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Contents:

PCR primers for off-targets of TAGGTTGCCCTTGGCCAGAG AGG

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.

Maximum amplicon length:     Primer Tm:

NamePrimer Sequence Tm CFD Score
ontarget_mm0_exon_5730457N03Rik/Evx1_chr6_52314152_F TCGTCGGCAGCGTCGAGCCACGGTCTGCTGGAG 62.6 1.00
ontarget_mm0_exon_5730457N03Rik/Evx1_chr6_52314152_R GTCTCGTGGGCTCGGTGCAGCTCACCTCGATTTCT 59.3 1.00
mm4_intron_Dnah5_chr15_28431220_F Primer3: not found at this Tm N.d. 0.74
mm4_intron_Dnah5_chr15_28431220_R Primer3: not found at this Tm N.d. 0.74
mm4_intergenic_Cdh7|Cdh19_chr1_110561423_F Primer3: not found at this Tm N.d. 0.70
mm4_intergenic_Cdh7|Cdh19_chr1_110561423_R Primer3: not found at this Tm N.d. 0.70
mm3_intergenic_Ppargc1a|mmu-mir-6417_chr5_52108065_F Primer3: not found at this Tm N.d. 0.64
mm3_intergenic_Ppargc1a|mmu-mir-6417_chr5_52108065_R Primer3: not found at this Tm N.d. 0.64
mm4_intergenic_Gm9621|Gm24200_chr9_93542462_F Primer3: not found at this Tm N.d. 0.59
mm4_intergenic_Gm9621|Gm24200_chr9_93542462_R Primer3: not found at this Tm N.d. 0.59
mm4_intron_Slc2a13_chr15_91511149_F TCGTCGGCAGCGTCGGTATGGCATGACCTCGGAG 59.9 0.55
mm4_intron_Slc2a13_chr15_91511149_R GTCTCGTGGGCTCGGTCAGCATTCTGAGATTCTCCCA 58.8 0.55
mm4_intron_Gm9994_chr1_93937699_F TCGTCGGCAGCGTCTGGTTTTATTGTACTTTACCACAGG 57.4 0.53
mm4_intron_Gm9994_chr1_93937699_R GTCTCGTGGGCTCGGGACATGGAGCCAACACAGGA 59.9 0.53
mm4_intron_Gm6086_chr1_94006022_F TCGTCGGCAGCGTCTGGTTTTATTGTACTTTACCACAGG 57.4 0.53
mm4_intron_Gm6086_chr1_94006022_R GTCTCGTGGGCTCGGGGCTCCTCAGCTGCCTATTT 59.8 0.53
mm4_intron_Gal3st2_chr1_93871535_F Primer3: not found at this Tm N.d. 0.53
mm4_intron_Gal3st2_chr1_93871535_R Primer3: not found at this Tm N.d. 0.53
mm4_intron_Ms4a10_chr19_10963678_F TCGTCGGCAGCGTCCCTCTGGCTGGTTTTGGGAA 60.1 0.52
mm4_intron_Ms4a10_chr19_10963678_R GTCTCGTGGGCTCGGCTCTTAGGTGACCCCTGCAC 59.7 0.52
mm3_intron_Ablim1_chr19_57266288_F Primer3: not found at this Tm N.d. 0.51
mm3_intron_Ablim1_chr19_57266288_R Primer3: not found at this Tm N.d. 0.51
mm4_intergenic_Gm23860|Gm11800_chr4_7967222_F Primer3: not found at this Tm N.d. 0.51
mm4_intergenic_Gm23860|Gm11800_chr4_7967222_R Primer3: not found at this Tm N.d. 0.51
mm4_intergenic_Ucma|Mcm10_chr2_4987767_F Primer3: not found at this Tm N.d. 0.51
mm4_intergenic_Ucma|Mcm10_chr2_4987767_R Primer3: not found at this Tm N.d. 0.51
mm4_intron_Arntl_chr7_113217840_F Primer3: not found at this Tm N.d. 0.51
mm4_intron_Arntl_chr7_113217840_R Primer3: not found at this Tm N.d. 0.51
mm4_intron_Timp3_chr10_86301842_F Primer3: not found at this Tm N.d. 0.47
mm4_intron_Timp3_chr10_86301842_R Primer3: not found at this Tm N.d. 0.47
mm4_intergenic_4930448E22Rik|Gm22659_chr9_46414230_F TCGTCGGCAGCGTCCCTGCCCTTTCACCTCTACG 60.1 0.41
mm4_intergenic_4930448E22Rik|Gm22659_chr9_46414230_R GTCTCGTGGGCTCGGAGGAAAGACACCTGCTGCTG 60.2 0.41
mm4_exon_Col3a1_chr1_45334593_F TCGTCGGCAGCGTCTGCATGTGTAGCAGGATCAA 57.2 0.40
mm4_exon_Col3a1_chr1_45334593_R GTCTCGTGGGCTCGGAAGGCCAGGTCCTCCAGG 60.6 0.40
mm4_intron_Zmat4_chr8_23686693_F Primer3: not found at this Tm N.d. 0.39
mm4_intron_Zmat4_chr8_23686693_R Primer3: not found at this Tm N.d. 0.39
mm4_intergenic_Gm25935|Gm22593_chr17_94235042_F Primer3: not found at this Tm N.d. 0.38
mm4_intergenic_Gm25935|Gm22593_chr17_94235042_R Primer3: not found at this Tm N.d. 0.38
mm4_intergenic_Axin2|Gm11668_chr11_108976744_F Primer3: not found at this Tm N.d. 0.37
mm4_intergenic_Axin2|Gm11668_chr11_108976744_R Primer3: not found at this Tm N.d. 0.37
mm4_intergenic_Zfp365|Rtkn2_chr10_67939001_F Primer3: not found at this Tm N.d. 0.36
mm4_intergenic_Zfp365|Rtkn2_chr10_67939001_R Primer3: not found at this Tm N.d. 0.36
mm4_intergenic_Gm14283|Gm14304_chr2_131422736_F Primer3: not found at this Tm N.d. 0.36
mm4_intergenic_Gm14283|Gm14304_chr2_131422736_R Primer3: not found at this Tm N.d. 0.36
mm4_intron_Alpk2_chr18_65370629_F TCGTCGGCAGCGTCCCCTCTGCTCCTCCAGGAAA 60.9 0.35
mm4_intron_Alpk2_chr18_65370629_R GTCTCGTGGGCTCGGTCATTTGTGTTCCCTGGGCA 59.8 0.35
mm3_intergenic_Cdh23|Slc29a3_chr10_60705929_F TCGTCGGCAGCGTCCCCTCAGCCAGAACAGGAAC 60.3 0.33
mm3_intergenic_Cdh23|Slc29a3_chr10_60705929_R GTCTCGTGGGCTCGGGACCACCACGCTCTGAAAGA 59.9 0.33
mm4_intergenic_D3Ertd751e|Gm25714_chr3_43269769_F Primer3: not found at this Tm N.d. 0.33
mm4_intergenic_D3Ertd751e|Gm25714_chr3_43269769_R Primer3: not found at this Tm N.d. 0.33
mm4_intergenic_Nipa1|Herc2_chr7_56038811_F Primer3: not found at this Tm N.d. 0.30
mm4_intergenic_Nipa1|Herc2_chr7_56038811_R Primer3: not found at this Tm N.d. 0.30
mm3_intron_Prex2_chr1_11036699_F TCGTCGGCAGCGTCTTCAGAGCTGAGGTGATGCC 59.7 0.30
mm3_intron_Prex2_chr1_11036699_R GTCTCGTGGGCTCGGGCAGATATGGACCTTGGGGAG 59.9 0.30
mm4_exon_Ecel1_chr1_87149617_F TCGTCGGCAGCGTCTCCACCAGTGCAACAGGTTT 60.0 0.29
mm4_exon_Ecel1_chr1_87149617_R GTCTCGTGGGCTCGGTAGTGTCCAGCCTGGCCATA 60.3 0.29
mm4_intergenic_Gm13218|Gata3_chr2_9847399_F TCGTCGGCAGCGTCTCATCCTCTGACATCTTAAATGCA 58.0 0.29
mm4_intergenic_Gm13218|Gata3_chr2_9847399_R GTCTCGTGGGCTCGGGCTTGCAGGAAACTTGTCCC 59.6 0.29
