGTCTTGGACCTCTGC | 60.2 | 0.01 |
| mm4_exon_Ccdc151_chr9_21995248_R | GTCTCGTGGGCTCGGACACCAGGTAATACTGCGGC | 60.1 | 0.01 |
| mm4_intron_Asb18_chr1_89992165_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intron_Asb18_chr1_89992165_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Dio3|Ppp2r5c_chr12_110319737_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Dio3|Ppp2r5c_chr12_110319737_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Gm22084|Gm24502_chr5_75374730_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Gm22084|Gm24502_chr5_75374730_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Gm25864|Kat6b_chr14_21462726_F | TCGTCGGCAGCGTCCTTTGTCCACACAGCACTGC | 59.9 | 0.01 |
| mm4_intergenic_Gm25864|Kat6b_chr14_21462726_R | GTCTCGTGGGCTCGGCAGGACTCCTTCTGCAGACA | 59.0 | 0.01 |
| mm4_intergenic_Gm10156|Olfr472_chr7_107879092_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Gm10156|Olfr472_chr7_107879092_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_exon_Dazap1_chr10_80288148_F | TCGTCGGCAGCGTCTAAAGCAGGGTTCGGGTGTG | 60.2 | 0.01 |
| mm4_exon_Dazap1_chr10_80288148_R | GTCTCGTGGGCTCGGGCCGCTCAAAGCAAGGAATG | 60.4 | 0.01 |
| mm4_intron_Lrp5_chr19_3643574_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intron_Lrp5_chr19_3643574_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intron_Cdh3_chr8_106520473_F | TCGTCGGCAGCGTCCTGGTCAGAACGGACAGACA | 59.3 | 0.01 |
| mm4_intron_Cdh3_chr8_106520473_R | GTCTCGTGGGCTCGGCATTCGGAACAGCCAGGTCT | 60.0 | 0.01 |
| mm4_intergenic_Sptssb|Gm23484_chr3_69866409_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Sptssb|Gm23484_chr3_69866409_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intergenic_Muc5ac|Muc5b_chr7_141822683_F | TCGTCGGCAGCGTCTGTTTCTGCCATGTCTGGACT | 59.5 | 0.01 |
| mm4_intergenic_Muc5ac|Muc5b_chr7_141822683_R | GTCTCGTGGGCTCGGCACAGAGGAAACCCAGACCC | 59.9 | 0.01 |
| mm4_intergenic_E130102H24Rik|Gm12795_chr4_101356921_F | TCGTCGGCAGCGTCGAGACACAACTCCAGGCGAA | 59.9 | 0.01 |
| mm4_intergenic_E130102H24Rik|Gm12795_chr4_101356921_R | GTCTCGTGGGCTCGGCCTGATGATGGGAGGATGCT | 58.9 | 0.01 |
| mm4_intron_Igfbpl1_chr4_45816069_F | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intron_Igfbpl1_chr4_45816069_R | Primer3: not found at this Tm | N.d. | 0.01 |
| mm4_intron_Fbln5_chr12_101799956_F | TCGTCGGCAGCGTCGCTTGCCAGGCTAGAACACT | 60.3 | 0.00 |
