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Contents:

PCR primers for off-targets of TGGCACTCTGGTTGGTAAGA GGG

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_52313891_F TCGTCGGCAGCGTCGAGAGTCCGGGGATGGAGAG 60.8 1.00
ontarget_mm0_exon_5730457N03Rik/Evx1_chr6_52313891_R GTCTCGTGGGCTCGGCCATCTTCTCTGGCGGTTCA 59.7 1.00
mm3_intergenic_Gm7627|Gm24120_chr7_69751823_F TCGTCGGCAGCGTCTCCCTTGTGAAAAGAATGTGGT 58.0 0.66
mm3_intergenic_Gm7627|Gm24120_chr7_69751823_R GTCTCGTGGGCTCGGCCCCTACCACAATGTAAGACCC 60.0 0.66
mm4_intergenic_Gm26288|Atp10a_chr7_58495328_F TCGTCGGCAGCGTCAAAGGTTCCATCCCACCTGG 59.5 0.60
mm4_intergenic_Gm26288|Atp10a_chr7_58495328_R GTCTCGTGGGCTCGGGCACACTGAAACACGCACTT 59.9 0.60
mm4_intron_Xpo1_chr11_23265624_F Primer3: not found at this Tm N.d. 0.53
mm4_intron_Xpo1_chr11_23265624_R Primer3: not found at this Tm N.d. 0.53
mm3_intron_Zfp277_chr12_40361207_F Primer3: not found at this Tm N.d. 0.51
mm3_intron_Zfp277_chr12_40361207_R Primer3: not found at this Tm N.d. 0.51
mm4_intergenic_Gm25382|Cited2_chr10_17569297_F Primer3: not found at this Tm N.d. 0.51
mm4_intergenic_Gm25382|Cited2_chr10_17569297_R Primer3: not found at this Tm N.d. 0.51
mm3_intron_Nell2_chr15_95492834_F Primer3: not found at this Tm N.d. 0.51
mm3_intron_Nell2_chr15_95492834_R Primer3: not found at this Tm N.d. 0.51
mm4_intron_BC089491_chr7_28288645_F TCGTCGGCAGCGTCCCACTCCCTTGGTACCTTGC 60.3 0.49
mm4_intron_BC089491_chr7_28288645_R GTCTCGTGGGCTCGGTTTGTAGCTGGGCAAGGTGG 60.5 0.49
mm4_intergenic_Dppa3|Gm10420_chr6_122657600_F Primer3: not found at this Tm N.d. 0.48
mm4_intergenic_Dppa3|Gm10420_chr6_122657600_R Primer3: not found at this Tm N.d. 0.48
mm4_intergenic_Fancg|Pigo_chr4_43014799_F Primer3: not found at this Tm N.d. 0.48
mm4_intergenic_Fancg|Pigo_chr4_43014799_R Primer3: not found at this Tm N.d. 0.48
mm4_intron_Mb21d2_chr16_28874579_F TCGTCGGCAGCGTCCTCTGGCTCGCCCTTAAGAG 59.8 0.40
mm4_intron_Mb21d2_chr16_28874579_R GTCTCGTGGGCTCGGTATCCCTCGATCTGGGGACA 59.1 0.40
mm4_intergenic_Gm22284|F630206G17Rik_chr11_45675286_F Primer3: not found at this Tm N.d. 0.35
mm4_intergenic_Gm22284|F630206G17Rik_chr11_45675286_R Primer3: not found at this Tm N.d. 0.35
mm4_intergenic_Gm12803|9630013D21Rik_chr4_109648205_F Primer3: not found at this Tm N.d. 0.34
mm4_intergenic_Gm12803|9630013D21Rik_chr4_109648205_R Primer3: not found at this Tm N.d. 0.34
mm3_intergenic_Gm25682|Adgb_chr10_10190652_F TCGTCGGCAGCGTCTGTGAACACATTCCCTCAAGAGA 59.6 0.32
mm3_intergenic_Gm25682|Adgb_chr10_10190652_R GTCTCGTGGGCTCGGCCTCATTCCTAGTCTCCCTGC 59.3 0.32
mm4_intron_Drd2_chr9_49394167_F Primer3: not found at this Tm N.d. 0.30
mm4_intron_Drd2_chr9_49394167_R Primer3: not found at this Tm N.d. 0.30
mm2_intergenic_Myl10|Col26a1_chr5_136701117_F TCGTCGGCAGCGTCGCGTCTGAGTGATGTTTGCG 60.1 0.29
mm2_intergenic_Myl10|Col26a1_chr5_136701117_R GTCTCGTGGGCTCGGGGAACAGCTGAGCAGAGCAA 60.6 0.29
mm4_intergenic_Gm22021|Gm25724_chr14_104611204_F TCGTCGGCAGCGTCGTTAGTTATGATAGCTCCTTTTGGC 58.0 0.27