mm4_intergenic_Idh2|Sema4b_chr7_80156790_F Primer3: not found at this Tm N.d. 0.28
mm4_intergenic_Idh2|Sema4b_chr7_80156790_R Primer3: not found at this Tm N.d. 0.28
mm4_intron_Myl2_chr5_122104737_F Primer3: not found at this Tm N.d. 0.28
mm4_intron_Myl2_chr5_122104737_R Primer3: not found at this Tm N.d. 0.28
mm4_intergenic_Gm16477|Gpr26_chr7_131707369_F Primer3: not found at this Tm N.d. 0.28
mm4_intergenic_Gm16477|Gpr26_chr7_131707369_R Primer3: not found at this Tm N.d. 0.28
mm4_intron_Slc36a3_chr11_55128680_F Primer3: not found at this Tm N.d. 0.28
mm4_intron_Slc36a3_chr11_55128680_R Primer3: not found at this Tm N.d. 0.28
mm4_intergenic_Gm8183|Tmem135_chr7_88935607_F TCGTCGGCAGCGTCGGCACCAGCATCTGACTCAT 60.1 0.28
mm4_intergenic_Gm8183|Tmem135_chr7_88935607_R GTCTCGTGGGCTCGGAGTTTTGCTACTCACCTCTTCCT 59.3 0.28
mm4_intron_Spats2_chr15_99186238_F TCGTCGGCAGCGTCTCCTAACTACAAGGCGGGGA 59.9 0.27
mm4_intron_Spats2_chr15_99186238_R GTCTCGTGGGCTCGGATCACTTGTCCTCTGCGGAG 59.4 0.27
mm4_intron_Ntrk2_chr13_59078068_F TCGTCGGCAGCGTCCTCGCCAGGTAATGCCTCTC 60.2 0.27
mm4_intron_Ntrk2_chr13_59078068_R GTCTCGTGGGCTCGGTACGGAGTGGCTAACAGGGA 59.9 0.27
mm3_intergenic_Myom2|Gm24231_chr8_15225042_F TCGTCGGCAGCGTCACCTTGCTTGTCCTCTCTGG 59.3 0.27
mm3_intergenic_Myom2|Gm24231_chr8_15225042_R GTCTCGTGGGCTCGGCGTCACTGCACCAAAGCTTG 60.3 0.27
mm4_intergenic_AY512915|Suclg2_chr6_95471706_F TCGTCGGCAGCGTCAAGACACACTAACATGACTGGA 57.0 0.26
mm4_intergenic_AY512915|Suclg2_chr6_95471706_R GTCTCGTGGGCTCGGGGTGTCGGCATCAAGGTGAA 60.6 0.26
mm4_intergenic_mmu-mir-6341|Gm2383_chr1_12548122_F Primer3: not found at this Tm N.d. 0.26
mm4_intergenic_mmu-mir-6341|Gm2383_chr1_12548122_R Primer3: not found at this Tm N.d. 0.26
mm4_intron_Tpk1_chr6_43655257_F TCGTCGGCAGCGTCTTGGCCAAGGAAGTTCAGCT 59.8 0.25
mm4_intron_Tpk1_chr6_43655257_R GTCTCGTGGGCTCGGTTGTGGAAGAGGGGAGGGAG 60.5 0.25
mm4_intron_Ypel5_chr17_72838409_F TCGTCGGCAGCGTCGTTCAAAGATGGGGCAGGGA 59.9 0.25
mm4_intron_Ypel5_chr17_72838409_R GTCTCGTGGGCTCGGTGCTCCAGGGATGGTTTTCC 59.9 0.25
mm4_intergenic_Pja2|mmu-mir-6420_chr17_64371092_F TCGTCGGCAGCGTCGCTAACCCCACCAGACCAAA 59.8 0.25
mm4_intergenic_Pja2|mmu-mir-6420_chr17_64371092_R GTCTCGTGGGCTCGGTGGGTTACTTTATTCCTGCAGGA 59.4 0.25
mm4_intergenic_Gm11599|Nrp2_chr1_62679604_F Primer3: not found at this Tm N.d. 0.24
mm4_intergenic_Gm11599|Nrp2_chr1_62679604_R Primer3: not found at this Tm N.d. 0.24
mm4_intron_Hcn1_chr13_117930377_F Primer3: not found at this Tm N.d. 0.24
mm4_intron_Hcn1_chr13_117930377_R Primer3: not found at this Tm N.d. 0.24
mm4_intron_Chrna7_chr7_63157689_F Primer3: not found at this Tm N.d. 0.24
mm4_intron_Chrna7_chr7_63157689_R Primer3: not found at this Tm N.d. 0.24
mm3_intergenic_Car8|Gm11810_chr4_8454520_F TCGTCGGCAGCGTCGCTCTGCCAAAAGTACCCCT 59.9 0.24
mm3_intergenic_Car8|Gm11810_chr4_8454520_R GTCTCGTGGGCTCGGTTGCTTTCTGTGGCATGGTT 58.5 0.24
mm4_intergenic_Gm12701|Ror1_chr4_100133141_F TCGTCGGCAGCGTCGCTTAACTCAGTGGGGAGCC 60.3 0.23
mm4_intergenic_Gm12701|Ror1_chr4_100133141_R GTCTCGTGGGCTCGGACTGCAGAGAAGTGGGTCTT 58.5 0.23
mm4_intergenic_Scgb1b7|Gm5329_chr7_31744657_F Primer3: not found at this Tm N.d. 0.23
mm4_intergenic_Scgb1b7|Gm5329_chr7_31744657_R Primer3: not found at this Tm N.d. 0.23
mm4_intergenic_Gm26894|9530036O11Rik_chr5_28539035_F TCGTCGGCAGCGTCTGATGGGTGTGAACCACGAG 59.9 0.23
mm4_intergenic_Gm26894|9530036O11Rik_chr5_28539035_R GTCTCGTGGGCTCGGGCCCTTCCACAATGCCAAAG 60.0 0.23
mm4_exon_Gm9146_chr7_32473721_F TCGTCGGCAGCGTCACTGCACCACTGACTGCTTA 59.2 0.23
mm4_exon_Gm9146_chr7_32473721_R GTCTCGTGGGCTCGGACGCCACATCTTTCCAGAGG 60.0 0.23
mm4_exon_Gm5652_chr12_5590129_F TCGTCGGCAGCGTCATAAGCCCTTCCACGATGCC 60.1 0.23
mm4_exon_Gm5652_chr12_5590129_R GTCTCGTGGGCTCGGTTTGTGGTGGGTGTGAACCA 59.9 0.23
mm4_exon_Gm5523_chr1_13786395_F TCGTCGGCAGCGTCGCCCTTCCACAATGCCAAAG 60.0 0.23
mm4_exon_Gm5523_chr1_13786395_R GTCTCGTGGGCTCGGTGATGGGTGTGAACCACGAG 59.9 0.23
mm4_exon_Gm18822_chr3_8616009_F Primer3: not found at this Tm N.d. 0.23
mm4_exon_Gm18822_chr3_8616009_R Primer3: not found at this Tm N.d. 0.23
mm4_intergenic_Gm16998|Gm26177_chr10_54239299_F Primer3: not found at this Tm N.d. 0.23
mm4_intergenic_Gm16998|Gm26177_chr10_54239299_R Primer3: not found at this Tm N.d. 0.23
mm3_intron_Nars2_chr7_97010923_F TCGTCGGCAGCGTCAGAAGATCCAGTTGGCACCA 58.9 0.21
mm3_intron_Nars2_chr7_97010923_R GTCTCGTGGGCTCGGCCTCCCCATTGCCCGTTTAA 60.3 0.21
mm4_intergenic_Gm10087|Sbf2_chr7_110532218_F TCGTCGGCAGCGTCTCACTTGCTTGATTGCCAGT 58.0 0.21
mm4_intergenic_Gm10087|Sbf2_chr7_110532218_R GTCTCGTGGGCTCGGTGTTTCTGCCACATTCTGGGA 59.8 0.21
mm4_intron_Tmem53_chr4_117262970_F Primer3: not found at this Tm N.d. 0.21
mm4_intron_Tmem53_chr4_117262970_R Primer3: not found at this Tm N.d. 0.21
mm4_intergenic_Gm12091|Gm12092_chr11_29606285_F Primer3: not found at this Tm N.d. 0.21
mm4_intergenic_Gm12091|Gm12092_chr11_29606285_R Primer3: not found at this Tm N.d. 0.21
mm4_intergenic_1700010I14Rik|6530411M01Rik_chr17_9030350_F TCGTCGGCAGCGTCGGTCTGTAGCGGCTGTTCAT 60.1 0.21
mm4_intergenic_1700010I14Rik|6530411M01Rik_chr17_9030350_R GTCTCGTGGGCTCGGAGGGCTGTTAGAGGTCTCACT 59.9 0.21
mm4_intergenic_Atf6b|Tnxb_chr17_34663745_F TCGTCGGCAGCGTCGGAGAGGCTATGCAAACACCT 60.0 0.20