| mm4_intron_Fbln5_chr12_101799956_R | GTCTCGTGGGCTCGGTGGCACTTGCACCTTCTCTG | 60.5 | 0.00 |
| mm4_intergenic_Gm24601|Gm26501_chr6_94916862_F | TCGTCGGCAGCGTCCACACAAAATTAGGACGCACCA | 59.7 | 0.00 |
| mm4_intergenic_Gm24601|Gm26501_chr6_94916862_R | GTCTCGTGGGCTCGGGGAATCGAACCCAGGGAAGG | 60.1 | 0.00 |
| mm4_intergenic_Bcl11b|Setd3_chr12_108031564_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intergenic_Bcl11b|Setd3_chr12_108031564_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intergenic_Ube2g2|Ube2g2/Sumo3_chr10_77622572_F | TCGTCGGCAGCGTCCGGATAAAAGGCCAGGCTGT | 60.3 | 0.00 |
| mm4_intergenic_Ube2g2|Ube2g2/Sumo3_chr10_77622572_R | GTCTCGTGGGCTCGGCACACAGGGGCTTAGGGAC | 59.7 | 0.00 |
| mm4_intergenic_Tlk2|Mrc2_chr11_105292238_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intergenic_Tlk2|Mrc2_chr11_105292238_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intergenic_Jazf1|Gm15572_chr6_52833301_F | TCGTCGGCAGCGTCGGGAACTTAGGGTGCAAGGG | 60.3 | 0.00 |
| mm4_intergenic_Jazf1|Gm15572_chr6_52833301_R | GTCTCGTGGGCTCGGAGGCAGAGTCGCTTCTTTCC | 60.0 | 0.00 |
| mm4_intron_Auh_chr13_52859530_F | TCGTCGGCAGCGTCGACCGTTCCCATGCTGAGAA | 60.0 | 0.00 |
| mm4_intron_Auh_chr13_52859530_R | GTCTCGTGGGCTCGGATCCTGGCTCGCTCTTCATG | 59.8 | 0.00 |
| mm4_intron_Susd1_chr4_59438084_F | TCGTCGGCAGCGTCCACTACACACCCCACAGTCC | 59.9 | 0.00 |
| mm4_intron_Susd1_chr4_59438084_R | GTCTCGTGGGCTCGGGAAGGATCATGGAGGCGGAG | 59.9 | 0.00 |
| mm4_intron_Add3_chr19_53243184_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intron_Add3_chr19_53243184_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intron_Gm12756_chr7_34672107_F | TCGTCGGCAGCGTCACTCTGGAATGTTGCTGCCA | 59.8 | 0.00 |
| mm4_intron_Gm12756_chr7_34672107_R | GTCTCGTGGGCTCGGCCTGCTCCTAAACAGAGGCC | 60.1 | 0.00 |
| mm4_intron_Camk2b_chr11_6002337_F | TCGTCGGCAGCGTCGCGAGTGTGCTGGACTAGTC | 60.4 | 0.00 |
| mm4_intron_Camk2b_chr11_6002337_R | GTCTCGTGGGCTCGGTGGGACCAGGGAGAAGGTAG | 59.9 | 0.00 |
| mm4_intron_1500017E21Rik_chr19_36633384_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intron_1500017E21Rik_chr19_36633384_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intergenic_Reep3|Jmjd1c_chr10_67101945_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intergenic_Reep3|Jmjd1c_chr10_67101945_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intergenic_Otos|Gpc1_chr1_92711818_F | TCGTCGGCAGCGTCGGCTTAGCCCATCCTCTCCT | 60.7 | 0.00 |