mm4_intergenic_Gm22021|Gm25724_chr14_104611204_R GTCTCGTGGGCTCGGAAACAGGGGAGATGCAAACA 57.6 0.27
mm4_intergenic_Gm22750|Rpl10a-ps2_chr13_8939610_F Primer3: not found at this Tm N.d. 0.27
mm4_intergenic_Gm22750|Rpl10a-ps2_chr13_8939610_R Primer3: not found at this Tm N.d. 0.27
mm4_intron_Prkch_chr12_73719389_F Primer3: not found at this Tm N.d. 0.27
mm4_intron_Prkch_chr12_73719389_R Primer3: not found at this Tm N.d. 0.27
mm4_intergenic_Gm25805|Usp7_chr16_8774605_F Primer3: not found at this Tm N.d. 0.25
mm4_intergenic_Gm25805|Usp7_chr16_8774605_R Primer3: not found at this Tm N.d. 0.25
mm4_intergenic_Capn10|Gpr35_chr1_92958318_F TCGTCGGCAGCGTCGGTGTAGGTAGGAGAGGTCACT 60.0 0.25
mm4_intergenic_Capn10|Gpr35_chr1_92958318_R GTCTCGTGGGCTCGGGGTGTCTTCTGTCAGATGCCT 59.7 0.25
mm4_intergenic_Ppap2b|Gm12722_chr4_105309342_F Primer3: not found at this Tm N.d. 0.24
mm4_intergenic_Ppap2b|Gm12722_chr4_105309342_R Primer3: not found at this Tm N.d. 0.24
mm4_intergenic_Gm23352|Wdr27_chr17_14795969_F TCGTCGGCAGCGTCTCCACCCTATCTCACACCTGT 59.9 0.23
mm4_intergenic_Gm23352|Wdr27_chr17_14795969_R GTCTCGTGGGCTCGGGCTTATTGGCTGTGAGAACTGT 58.9 0.23
mm4_intergenic_Med13l|n-R5s175_chr5_119217955_F Primer3: not found at this Tm N.d. 0.22
mm4_intergenic_Med13l|n-R5s175_chr5_119217955_R Primer3: not found at this Tm N.d. 0.22
mm4_intron_Gm5431_chr11_48899186_F Primer3: not found at this Tm N.d. 0.20
mm4_intron_Gm5431_chr11_48899186_R Primer3: not found at this Tm N.d. 0.20
mm4_intron_Gm12185_chr11_48918885_F Primer3: not found at this Tm N.d. 0.20
mm4_intron_Gm12185_chr11_48918885_R Primer3: not found at this Tm N.d. 0.20
mm4_intergenic_Gm12187|Ifi47_chr11_49073040_F Primer3: not found at this Tm N.d. 0.20
mm4_intergenic_Gm12187|Ifi47_chr11_49073040_R Primer3: not found at this Tm N.d. 0.20
mm4_intron_Megf11_chr9_64571503_F TCGTCGGCAGCGTCTGCGACTCTACTCCTGACTGT 60.2 0.20
mm4_intron_Megf11_chr9_64571503_R GTCTCGTGGGCTCGGGGTGAGAGCAGACATGAGCA 59.7 0.20
mm4_intron_Herc2_chr7_56203712_F Primer3: not found at this Tm N.d. 0.20
mm4_intron_Herc2_chr7_56203712_R Primer3: not found at this Tm N.d. 0.20
mm4_intergenic_n-R5s209|Gm7846_chr1_27450417_F Primer3: not found at this Tm N.d. 0.18
mm4_intergenic_n-R5s209|Gm7846_chr1_27450417_R Primer3: not found at this Tm N.d. 0.18
mm4_intergenic_Gm23154|Gm12604_chr4_87538426_F Primer3: not found at this Tm N.d. 0.18
mm4_intergenic_Gm23154|Gm12604_chr4_87538426_R Primer3: not found at this Tm N.d. 0.18
mm4_intergenic_Gm22527|Rnf144a_chr12_25732364_F TCGTCGGCAGCGTCCCCTGCTGACGGAACTGTTC 60.9 0.18
mm4_intergenic_Gm22527|Rnf144a_chr12_25732364_R GTCTCGTGGGCTCGGTAAGGGATCCTTCGGCCTGT 60.3 0.18
mm4_intron_Nsun6_chr2_15011482_F Primer3: not found at this Tm N.d. 0.18
mm4_intron_Nsun6_chr2_15011482_R Primer3: not found at this Tm N.d. 0.18
mm4_intergenic_Slc22a22|Zhx2_chr15_57482661_F Primer3: not found at this Tm N.d. 0.18