mm4_intergenic_Atf6b|Tnxb_chr17_34663745_R GTCTCGTGGGCTCGGCCCTCTCCCAATGGACACAC 60.0 0.20
mm4_intergenic_Gm24092|Cenpf_chr1_189516710_F TCGTCGGCAGCGTCTTCCCTGCTCAGAAGTGGTG 59.6 0.19
mm4_intergenic_Gm24092|Cenpf_chr1_189516710_R GTCTCGTGGGCTCGGACTCAACCACTGCCCATTTAGT 59.8 0.19
mm4_intergenic_Dhx40|Ypel2_chr11_86898562_F Primer3: not found at this Tm N.d. 0.19
mm4_intergenic_Dhx40|Ypel2_chr11_86898562_R Primer3: not found at this Tm N.d. 0.19
mm4_intergenic_Ubn2|Ubn2/mmu-mir-7670_chr6_38501484_F TCGTCGGCAGCGTCCCTGGCTTCTGTTTGGGTCT 59.8 0.19
mm4_intergenic_Ubn2|Ubn2/mmu-mir-7670_chr6_38501484_R GTCTCGTGGGCTCGGAACTCTCAGCCAAACACTTCT 57.4 0.19
mm4_intron_Rgs7_chr1_175333235_F Primer3: not found at this Tm N.d. 0.19
mm4_intron_Rgs7_chr1_175333235_R Primer3: not found at this Tm N.d. 0.19
mm3_intergenic_Trip11|Gm20701_chr12_101862799_F TCGTCGGCAGCGTCGCTGGGAGGTGCTTCAGAAT 60.0 0.19
mm3_intergenic_Trip11|Gm20701_chr12_101862799_R GTCTCGTGGGCTCGGAAAGGGCATGGATCCATTGT 57.4 0.19
mm4_exon_P2rx1_chr11_72999251_F TCGTCGGCAGCGTCCACTTGGCCTGCTCTGTTCT 60.2 0.18
mm4_exon_P2rx1_chr11_72999251_R GTCTCGTGGGCTCGGGAAGGGGCTCAGAGACAAGC 60.3 0.18
mm4_intergenic_Rerg|Ptpro_chr6_137185894_F Primer3: not found at this Tm N.d. 0.18
mm4_intergenic_Rerg|Ptpro_chr6_137185894_R Primer3: not found at this Tm N.d. 0.18
mm4_intergenic_Gm14654|Gm4987_chrX_46408871_F Primer3: not found at this Tm N.d. 0.18
mm4_intergenic_Gm14654|Gm4987_chrX_46408871_R Primer3: not found at this Tm N.d. 0.18
mm4_intron_Camkmt_chr17_85378898_F Primer3: not found at this Tm N.d. 0.17
mm4_intron_Camkmt_chr17_85378898_R Primer3: not found at this Tm N.d. 0.17
mm4_intergenic_Kcna6/Gm26673|Ndufa9_chr6_126759717_F Primer3: not found at this Tm N.d. 0.17
mm4_intergenic_Kcna6/Gm26673|Ndufa9_chr6_126759717_R Primer3: not found at this Tm N.d. 0.17
mm4_intron_Kcnh1_chr1_192455000_F TCGTCGGCAGCGTCGCCAATACCCAGGGTTCCAA 59.9 0.17
mm4_intron_Kcnh1_chr1_192455000_R GTCTCGTGGGCTCGGCTGGGCAGAGTCAACCTCAG 60.0 0.17
mm4_intron_Gm3235_chr8_91622454_F TCGTCGGCAGCGTCTCAAGTGTAAAATTGGGCCCC 58.7 0.16
mm4_intron_Gm3235_chr8_91622454_R GTCTCGTGGGCTCGGCAATGGCGCCTTAATGTGGG 59.8 0.16
mm2_intron_Gm15514_chr7_107275902_F Primer3: not found at this Tm N.d. 0.16
mm2_intron_Gm15514_chr7_107275902_R Primer3: not found at this Tm N.d. 0.16
mm3_intron_Caln1_chr5_130601818_F Primer3: not found at this Tm N.d. 0.16
mm3_intron_Caln1_chr5_130601818_R Primer3: not found at this Tm N.d. 0.16
mm4_intron_Serpinb5_chr1_106868893_F Primer3: not found at this Tm N.d. 0.15
mm4_intron_Serpinb5_chr1_106868893_R Primer3: not found at this Tm N.d. 0.15
mm4_intron_Tmem28_chrX_99840022_F TCGTCGGCAGCGTCGGCTCCTTTAGAACTGTCCCT 59.0 0.15
mm4_intron_Tmem28_chrX_99840022_R GTCTCGTGGGCTCGGTCCATTCTGGAGGGTCCTCA 59.5 0.15
mm4_exon_Adamts20_chr15_94333716_F TCGTCGGCAGCGTCTCTTACGGACGCAGGCAATT 60.0 0.14
mm4_exon_Adamts20_chr15_94333716_R GTCTCGTGGGCTCGGCTGCCTTCCTAGCTGAGTCA 58.8 0.14
mm4_intergenic_mmu-mir-6393|Zdhhc25_chr15_88500796_F Primer3: not found at this Tm N.d. 0.13
mm4_intergenic_mmu-mir-6393|Zdhhc25_chr15_88500796_R Primer3: not found at this Tm N.d. 0.13
mm4_intron_Dlg2_chr7_91853767_F TCGTCGGCAGCGTCAGGAGAAGTGAAGCAGTTGC 58.1 0.12
mm4_intron_Dlg2_chr7_91853767_R GTCTCGTGGGCTCGGGGAACTGAAGTGCGGGAGAA 59.9 0.12
mm4_intergenic_Ttll7|Gm23131_chr3_147444537_F Primer3: not found at this Tm N.d. 0.12
mm4_intergenic_Ttll7|Gm23131_chr3_147444537_R Primer3: not found at this Tm N.d. 0.12
mm3_intergenic_Gm14597|Cxx1c_chrX_53580057_F TCGTCGGCAGCGTCAACCAGTGGGCATTGTTCCA 60.1 0.11
mm3_intergenic_Gm14597|Cxx1c_chrX_53580057_R GTCTCGTGGGCTCGGTGTTCTTGCTGTGCTAGAGACA 59.6 0.11
mm4_intergenic_Ces5a|Gm26843_chr8_93661870_F TCGTCGGCAGCGTCGGGGTGTGACCTCAAGAGAC 59.6 0.11
mm4_intergenic_Ces5a|Gm26843_chr8_93661870_R GTCTCGTGGGCTCGGGGTCGAGATGAGCTCACCAC 60.1 0.11
mm4_intron_Acpp_chr9_104314647_F Primer3: not found at this Tm N.d. 0.11
mm4_intron_Acpp_chr9_104314647_R Primer3: not found at this Tm N.d. 0.11
mm4_exon_Hist1h2be/Gm11398_chr13_23619863_F TCGTCGGCAGCGTCTTCAGCCTGCTTCCTGCTTT 60.1 0.11
mm4_exon_Hist1h2be/Gm11398_chr13_23619863_R GTCTCGTGGGCTCGGAGTTCACGTCTTTGGCAGCT 60.1 0.11
mm4_intron_Gpr98_chr13_81575660_F TCGTCGGCAGCGTCCTCCCCTTCTTTGCCAGACC 60.3 0.10
mm4_intron_Gpr98_chr13_81575660_R GTCTCGTGGGCTCGGACCATCTTTGTCAACTACAGGCA 60.1 0.10
mm4_intergenic_Gm17037|Gm23822_chr5_18851868_F TCGTCGGCAGCGTCGGCATTGGAAAATATCAGCTGCT 59.9 0.10
mm4_intergenic_Gm17037|Gm23822_chr5_18851868_R GTCTCGTGGGCTCGGAGTCCAGGCGTTAGGAAATCA 59.0 0.10
mm4_intergenic_Gm17037|Gm23822_chr5_18755905_F TCGTCGGCAGCGTCAGTCCAGGCGTTAGGAAATCA 59.0 0.10
mm4_intergenic_Gm17037|Gm23822_chr5_18755905_R GTCTCGTGGGCTCGGGCATTGGAAAATATCAGCTGCCT 59.9 0.10
mm4_intergenic_Gm23986|Gm24929_chr8_51224259_F Primer3: not found at this Tm N.d. 0.09
mm4_intergenic_Gm23986|Gm24929_chr8_51224259_R Primer3: not found at this Tm N.d. 0.09
mm4_intergenic_Kazn|Gm13052_chr4_142287559_F TCGTCGGCAGCGTCACCACAGAGGAGGGGAAGAA 59.8 0.09
mm4_intergenic_Kazn|Gm13052_chr4_142287559_R GTCTCGTGGGCTCGGAGACTCCTGAGAGCCAAGGT 59.8 0.09
mm4_intergenic_Dner|Dner/Mir5126_chr1_84598108_F TCGTCGGCAGCGTCCCCTCTGAAGGTTACTGCGG 60.1 0.09