| mm4_intergenic_Otos|Gpc1_chr1_92711818_R | GTCTCGTGGGCTCGGTGGTCTCTGGGAGCCTCTAC | 60.0 | 0.00 |
| mm4_intergenic_Gm15849|Tmcc2_chr1_132383026_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intergenic_Gm15849|Tmcc2_chr1_132383026_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intergenic_Gm11691|Gm11692_chr11_114272100_F | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_intergenic_Gm11691|Gm11692_chr11_114272100_R | Primer3: not found at this Tm | N.d. | 0.00 |
| mm4_exon_Htr6_chr4_139074707_F | TCGTCGGCAGCGTCTCAGCACGATGACCACGC | 60.4 | 0.00 |
| mm4_exon_Htr6_chr4_139074707_R | GTCTCGTGGGCTCGGTCAACCCTAGTCCCCATGGT | 59.8 | 0.00 |
| mm4_exon_Bai2_chr4_130012545_F | TCGTCGGCAGCGTCGTCCATCCTGGCTTCCAACA | 59.9 | 0.00 |
| mm4_exon_Bai2_chr4_130012545_R | GTCTCGTGGGCTCGGCTTTAGGCCCCTTCCCACAC | 60.3 | 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_52314223 |
ACCTAGTAGCTCAGACACCGAATCGGATTTCTATGAAGAAATCGAGGTGAGCTGCACCCCAGACTGCGCCACCGGGAACG CCGAGTACCAGCACAGCAAAGGT |
| mm4_intergenic_Arhgef4/Fam168b|Fam168b_chr1_34817472 |
CTGCACAGCTCCATCCTCAAATCTGGGAAAGAATAACAACAGTCAGACAGGCTCTTGGCACTTGTGCTTTACCAGTTCCA GAAGGCAGCGGTACCCAAAGCTGCGCCACCTGGTTCCCACCCACCTTACAGCAACACCCT |
| mm4_intron_Poc1a_chr9_106302709 |
GGCCTGCACTTGACAAACAGAGGTGGCCACAATGGCCCGGTGATGCAGTCTGAGGAGCACAGGCTGCACTCAGCGCCAAG GCTGCTTCCTAGGGCTCTGGACAAGCTAACA |
| mm4_intergenic_Gm22145|Tln2_chr9_67159669 |
CTTTGTGTGAGCTGCTCCCACTGCCACCCTTCCTGTGGGCTCCAGGTGGCGCAGGGTGGGATGACAAACCTTAAAGTACA TGTCTTATCTTGCCTTGAACTGGCACCAGGGGCCAACATCAATCA |
| mm4_intron_Nfatc2_chr2_168554510 |
AATGCCACCACCAACCAGAAGGCTGTCCAGACTGCGCCTCCAGGGGACAGAGTGATGGAAACAGGACAGTTCTGCTTATG CGGGATCCTGTC |
| mm4_exon_Coq6_chr12_84370799 |
GGCTCTGCTTGAATACGGCTGTTGCTGGCACCTTTTGGTTCAGATAGCCACTTAGTCCTGTTGGCTCTGTCTGGGGTCCC ATTCTGTATGGTTTCCCTATGGGGGCTGTGAGTGGGACAGGCTGAGCAGTTTGA |
| mm4_exon_Megf11_chr9_64501524 |
CCGCAACCGAAGTCTGAGTAAGCCTGTCTTCTCTGTTCTCCCACACAGGCCCCGATGGCGCCGTCTGCGGTGGGCCTCCT TGTCTTCCTTCTGCAAGCTGCTCTTGCTCTGAACCCTG |
| mm4_intergenic_Efcab6|Sult4a1_chr15_84074116 |
CACCTCTTGGGCTGTGAACAAAACCACAAACTAAGCCCAAGCTGTGAGATGACAATCCCACTACAGCCACCAGGTGGCGC TGGCTGGCCTGCAGTTTGGGGATGGGCAGAAC |
| mm4_exon_Adnp2_chr18_80129631 |
GGGGACAGTCTGGTTTGAGGAAAGCAGCCCAGATGGCACCACCTGGCCTGCAGGGAGAACCCTCAAGGGCACTGTCTGGC CAGGAGGAAGACCTCGAGAAGGAGCTGT |
| mm4_intron_Ptch1_chr13_63564603 |