mm4_intergenic_Dner|Dner/Mir5126_chr1_84598108_R GTCTCGTGGGCTCGGAGGTTAAACTGGTGGCATCCA 59.5 0.09
mm4_intron_Lcor_chr19_41516542_F Primer3: not found at this Tm N.d. 0.09
mm4_intron_Lcor_chr19_41516542_R Primer3: not found at this Tm N.d. 0.09
mm4_intron_Ryr2_chr13_11759224_F Primer3: not found at this Tm N.d. 0.09
mm4_intron_Ryr2_chr13_11759224_R Primer3: not found at this Tm N.d. 0.09
mm4_intergenic_AL596090.1|Gm12266_chr11_60308898_F TCGTCGGCAGCGTCTGTGGAAAGTCTTTCTCAGCCT 59.5 0.09
mm4_intergenic_AL596090.1|Gm12266_chr11_60308898_R GTCTCGTGGGCTCGGGGGTGGGGATCAAGTTGCTT 60.2 0.09
mm4_intron_Limch1_chr5_66817576_F TCGTCGGCAGCGTCTGAGGAGAGAGGAGGCAACA 59.8 0.08
mm4_intron_Limch1_chr5_66817576_R GTCTCGTGGGCTCGGCGGTGGTCAACATGAGGACA 59.9 0.08
mm4_intergenic_Gm15077|Col4a6_chrX_141316177_F Primer3: not found at this Tm N.d. 0.08
mm4_intergenic_Gm15077|Col4a6_chrX_141316177_R Primer3: not found at this Tm N.d. 0.08
mm3_intergenic_Ctdp1|Nfatc1_chr18_80579659_F TCGTCGGCAGCGTCCCTTTGAGGACAGCAGCAAG 59.1 0.07
mm3_intergenic_Ctdp1|Nfatc1_chr18_80579659_R GTCTCGTGGGCTCGGTCAGCATCTCAGCAGCAACT 59.6 0.07
mm4_intergenic_Creb3l2|Akr1d1_chr6_37480950_F Primer3: not found at this Tm N.d. 0.07
mm4_intergenic_Creb3l2|Akr1d1_chr6_37480950_R Primer3: not found at this Tm N.d. 0.07
mm4_intron_Smarca2_chr19_26671350_F Primer3: not found at this Tm N.d. 0.07
mm4_intron_Smarca2_chr19_26671350_R Primer3: not found at this Tm N.d. 0.07
mm4_intron_Ttc6_chr12_57566297_F TCGTCGGCAGCGTCGCTTGCCCAGTGGGTATGAA 60.3 0.07
mm4_intron_Ttc6_chr12_57566297_R GTCTCGTGGGCTCGGGGGTTAGGAATGCTGTTCTCCA 60.0 0.07
mm4_intergenic_Ssu2|Cav3_chr6_112397559_F TCGTCGGCAGCGTCCTTCCCAAGGCCTGCTTC 57.9 0.07
mm4_intergenic_Ssu2|Cav3_chr6_112397559_R GTCTCGTGGGCTCGGGTGCTCTGGAGGCAGAAG 57.3 0.07
mm4_intron_Msra_chr14_64220859_F Primer3: not found at this Tm N.d. 0.06
mm4_intron_Msra_chr14_64220859_R Primer3: not found at this Tm N.d. 0.06
mm4_intergenic_Cyp1b1|Atl2_chr17_79845943_F Primer3: not found at this Tm N.d. 0.06
mm4_intergenic_Cyp1b1|Atl2_chr17_79845943_R Primer3: not found at this Tm N.d. 0.06
mm4_exon_Mob1b_chr5_88743389_F Primer3: not found at this Tm N.d. 0.06
mm4_exon_Mob1b_chr5_88743389_R Primer3: not found at this Tm N.d. 0.06
mm4_intron_Itsn1_chr16_91894618_F Primer3: not found at this Tm N.d. 0.04
mm4_intron_Itsn1_chr16_91894618_R Primer3: not found at this Tm N.d. 0.04
mm4_intergenic_Gm25818|Creb5_chr6_53572470_F TCGTCGGCAGCGTCCTCTTAGCCTAGTTCCCCGC 59.6 0.04
mm4_intergenic_Gm25818|Creb5_chr6_53572470_R GTCTCGTGGGCTCGGGGCAGCTCTGGTGGTTCTTT 60.5 0.04
mm4_intron_Sort1_chr3_108345150_F Primer3: not found at this Tm N.d. 0.04
mm4_intron_Sort1_chr3_108345150_R Primer3: not found at this Tm N.d. 0.04
mm4_intergenic_Mir802|Setd4_chr16_93519053_F Primer3: not found at this Tm N.d. 0.04
mm4_intergenic_Mir802|Setd4_chr16_93519053_R Primer3: not found at this Tm N.d. 0.04
mm4_intron_Tmcc3_chr10_94350054_F Primer3: not found at this Tm N.d. 0.04
mm4_intron_Tmcc3_chr10_94350054_R Primer3: not found at this Tm N.d. 0.04
mm4_intron_Mug2_chr6_122076512_F Primer3: not found at this Tm N.d. 0.04
mm4_intron_Mug2_chr6_122076512_R Primer3: not found at this Tm N.d. 0.04
mm3_intergenic_Cish/Gm17041|Hemk1_chr9_107309801_F TCGTCGGCAGCGTCCGGTTCCTGTCCTTGTAGGG 59.7 0.04
mm3_intergenic_Cish/Gm17041|Hemk1_chr9_107309801_R GTCTCGTGGGCTCGGCTCTGCCACCCGAATTGAGT 60.0 0.04
mm3_intron_Duox1_chr2_122346065_F TCGTCGGCAGCGTCCTTGAGGAAGCTGCCTTGGA 59.9 0.04
mm3_intron_Duox1_chr2_122346065_R GTCTCGTGGGCTCGGGTACAGGAAGTAGGGCCAGC 59.8 0.04
mm4_intron_Camk2d_chr3_126697298_F Primer3: not found at this Tm N.d. 0.04
mm4_intron_Camk2d_chr3_126697298_R Primer3: not found at this Tm N.d. 0.04
mm4_intergenic_Edn1|Phactr1_chr13_42481278_F Primer3: not found at this Tm N.d. 0.03
mm4_intergenic_Edn1|Phactr1_chr13_42481278_R Primer3: not found at this Tm N.d. 0.03
mm4_intergenic_Kcnb1|Kcnb1/1110018N20Rik_chr2_167113698_F TCGTCGGCAGCGTCGACCGATGGGGAGAACAACT 59.3 0.03
mm4_intergenic_Kcnb1|Kcnb1/1110018N20Rik_chr2_167113698_R GTCTCGTGGGCTCGGTGCACACTAAGCTCCTGTGG 59.9 0.03
mm3_intergenic_Gm15083|Slc6a11_chr6_114059025_F TCGTCGGCAGCGTCTGCCTTTCACCTCTGGTCAC 59.8 0.03
mm3_intergenic_Gm15083|Slc6a11_chr6_114059025_R GTCTCGTGGGCTCGGGGGACTGAAAGGGGAAAGGG 59.9 0.03
mm4_intron_Irf8_chr8_120739370_F TCGTCGGCAGCGTCAGCACAGGACTCCAGCTCTA 59.9 0.03
mm4_intron_Irf8_chr8_120739370_R GTCTCGTGGGCTCGGCACCCGAGAAAGAGGACACC 60.0 0.03
mm4_intergenic_Osm|Lif_chr11_4253639_F TCGTCGGCAGCGTCACCCCTACCCTGTAGCCTG 59.9 0.03
mm4_intergenic_Osm|Lif_chr11_4253639_R GTCTCGTGGGCTCGGAGGGTAGGGGTGTGCTGG 60.6 0.03
mm4_exon_Npr2_chr4_43643314_F TCGTCGGCAGCGTCATAGACCCTTGCACCACCAC 59.6 0.03
mm4_exon_Npr2_chr4_43643314_R GTCTCGTGGGCTCGGGTCATGAGCGAGCCGTAACT 60.1 0.03
mm4_intergenic_Bcl6|1110054M08Rik_chr16_24305585_F Primer3: not found at this Tm N.d. 0.03
mm4_intergenic_Bcl6|1110054M08Rik_chr16_24305585_R Primer3: not found at this Tm N.d. 0.03
mm4_intron_Cobl_chr11_12257496_F Primer3: not found at this Tm N.d. 0.03
mm4_intron_Cobl_chr11_12257496_R Primer3: not found at this Tm N.d. 0.03
mm4_intergenic_Gm13002|Wnt4_chr4_137268070_F TCGTCGGCAGCGTCGCTGGCTTTCCCTGACTTCT 59.9 0.03
mm4_intergenic_Gm13002|Wnt4_chr4_137268070_R GTCTCGTGGGCTCGGGGGGACAAGTGACCTGTCAA 59.5 0.03
mm4_intron_4933406C10Rik_chr12_32938863_F Primer3: not found at this Tm N.d. 0.03
mm4_intron_4933406C10Rik_chr12_32938863_R Primer3: not found at this Tm N.d. 0.03
mm4_intergenic_Tbc1d22a|Gm23416_chr15_86583725_F TCGTCGGCAGCGTCGGCTCCGTCTTCTCAAAGCA 60.3 0.03
mm4_intergenic_Tbc1d22a|Gm23416_chr15_86583725_R GTCTCGTGGGCTCGGGTCAAGGACCTGGGTCAGTC 59.6 0.03
mm2_intergenic_Trim33|Gm25009_chr3_103372290_F Primer3: not found at this Tm N.d. 0.03
mm2_intergenic_Trim33|Gm25009_chr3_103372290_R Primer3: not found at this Tm N.d. 0.03
mm4_intron_Bptf_chr11_107072076_F Primer3: not found at this Tm N.d. 0.02
mm4_intron_Bptf_chr11_107072076_R Primer3: not found at this Tm N.d. 0.02
mm4_intergenic_Elof1|Acp5_chr9_22120159_F Primer3: not found at this Tm N.d. 0.02
mm4_intergenic_Elof1|Acp5_chr9_22120159_R Primer3: not found at this Tm N.d. 0.02
mm4_intergenic_Gm7146|Klhl4_chrX_114340156_F Primer3: not found at this Tm N.d. 0.02
mm4_intergenic_Gm7146|Klhl4_chrX_114340156_R Primer3: not found at this Tm N.d. 0.02
mm4_intron_Mlph_chr1_90932942_F TCGTCGGCAGCGTCTCTGGGAGCCCTGAATACCA 59.9 0.02
mm4_intron_Mlph_chr1_90932942_R GTCTCGTGGGCTCGGAGGGTAGAGGTGAGGTTTCCT 59.5 0.02
mm4_intergenic_Gm23530|Csmd3_chr15_47819083_F Primer3: not found at this Tm N.d. 0.02
mm4_intergenic_Gm23530|Csmd3_chr15_47819083_R Primer3: not found at this Tm N.d. 0.02
mm4_exon_Gnb4_chr3_32593953_F Primer3: not found at this Tm N.d. 0.01
mm4_exon_Gnb4_chr3_32593953_R Primer3: not found at this Tm N.d. 0.01
mm4_intron_Dnajc15_chr14_77874615_F TCGTCGGCAGCGTCCGCGCCCTGGTTCTTAACTA 60.1 0.01
mm4_intron_Dnajc15_chr14_77874615_R GTCTCGTGGGCTCGGCAGAACAGGCCCACGGTTAT 60.0 0.01
mm4_intergenic_Gm13471|Gm13481_chr2_48156115_F TCGTCGGCAGCGTCAGCCAGGCCTTTCAATTCCT 59.5 0.01
mm4_intergenic_Gm13471|Gm13481_chr2_48156115_R GTCTCGTGGGCTCGGACGTTCAGGCAGCTACAAGA 59.3 0.01
mm4_intergenic_Gm22296|Gm23799_chr12_56050991_F Primer3: not found at this Tm N.d. 0.01
mm4_intergenic_Gm22296|Gm23799_chr12_56050991_R Primer3: not found at this Tm N.d. 0.01
mm4_exon_Gm14613_chrX_41741891_F Primer3: not found at this Tm N.d. 0.01
mm4_exon_Gm14613_chrX_41741891_R Primer3: not found at this Tm N.d. 0.01
mm4_intron_Synj1_chr16_90955634_F TCGTCGGCAGCGTCAATTCCACGTGGAGGCTGTT 59.8 0.01
mm4_intron_Synj1_chr16_90955634_R GTCTCGTGGGCTCGGAGCTTATGGATCCAAGCCAGA 58.8 0.01
mm3_intergenic_Slc24a3|Gm14093_chr2_145268171_F TCGTCGGCAGCGTCCAGTGAAAGTAGGGCTTCCC 57.8 0.01
mm3_intergenic_Slc24a3|Gm14093_chr2_145268171_R GTCTCGTGGGCTCGGTTCTGTGGAGGCTGTTGCTC 60.2 0.01
mm4_intergenic_Ap5b1|Rnaseh2c_chr19_5598447_F Primer3: not found at this Tm N.d. 0.01
mm4_intergenic_Ap5b1|Rnaseh2c_chr19_5598447_R Primer3: not found at this Tm N.d. 0.01
mm4_intron_Mdga1_chr17_29953342_F TCGTCGGCAGCGTCGCTGTTCCTGCCCAACAAAG 59.9 0.01
mm4_intron_Mdga1_chr17_29953342_R GTCTCGTGGGCTCGGGCTACTCAGGTGAGCGTCTC 59.9 0.01
mm4_intergenic_Gm23698|Gm22186_chr10_110882296_F TCGTCGGCAGCGTCCCCAGCAACAGCCAATACAC 59.4 0.01
mm4_intergenic_Gm23698|Gm22186_chr10_110882296_R GTCTCGTGGGCTCGGGCTATTGCTAGTCCAGGCCC 60.2 0.01
mm4_intron_E430025E21Rik_chr15_59341638_F Primer3: not found at this Tm N.d. 0.01
mm4_intron_E430025E21Rik_chr15_59341638_R Primer3: not found at this Tm N.d. 0.01
mm3_exon_Numa1_chr7_102013921_F Primer3: not found at this Tm N.d. 0.00
mm3_exon_Numa1_chr7_102013921_R Primer3: not found at this Tm N.d. 0.00
mm4_intergenic_Samd12|Gm23200_chr15_53529919_F Primer3: not found at this Tm N.d. 0.00
mm4_intergenic_Samd12|Gm23200_chr15_53529919_R Primer3: not found at this Tm N.d. 0.00
mm4_intergenic_Gm20713/Gpc5|Gm20713_chr14_115809793_F TCGTCGGCAGCGTCAGCTGCTGTGGTGAAAGTCA 59.8 0.00
mm4_intergenic_Gm20713/Gpc5|Gm20713_chr14_115809793_R GTCTCGTGGGCTCGGGCCACACTCCAGTCTGAACT 59.6 0.00
mm4_intron_Golga7_chr8_23245775_F Primer3: not found at this Tm N.d. 0.00
mm4_intron_Golga7_chr8_23245775_R Primer3: not found at this Tm N.d. 0.00
mm4_intron_Map3k7cl_chr16_87553624_F Primer3: not found at this Tm N.d. 0.00
mm4_intron_Map3k7cl_chr16_87553624_R Primer3: not found at this Tm N.d. 0.00
mm4_intergenic_Mdfic|Tfec_chr6_16624126_F TCGTCGGCAGCGTCGCGTAAGGCATGTGATTGTGT 59.5 0.00
mm4_intergenic_Mdfic|Tfec_chr6_16624126_R GTCTCGTGGGCTCGGTGCTTGAATGAACAAAGTTGCTCT 59.9 0.00
mm4_intron_Suds3_chr5_117105993_F TCGTCGGCAGCGTCTCGCCTGCCAGTTAACTTGA 59.6 0.00
mm4_intron_Suds3_chr5_117105993_R GTCTCGTGGGCTCGGTTCGGTGCTATGGTGCTGAG 60.1 0.00
mm4_intron_Ppargc1b_chr18_61340835_F TCGTCGGCAGCGTCTTCACCTGGCCTACCTGTCA 60.4 0.00
mm4_intron_Ppargc1b_chr18_61340835_R GTCTCGTGGGCTCGGGGACCTGTCTGTGAAGTCCG 60.0 0.00
mm4_intergenic_Gm26463|Gap_chr5_151703525_F TCGTCGGCAGCGTCTCACCTCTTCACTTGCTGGC 60.2 0.00
mm4_intergenic_Gm26463|Gap_chr5_151703525_R GTCTCGTGGGCTCGGTGGCATTTGGCAGAACCTGT 60.4 0.00
mm3_intron_Map9_chr3_82377323_F Primer3: not found at this Tm N.d. 0.00
mm3_intron_Map9_chr3_82377323_R Primer3: not found at this Tm N.d. 0.00

Off-target amplicon sequences with primers

These only list off-targets that have primers in the table above. Primers underlined, off-targets in bold.