TAGCCGAGTGCACAAGGAAGAGGCCCAGGCCGGCGCCGGCGGGGGTCCTGGCTGGGCGCAGGCTGCTCTCCGGGCGGCGG AGCCCGGGGTGCTGGCCAGGGCCCCTGCGGGCCCCAGGCTAGGTGCTTGCCTTCCCC |
| mm4_intergenic_Mirlet7b|Ppara_chr15_85709449 |
GGGTGGAGTCAGGATTCAAGGGCACCCCAGATTGTGCCTCAGGGAAAGTACCCAGGAAGGTCCTGGTCCCTGGCCGGCCT TCTGCTGCCACCTGCTGGCTAATCTAAGAAGTGACTCCTGGGGTTGT |
| mm4_intergenic_Bri3|Nptx2_chr5_144480005 |
GCGCCGGAACAAAGTGAAATTCCAGGTGGCAGAGGGTGGGGTGCTGCCCCCTGCTTCCTGGAAGTGTGCTCATTGGTGAG ACTTGATAGGGGCTGTGACTTCAAGTG |
| mm4_intron_Hrh1_chr6_114410664 |
GGGTGTATGCCCTTCAGAGGGCGGTGACCTGGGAACTTAGCAGGAAGTAATGAAAGAGAGCCTGGTGGGACAGGCTGGGA TGCTCTGTGTAGAGAGATGAGTGCGGCTGTGATAGG |
| mm3_intergenic_Gm1043|Crmp1_chr5_37194271 |
AGTGTCCTCCAAAGCCTGTGGGGTGCCGAGTCCTGGTCCCATCCAGGGGTTGAGTGGGCACTGCAGACTGCTCCACCAGG TTCCCCAAAGGTAAGCACATGCCTTCACCTCA |
| mm4_exon_Pou4f1_chr14_104465690 |
AGGAACTCCCCAAATGCAGGCAGGATAACGGACAGTCTAAATGAGGGGAAGTGGGCCAGAGGGAGCCCCAGAAACGCACC CCTCAGCTCCCCAGTGTGCCCCACCCGGCGTCTCACACCCTCCTCAGTAAGTGGCA |
| mm4_exon_Aebp1_chr11_5869519 |
TATGCCAGGAGTACCGCGATGGGAACCCGAGAGTGCGCAACCTGGTGCAGGACACACGCATCCACCTGGTGCCCTCGCTG AACCCTGATGGCTAT |
| mm4_intergenic_Gm15461|Mapre3_chr5_30850355 |
CCTGTGCAGTCTAATGGCCATGCCATTACGTTCTGGTCAGATCATTAACTGGATGGCCGCCCTACTCCTGAACACCAGCC CCTCCCTTGGCTCCTCAGACTCCTCCACCTGGCCCAGCCTCCTCTCCTTTGTTGGCA |
| mm4_intron_Pdxk_chr10_78444766 |
GGGTGGGTGAGTCTGCTTATGTCCCCAGCACCCCATCCAGCCCCACCAGGCTCCACAGAGCCCTGTCCTGAGCCCGCCTT CTGTCTGTCTGACTCTCCTGGGG |
| mm4_intron_Zfp219_chr14_52014197 |
CACCTCCACTGTGCTCACGGCTCTCCCACCGCGCACCCCCAGGCCCCCTGCACCCCAGGCCGCGGCGCCCGGCCTCACGG TCCCTACAAAGCC |
| mm4_exon_Repin1_chr6_48597490 |
GTGGCAAGAACTTCGGCAAGAAGACGCACCTGGTGGCGCACTCACGCGTGCACTCCGGCGAACGTCCCTTCGCCTGCGAG GAGTGTGGTCGCCGTTTCTCACAGGGCAGCCA |
| mm4_intergenic_Anxa9|Gm10691_chr3_95307592 |
AATGCAGGTCAGACAGGCTCCAGGCTGATTTCAAGGTTGATAGAGAAGAACCTGTTGGGACACATACCATCAGGGCACCC CAGCCTGCACCCCACGGGGGGTCCTGGCCCATAAGCTCCAGTGA |
| mm4_intron_Lgr6_chr1_135057322 |
CTCCTGTCAGCTCTCCCTCTGCCTCATTCCTGCAGGCGCAGGCTGGGGTGATGAGCTTTCTCCCCTCTCTGTTTGCTTCC |
| mm4_exon_Ccdc151_chr9_21995248 |
TTGCTGTCTTGGACCTCTGCCATCTCCAGCTGGCGCAGGCTGTGCTGCAGCCTCAGGTCCTCCAGCCGTTTCTGCCGCAG TATTACCTGGTGT |
| mm4_intergenic_Gm25864|Kat6b_chr14_21462726 |
CTTTGTCCACACAGCACTGCCAGGTGTTGAGAGAATTGGCTGTGAGGGCTCACACAGCTCTGGGAGCCTTGCAAACAGGG AGGGGTGTCTGCACCCCAGACTGTGAGGCCAGGGAACTTGTCTGCAGAAGGAGTCCTG |
| mm4_exon_Dazap1_chr10_80288148 |
TAAAGCAGGGTTCGGGTGTGGGAAGCGGGAGCCCTGGCTCCCGCCGGCGCGGGCTGGGGTGCGGGCAGAGACTACTGCGT GCATTTGGTTTTTTGTTCATTCCTTGCTTTGAGCGGC |
| mm4_intron_Cdh3_chr8_106520473 |
CTGGTCAGAACGGACAGACATACTATAGACCTGAGCACTCTAAGGGGAACTTTCTGTCTTGATGCTCACCCCAGANNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGACCTGGCTGTTCCGAATG |
| mm4_intergenic_Muc5ac|Muc5b_chr7_141822683 |
TGTTTCTGCCATGTCTGGACTTGGATTTCTTCCTGCACCCCAGCCAGCTTCACCAGGATAGGGGGGCAGCCTCCTCCCCA CAGAGCCTTGCTCAGCATGAAGCCGGGTCTGGGTTTCCTCTGTG |
| mm4_intergenic_E130102H24Rik|Gm12795_chr4_101356921 |
GAGACACAACTCCAGGCGAAGGACGTGGTGCGTGTGCGCGCGTGCGCGCCGGTCTCTCCGTGCCCAGGAGCCGGAGGCTG GGGTGCTCCAAGCATCCTCCCATCATCAGG |
| mm4_intron_Fbln5_chr12_101799956 |
GCTTGCCAGGCTAGAACACTGTAGAACCTAAGTGACCAGATAAACTAGCAGTTCAAGAGAGAAGAAAGGGAACAGGGTAT CCAAGTTGCTCTGGCACCACAGACTTCGCCATGAGGCCCCAGAGAAGGTGCAAGTGCCA |
| mm4_intergenic_Gm24601|Gm26501_chr6_94916862 |
CACACAAAATTAGGACGCACCAGGCACCCCATAGTGCCCCCCCTGGGTCTGCTTCCTGGTACCTCAGAATACTCTGCTAG GTATGCTTCCTGGTACCCCAGAACCTTCCCTGGGTTCGATTCC |
| mm4_intergenic_Ube2g2|Ube2g2/Sumo3_chr10_77622572 |
CGGATAAAAGGCCAGGCTGTCGCCGTCACCTGCGCACCCCAGCCAGCGGCAGCGGGGCTGGCCCTGGGCTCAGAAGCCGG CCGGGGCAGCGCCGCCGTGGCCCTGCCACCCGGGTCTGGTCCCTAAGCCCCTGTGTG |
| mm4_intergenic_Jazf1|Gm15572_chr6_52833301 |
GGGAACTTAGGGTGCAAGGGATGATAGAGTGAGATGCACCCCAGGCTGCTGCACTGGGTGAGGGGACTATAGCCAATGTA ATCTTAGGAAGCAAAGAATCCTCATTCTAATGACTAGGATGGAAAGAAGCGACTCTGCCT |
| mm4_intron_Auh_chr13_52859530 |
GACCGTTCCCATGCTGAGAAAGCTTGCACTGTGCTGAGCACCCCAGCCTACGCCAGGGGGCATTTCCCAGTGCTGCTGCT GCATGAAGAGCGAGCCAGGAT |
| mm4_intron_Susd1_chr4_59438084 | CACTACACACCCCACAGTCCCCGGGGCGGGCAGTCTGGCGTGCTTCTCGCCGCTCCGCCTCCATGATCCTTC |
| mm4_intron_Gm12756_chr7_34672107 | ACTCTGGAATGTTGCTGCCACCTGGTGGCCCAGTTAGGGATGCACCGGCCTCTGTTTAGGAGCAGG |
| mm4_intron_Camk2b_chr11_6002337 |
GCGAGTGTGCTGGACTAGTCCTGGCCCTGGTGCTCTTGGGAGCTTAAGTTCTTGCTGTATTCCACCACCCAAGACTGGGC CACGAGGCTGGAGAGTGAAGAGCAGCTACCTTCTCCCTGGTCCCA |
| mm4_intergenic_Otos|Gpc1_chr1_92711818 |
GGCTTAGCCCATCCTCTCCTTGGGGCTCCCCTCACCCCAGAATGGGCCTCCCGGGGTCCCCTCCTTAGCTAGATGATTCC AACTGTAAATGCTCCCTGCAGGAGGTAGAGGCTCCCAGAGACCA |
| mm4_exon_Htr6_chr4_139074707 |
TCAGCACGATGACCACGCACAGCGCAGCGGCCACCCAGCCGCTGCCCCCTGGGGCTGGCGGTGGCCCGGGGCCCCAGGCT GGGGTGCTACTGTTGACAGGGCCGGGCTCTGGAACCATGGGGACTAGGGTTGA |
| mm4_exon_Bai2_chr4_130012545 |
GTCCATCCTGGCTTCCAACATTCTGATCCTGGTGGGCCAGTCCCGGGTGCTGAGCAAGGCAGGTGCAGGCTCCTGGGGGT GTGTGGGAAGGGGCCTAAAG |