ontarget_mm0_exon_5730457N03Rik/Evx1_chr6_52314152 GAGCCACGGTCTGCTGGAGCGGCCATGCTTGGCCCGGGACCCCCAGTCCCCTCCGCGGACAGCCTCTCTGGCCAAGGGCA
ACCTAGTAGCTCAGACACCGAATCGGATTTCTATGAAGAAATCGAGGTGAGCTGCA
mm4_intron_Slc2a13_chr15_91511149 GGTATGGCATGACCTCGGAGAGATCTGCCTCAGACAAACCTCTCTTGCCATTGGCAACCTGCATTTTCTTTTCACTGGGA
GAATCTCAGAATGCTGA
mm4_intron_Gm9994_chr1_93937699 TGGTTTTATTGTACTTTACCACAGGTGGAGGGTGCCCTCAGCCAGAGTGGCTGTGCCTCCTGTGTTGGCTCCATGTC
mm4_intron_Gm6086_chr1_94006022 TGGTTTTATTGTACTTTACCACAGGTGGAGGGTGCCCTCAGCCAGAGTGGCTGTGCCTCCTGTGTTGGCTCCGTGTCCCA
TATTAACCTGGGCTATGAAATAGGCAGCTGAGGAGCC
mm4_intron_Ms4a10_chr19_10963678 CCTCTGGCTGGTTTTGGGAAATCCAGCATGACTGACTACCCTAGACATAGCTTATGCCATCCACTCTGGCCATGGGCAGC
CACTGTACACCTGCTGTGGGTGGGAGGCTGGGGTGTGCAGGGGTCACCTAAGAG
mm4_intergenic_4930448E22Rik|Gm22659_chr9_46414230 CCTGCCCTTTCACCTCTACGACTCCTCTCTTGCCAAGGGAAACTTCCAAGCCTCAGTCCAGAGTCTGATCGAACAGTGGA
GCCCCTCCCCTCTGGTGAAGCAGGACCCAGCAGCAGGTGTCTTTCCT
mm4_exon_Col3a1_chr1_45334593 TGCATGTGTAGCAGGATCAAAAAATGGGGTTTGGACTTTTATTAGTGAATTACTTTTTGAGTATCTAAACCCTTGCTTTT
TTCTTTAGGGTGCCCCTGGCAAGAATGGAGAACGGGGTGGCCCTGGAGGACCTGGCCTT
mm4_intron_Alpk2_chr18_65370629 CCCTCTGCTCCTCCAGGAAATGAAGGTTTAGCATCTTCTCCCTACTGCATCACCTACGATTGACATCAATCAATAGATAG
GCCTTGGCCAGATTGGAATGGAGAAGCCCTGCCCAGGGAACACAAATGA
mm3_intergenic_Cdh23|Slc29a3_chr10_60705929 CCCTCAGCCAGAACAGGAACAGATGAAGTCTTCACACCCTCTCTGGCCAGGGGCAAGCTCCTGACAACCGTCATCCATCT
TTCAGAGCGTGGTGGTC
mm3_intron_Prex2_chr1_11036699 TTCAGAGCTGAGGTGATGCCCCACAGCTGTAGCACTGAGCACACCTTTGTGCAGCTCCACTGGAATCTAAGACTTCCACC
CTGGCCAAAGGCTACCTACTCCCCAAGGTCCATATCTGC
mm4_exon_Ecel1_chr1_87149617 TCCACCAGTGCAACAGGTTTCCTGAGCGGTCATACTGTCCCCCTGTGGCCAATGGCAATCCAGCACACTCAGACCACGCC
TCACCCTATGGCCAGGCTGGACACTA
mm4_intergenic_Gm13218|Gata3_chr2_9847399 TCATCCTCTGACATCTTAAATGCATTTATTTGCTGATAGGATTTACCCTCTCTGGCCAAGAGCCACTGATTAACATCTAG
TCTGCACACTATGTAGAAATGTAATCCTTAACAAAATGGGACAAGTTTCCTGCAAGC
mm4_intergenic_Gm8183|Tmem135_chr7_88935607 GGCACCAGCATCTGACTCATAAAGGTTGCTCTTGACCAGACAGGCTCTTGCTTTCTACTCAACAAATCCTAGGTCATTTA
GTCAGGAAAATAGGAAGAGGTGAGTAGCAAAACT
mm4_intron_Spats2_chr15_99186238 TCCTAACTACAAGGCGGGGAGAAGCGGAGACGCCTGTGCTGTGTGTAACTCTGCTTCGTTCAGTTGCTCTTGGCCAGTGT
GGGATTGAGAGGCACAGAGAACTCACAGTGCTCCGCAGAGGACAAGTGAT
mm4_intron_Ntrk2_chr13_59078068 CTCGCCAGGTAATGCCTCTCTATTCTCCAATCTCAGCAAAACTCACCAACTCATTCATTTACAGAGGCAACATTCACCCT
AGGGTGCACTTGACCATAGTGGGCTTTCCCTGTTAGCCACTCCGTA
mm3_intergenic_Myom2|Gm24231_chr8_15225042 ACCTTGCTTGTCCTCTCTGGAGAGAATGTCAGCAATTTGTTGCCCATGGCCAGAGAGGATCATACAGTTATGCAGGCAAG
CTTTGGTGCAGTGACG
mm4_intergenic_AY512915|Suclg2_chr6_95471706 AAGACACACTAACATGACTGGATAGGTTTCCATTGGCAAGTGTGGCCTTCTGTAGATTAGTAAGGTCCCATAGGGTCAAA
ATTAGGAAAAACATATTCCCTACTTTTTCGTTTCTGTTTCACCTTGATGCCGACACC
mm4_intron_Tpk1_chr6_43655257 TTGGCCAAGGAAGTTCAGCTGTTTATCCTGGGCCGGAAGCTGGAAATGCCCTTGGCTTGGCCTTGGCCAGAATGGAGCTC
AGGTTCTTATCTGTACTCCTGTCAGCCTTCCTCCCTCCCCTCTTCCACAA
mm4_intron_Ypel5_chr17_72838409 GTTCAAAGATGGGGCAGGGAGACACCAGGAGGAGGAAGTAGGAAGTATTCTGAGGAGAACAGATGTTGGGCCTAGAAAAT
GAAAAGCCTATGGGTTGCTGTTGGCCAGAAAGGCTTAGGAAAACCATCCCTGGAGCA
mm4_intergenic_Pja2|mmu-mir-6420_chr17_64371092 GCTAACCCCACCAGACCAAATAAATGTTTTTGTTCTTTATATTGAAAGGTTGCTTTTGGATTGCCTTTGGCCAGGGTGGG
TTATCCTGCAGGAATAAAGTAACCCA
mm3_intergenic_Car8|Gm11810_chr4_8454520 GCTCTGCCAAAAGTACCCCTCAGAATCTGCCCACTCTGGCCATGGGACACCTACGCTCTAGCAGACCTGGTTACTTAACC
ATGCCACAGAAAGCAA
mm4_intergenic_Gm12701|Ror1_chr4_100133141 GCTTAACTCAGTGGGGAGCCACTTATTACATAAGCTGAACCCCAGGTCTGTGGGTTTCCCTTGACCAAAGAGGCAGTACC
TGGAGTTATGAGGAAAACAGAAAGACCCACTTCTCTGCAGT
mm4_intergenic_Gm26894|9530036O11Rik_chr5_28539035 TGATGGGTGTGAACCACGAGAAATATGACAACTCACTCAAGATTGTCAGCAATGCATCCTGCACTACCAACTGCTTAGCC
CCTCTGGCCAAGGTCATCCATGACAACTTTGGCATTGTGGAAGGGC
mm4_exon_Gm9146_chr7_32473721 ACTGCACCACTGACTGCTTAGCCTCTCTGGCCAAGGTCATCCATGACAACTTCGGCATCATGGACGAGCTCATGACCACA
GTCCATGACATCACTGCCACTCAGAACTCTGTGGATTGCCCCTCTGGAAAGATGTGGCGT
mm4_exon_Gm5652_chr12_5590129 ATAAGCCCTTCCACGATGCCAAAGTTGTCATGGATGACCTTGGCCAGAGGGGCTAAGCAGTTGGTGGTGCAGGATGCATT
GCTGACAATCTTGAGTGAATTGTCATATTTCTCATGGTTCACACCCACCACAAA
mm4_exon_Gm5523_chr1_13786395 GCCCTTCCACAATGCCAAAGTTGTCATGGATGACCTTGGCCAGAGGGGCTAAGCAGTTGGTGGTGCAGGATGCATTGCTG
ACAATCTTGAGTGAGTTGTCATATTTCTCGTGGTTCACACCCATCA
mm3_intron_Nars2_chr7_97010923 AGAAGATCCAGTTGGCACCATATGAGACATATATATCACATAAAATTTATAGGTTTCTCTTGCCCAGAGTGGCTAGACAG
ATTAAGTCCCTAGTATACATTTGTTGAATTAAACGGGCAATGGGGAGG
mm4_intergenic_Gm10087|Sbf2_chr7_110532218 TCACTTGCTTGATTGCCAGTTCTCTAGCTACCTTCCCTAAGAAACCCTTCCTACCTAGGAATTTGGGAACTGTGTCTATC
TAGCTTTCCTATGGCCAGAGAGGATATATCCCAGAATGTGGCAGAAACA
mm4_intergenic_1700010I14Rik|6530411M01Rik_chr17_9030350 GGTCTGTAGCGGCTGTTCATGTGAGTAGTATGCATTGAAGCTGTTCTCTGAAGGATCAGATTATAAGCTGCCCTTTGCCA
GAAGGGGGCAACATACCAGAGAGACCAGTGAGACCTCTAACAGCCCT
mm4_intergenic_Atf6b|Tnxb_chr17_34663745 GGAGAGGCTATGCAAACACCTTCCTCTTTGGCCCAGAGGAACCTAGGATGTGTGTCCATTGGGAGAGGG
mm4_intergenic_Gm24092|Cenpf_chr1_189516710 TTCCCTGCTCAGAAGTGGTGCAATAGTCTTATCAGGTTTCTCCATGTGTCTCCATCTTGCTCTTGGCCAGAGTGGTCCAG
TCAGTATTAAGATATAAGAAAGATTCTTGCTTCTTACTAAATGGGCAGTGGTTGAGT
mm4_intergenic_Ubn2|Ubn2/mmu-mir-7670_chr6_38501484 CCTGGCTTCTGTTTGGGTCTTTGTTTCTCTATCCAGTGCTCTGGGCTGTTGGGTACCACTCTGGCCTGGGGAACCCTATC
TTCTCTTCCTCCAATGTTTTTAGAAGTGTTTGGCTGAGAGTT
mm3_intergenic_Trip11|Gm20701_chr12_101862799 GCTGGGAGGTGCTTCAGAATCAATCAATAGCTCAGCCAGTGGCGAAGCTGCACCTCAGTGGCCATGGGCAACCTACTGAC
CTCATAACCCTTTACAATGGATCCATGCCCTTT
mm4_exon_P2rx1_chr11_72999251 CACTTGGCCTGCTCTGTTCTTAAGGGGCTGGGAAGCCTCCAGCCACTCCACTGCTCTCTCTGTAGACACAGATGCTAGCC
TGCCCTTGACCACAGAGGCCGTGCGGGGGGCTTGTCTCTGAGCCCCTTC
mm4_intron_Kcnh1_chr1_192455000 GCCAATACCCAGGGTTCCAAGTAGAGCTATGGGGATCCCTTCAGGGGAAACCACTGTGGCCAAGGTCACCCTGAGCATAT
GGTCCCATTTGCTGAGGTTGACTCTGCCCAG
mm4_intron_Gm3235_chr8_91622454 TCAAGTGTAAAATTGGGCCCCTCGATTGCCCTGGGCCACAGTGGCTGCGTTAAGGAAGCTCGATTTACCTTGCAGCCGAG
TGAAAAATGATCAGAATATTAGACTCATCTAGCCCACATTAAGGCGCCATTG
mm4_intron_Tmem28_chrX_99840022 GGCTCCTTTAGAACTGTCCCTGGATTATGAATACTACTTCTCTATTAGTCTACCCTTGGCCAGACTGGGCATATCTAGCC
TTTGAACAGATGGTCTAGGAGGCTTGTACATATGAGGACCCTCCAGAATGGA
mm4_exon_Adamts20_chr15_94333716 TCTTACGGACGCAGGCAATTTTTCTTCTATGAAGACCTTGGCCAGAGTGGAATAGAAATTAAAAATTAAAGAGAAATGTA
TTTAAGTAGATGTCCTGTAATTACAATAACTAGCACAAATGACTCAGCTAGGAAGGCAG
mm4_intron_Dlg2_chr7_91853767 AGGAGAAGTGAAGCAGTTGCTTTCTTTTCCATTCTGGCCAAGGGCCCACTAAGGAACTCTATGCCTTTCTCCCGCACTTC
AGTTCC
mm3_intergenic_Gm14597|Cxx1c_chrX_53580057 AACCAGTGGGCATTGTTCCACAAACCAACCAATGGGAGCGCAGCATGCGCTCACAATGCTCCTCTGGCCAATGGCAAGCT
TCGGGAGGAAAAACATGGATCCTCCTATGCATTTTGTCTCTAGCACAGCAAGAACA
mm4_intergenic_Ces5a|Gm26843_chr8_93661870 GGGGTGTGACCTCAAGAGACACAGATCAGCTGGTGTGCAGCTTTTTACTCAGTACCCACCTCCACCCTGGCCAAGGGGAA
GCTGCCAAGGAGCAGATTCACCTCCGTACAGCAGAGGGCAGTGGTGAGCTCATCTCGACC
mm4_exon_Hist1h2be/Gm11398_chr13_23619863 TTCAGCCTGCTTCCTGCTTTCCAGGTGTAACAAGTGCACCACCACTATGGGCAAGGGGCACCTAGGACACATACTTGTTG
AAAGCTGCCAAAGACGTGAACT
mm4_intron_Gpr98_chr13_81575660 CTCCCCTTCTTTGCCAGACCTAAATTACTACAAAAACACCTTTCAGAACTCCATTCATGCCAAGAGCAACCTAATGCTTA
AAGAAGTACAGCACACATATAACACACTATTAATCTGCCTGTAGTTGACAAAGATGGT
mm4_intergenic_Gm17037|Gm23822_chr5_18851868 GGCATTGGAAAATATCAGCTGCTTAATATACCTGGTTCCAGAATGTGGACATAGGGTGTCCTTGGCCAGCAGGGGTATTA
AGGTTTTGTTTAACATTGACTCATTGATTTCCTAACGCCTGGACT
mm4_intergenic_Gm17037|Gm23822_chr5_18755905 AGTCCAGGCGTTAGGAAATCAATGAGTCAATGTTAAACAAAACCTTAATACCCCTGCTGGCCAAGGACACCCTATGTCCA
CATTCTGGAACCAGGTATATTAGGCAGCTGATATTTTCCAATGC
mm4_intergenic_Kazn|Gm13052_chr4_142287559 ACCACAGAGGAGGGGAAGAACCCTGAGTTGTGGCATGGGTGGCGATCCCCATGGTATAAATACCGCCACTGTGGCCAATG
TCAAACTACCAGAGTAGTTCTGGAACATTGGACCTTGGCTCTCAGGAGTCT
mm4_intergenic_Dner|Dner/Mir5126_chr1_84598108 CCCTCTGAAGGTTACTGCGGATCCAGAACTGAGTGAAACATTCTAGATTTGTTGTCCTTTGTCCTTGGCCAGAGTGGCCA
GAATATGGATGCCACCAGTTTAACCT
mm4_intergenic_AL596090.1|Gm12266_chr11_60308898 TGTGGAAAGTCTTTCTCAGCCTTCTCTATATACTACCGACCCACTCTAGCCTAGGGCAGACTAGGCTGGGTGCCAGTAAA
GGCTGAGCAAATATTAAAGCAACTTGATCCCCACCC
mm4_intron_Limch1_chr5_66817576 TGAGGAGAGAGGAGGCAACATGCCACCTGCTCTGGCCAAGGACAACAGTTGAAGTCCCAAGAGCATCCTAGAAGGAGTCA
CCCCAACAGCTCCAGTGTCCTCATGTTGACCACCG
mm3_intergenic_Ctdp1|Nfatc1_chr18_80579659 CCTTTGAGGACAGCAGCAAGATTCACCTCTCAGGCCAATGGGAACCTAGTGGCGAGGCCAGGAAACTGCCTGCCTGCTCA
GTAGTTAGCAGTTGCTGCTGAGATGCTGA
mm4_intron_Ttc6_chr12_57566297 GCTTGCCCAGTGGGTATGAAATAATGGTACAGATTTCCACTTTACATCTGTAAAGAAAGATAGTGCTAGTGTTTGTGACC
CAGTCTTGCAAAGGGCCACCTACCATGGAGAACAGCATTCCTAACCC
mm4_intergenic_Ssu2|Cav3_chr6_112397559 CTTCCCAAGGCCTGCTTCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNCCCACCCTGTCCAAGGACAACCTTCTTCTGCCTCCAGAGCAC
mm4_intergenic_Gm25818|Creb5_chr6_53572470 CTCTTAGCCTAGTTCCCCGCCCCCCTTCCCGAGAGTGGAGAGCTAACCTCAGAAGGACAAGGTTGCACTTGGCTGGAGGG
GTCCTTTCTCTTAGCACATTAAAGAACCACCAGAGCTGCC
mm3_intergenic_Cish/Gm17041|Hemk1_chr9_107309801 CGGTTCCTGTCCTTGTAGGGTAGGCTGGCCTTGGCCAGAAAGAGCCTGCTGCTGTGGAGAATCTGTGACCCACTCAATTC
GGGTGGCAGAG
mm3_intron_Duox1_chr2_122346065 CTTGAGGAAGCTGCCTTGGACCTGACAGACGTTCAGATCAGTGGTGGAAGGCTCTTTGGTGAGATCGCTTCTCACTCACA
CCACTCTGTCCAAGGGCAAAATACATCTCTGTATTGAGGCTGGCCCTACTTCCTGTAC
mm4_intergenic_Kcnb1|Kcnb1/1110018N20Rik_chr2_167113698 GACCGATGGGGAGAACAACTATTCTGGATATGAACGGGTTAACCCCAGCACTAGGCTGACCTTGTACAGAGAGGCCTGGC
AGCTCTTGGTCTGTGTGGTTTGCATCTCCAGCCACAGGAGCTTAGTGTGCA
mm3_intergenic_Gm15083|Slc6a11_chr6_114059025 TGCCTTTCACCTCTGGTCACCTCTGTGGTGCTTTTTCTCAGCACAGTGAAGCCTTCCTTTGAAGACTGCAGGCACTGGGC
TCCCTCTGGCCAAGGCCAGCCTGTGACCCTTTCCCCTTTCAGTCCC
mm4_intron_Irf8_chr8_120739370 AGCACAGGACTCCAGCTCTAACTCCATCCCAGTGGGAACAGGACCCTATACTGTCTGATATTACTATTACTATCCTAGCT
GGCAAAGGGCAACCTGCAAGCAGCCTTGAGGGTGTCCTCTTTCTCGGGTG
mm4_intergenic_Osm|Lif_chr11_4253639 ACCCCTACCCTGTAGCCTGCCTCCCCTCAGGCCCAGCACAACCTACCCTGCAGCCTGCCCCCCCCCTCCGGCCCAGCACA
CCCCTACCCT
mm4_exon_Npr2_chr4_43643314 ATAGACCCTTGCACCACCACCACCACCATCTAATGTTCCTTTCATCCTTCCGCCTCCATGTTGCCCTTGGCCCCAGCGGG
GATCCAGTTACGGCTCGCTCATGAC
mm4_intergenic_Gm13002|Wnt4_chr4_137268070 GCTGGCTTTCCCTGACTTCTTTCCCTAAAGCAAATGTGAATCAAGTTCACATCGGCCACACGGGCCATGGGCATCCTACA
TGTTCTGCCATGTTTAAAAAAAAAGGTGAGTTTGACAGGTCACTTGTCCCC
mm4_intergenic_Tbc1d22a|Gm23416_chr15_86583725 GGCTCCGTCTTCTCAAAGCACTGATGCAAAGCTTTATCCAGACCCTGGGGTCATGTGATCAAACACCTCTTGCTGCCATT
CTGCCCATGGGCAACCTCACCTCGGGACTGACCCAGGTCCTTGAC
mm4_intron_Mlph_chr1_90932942 TCTGGGAGCCCTGAATACCAAGATCCCATGAGGATGGTGGCACCATGCAGACCCCCTCAGTCTAAGGGCAACCTGCTCAG
GAAACCTCACCTCTACCCT
mm4_intron_Dnajc15_chr14_77874615 CGCGCCCTGGTTCTTAACTACTTTTCCCCAAGGGAGGCTCCTGGCTCCACCGGGCCCCCTCTGCCCAGGGGGAACCCATG
GGTCTCTTCACTGGATAACCGTGGGCCTGTTCTG
mm4_intergenic_Gm13471|Gm13481_chr2_48156115 AGCCAGGCCTTTCAATTCCTCTTTTCTGTCATTCCCATTGTGTGTTATTAATTTTTAGATCTCTAGGTTCCCACTCAGGC
CAAGGTCAAGGTAGCATTACCTGTATTACTGCAGCACATATCTTGTAGCTGCCTGAACGT
mm4_intron_Synj1_chr16_90955634 AATTCCACGTGGAGGCTGTTCACAGTCTGCCTTTAAGAGCTTATGATGCCAAATAGAAGTAGTTAGGATTCCTTCACTCT
GGCCAAAGGCAAACCGCTGATAATGTGCTATGTAGTTCTGGCTTGGATCCATAAGCT
mm3_intergenic_Slc24a3|Gm14093_chr2_145268171 CAGTGAAAGTAGGGCTTCCCTTTTCTCTCTGGCCAAGAGCAAACAAAACTCCAACTTAGACATTCAAGGTCTTCCCTTTG
TCGAGAATGCATGAGCAACAGCCTCCACAGAA
mm4_intron_Mdga1_chr17_29953342 GCTGTTCCTGCCCAACAAAGATTATCACAGCTGGGCTACTAGAACCTAGGTTGCTCTTGGAGAGGGTGGGGAGGATCATG
AGACGCTCACCTGAGTAGC
mm4_intergenic_Gm23698|Gm22186_chr10_110882296 CCCAGCAACAGCCAATACACACAAAGCTCTGACCAAGTCACAACTGAAGCAGGATGCAGAGTCCTCTCTGACCACGGGCC
ACCAAGGAGCCCTGGCAGAGCTGGGCTGGGACCTGGGCCTGGACTAGCAATAGC
mm4_intergenic_Gm20713/Gpc5|Gm20713_chr14_115809793 AGCTGCTGTGGTGAAAGTCAAGCAGCCCTCACTGCCGAAGGGCAACCCAAGTAGATGGATCTGGAGTTGTCCTCATGATT
AGTTCAGACTGGAGTGTGGC
mm4_intergenic_Mdfic|Tfec_chr6_16624126 GCGTAAGGCATGTGATTGTGTGTAGGTTGCCTTTGGGTAGACTGGGAACACTAAAGAGAGAATGTGTAGCTTTAATACAC
ACAGAGCAACTTTGTTCATTCAAGCA
mm4_intron_Suds3_chr5_117105993 TCGCCTGCCAGTTAACTTGAATCTGACAAACCAAAAAGCACCTCTTATGTCCCACTGGGACCAAGGGCAGCCTATCATTC
AAGAGCCAGGCCCTTGTCTCAGCACCATAGCACCGAA
mm4_intron_Ppargc1b_chr18_61340835 TTCACCTGGCCTACCTGTCAGGGGTCAGCTCCCCAGCCCCACCCATCAGTCACAGGATGAGACCAGCAGAAACAAGGAGG
TTGTCCTTGTGCATCAGGGTGCCCTTGGGGAGAGCGGCGGACTTCACAGACAGGTCC
mm4_intergenic_Gm26463|Gap_chr5_151703525 TCACCTCTTCACTTGCTGGCATAAATTTTGATTGTGTATGCTATACTGTGAATTCTTCCCCCTCAGCCTCACTACTACTG
AGATGGCTGCTGCCACTCAGACCAGGGGAAACCTATACAAACAGGTTCTGCCAAATGCCA

Input file for Crispresso

Crispresso, written by Luca Pinello, is a software package to quantify the Cas9-induced mutations on off- or on-targets.

Click here to download an amplicon input file for Crispresso. For each off-target, it includes the off-target name, its PCR amplicon and the guide sequence. Keep a copy of this file.

After sequencing, run CRISPRessoPooled. The tool will map the reads to the amplicons and analyse the mutations:
CRISPRessoPooled -r1 Reads1.fastq.gz -r2 Reads2.fastq.gz -f crisporAmplicons_mN1FkRligAThyqKv3eg3.txt --name MY_EXPERIMENT

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CRISPR/Cas9 Guide Designer for chordate vertebrate ecdysozoans lophotrochozoans protostomes spongi corals plants butterflies metazoans genomes fruitflies insects nematodes mammals.