mm4_intergenic_Slc22a22|Zhx2_chr15_57482661_R Primer3: not found at this Tm N.d. 0.18
mm4_intergenic_AC112986.1|Tsn_chr1_117611897_F Primer3: not found at this Tm N.d. 0.17
mm4_intergenic_AC112986.1|Tsn_chr1_117611897_R Primer3: not found at this Tm N.d. 0.17
mm3_intron_Podn_chr4_108016400_F Primer3: not found at this Tm N.d. 0.17
mm3_intron_Podn_chr4_108016400_R Primer3: not found at this Tm N.d. 0.17
mm4_intergenic_Ccdc141|Sestd1_chr2_77172282_F Primer3: not found at this Tm N.d. 0.17
mm4_intergenic_Ccdc141|Sestd1_chr2_77172282_R Primer3: not found at this Tm N.d. 0.17
mm4_intergenic_Ptprj|Nup160_chr2_90638612_F Primer3: not found at this Tm N.d. 0.17
mm4_intergenic_Ptprj|Nup160_chr2_90638612_R Primer3: not found at this Tm N.d. 0.17
mm4_intron_Gm765_chr6_98267716_F TCGTCGGCAGCGTCTAAGTGTCTCACTCTGCCGC 59.7 0.16
mm4_intron_Gm765_chr6_98267716_R GTCTCGTGGGCTCGGGGTCTCAGAGGGTGGATCCT 60.0 0.16
mm4_intron_Efna1_chr3_89275963_F TCGTCGGCAGCGTCCCTTCCCAGCTTCCTCAAGG 60.0 0.16
mm4_intron_Efna1_chr3_89275963_R GTCTCGTGGGCTCGGGCATCAGGGATGTGGTGTGA 60.0 0.16
mm4_intergenic_Gm24490|Abcc12_chr8_86461793_F TCGTCGGCAGCGTCTGTGTAGGGTGGGAACAGGA 60.1 0.16
mm4_intergenic_Gm24490|Abcc12_chr8_86461793_R GTCTCGTGGGCTCGGCTTCCTACGGCTGTCTGACC 59.8 0.16
mm4_intron_Dennd2a_chr6_39495410_F TCGTCGGCAGCGTCGACAAAGGGAAAGGGGAGGG 59.9 0.16
mm4_intron_Dennd2a_chr6_39495410_R GTCTCGTGGGCTCGGGGACAGCCACCTTCAGTGTT 60.1 0.16
mm4_intron_Ankrd27_chr7_35603502_F TCGTCGGCAGCGTCATGTGCATATGCCCGAGAGC 60.6 0.16
mm4_intron_Ankrd27_chr7_35603502_R GTCTCGTGGGCTCGGCCAGGTGAGAGTCTCGGAGA 60.0 0.16
mm4_intergenic_Gm12111|Rpsa-ps4_chr11_32950868_F Primer3: not found at this Tm N.d. 0.15
mm4_intergenic_Gm12111|Rpsa-ps4_chr11_32950868_R Primer3: not found at this Tm N.d. 0.15
mm4_intergenic_Rpl36-ps3|Mycn_chr12_12930812_F Primer3: not found at this Tm N.d. 0.15
mm4_intergenic_Rpl36-ps3|Mycn_chr12_12930812_R Primer3: not found at this Tm N.d. 0.15
mm4_intron_Tars2_chr3_95753443_F Primer3: not found at this Tm N.d. 0.15
mm4_intron_Tars2_chr3_95753443_R Primer3: not found at this Tm N.d. 0.15
mm4_intergenic_Adamts18|Nudt7_chr8_113888295_F Primer3: not found at this Tm N.d. 0.15
mm4_intergenic_Adamts18|Nudt7_chr8_113888295_R Primer3: not found at this Tm N.d. 0.15
mm4_intergenic_Gm26129|n-R5s52_chr13_14088814_F Primer3: not found at this Tm N.d. 0.14
mm4_intergenic_Gm26129|n-R5s52_chr13_14088814_R Primer3: not found at this Tm N.d. 0.14
mm4_intergenic_Slc27a5|Zbtb45_chr7_12998871_F Primer3: not found at this Tm N.d. 0.14
mm4_intergenic_Slc27a5|Zbtb45_chr7_12998871_R Primer3: not found at this Tm N.d. 0.14
mm4_intergenic_Idi2|Gtpbp4_chr13_8961516_F Primer3: not found at this Tm N.d. 0.14
mm4_intergenic_Idi2|Gtpbp4_chr13_8961516_R Primer3: not found at this Tm N.d. 0.14
mm4_intergenic_Gm27039|Adcyap1_chr17_92846542_F TCGTCGGCAGCGTCTGCACCACTTTCAAGGGTTG 58.8 0.14
mm4_intergenic_Gm27039|Adcyap1_chr17_92846542_R GTCTCGTGGGCTCGGTCATCTCTGCACTGGTTTGT 57.0 0.14
mm4_intergenic_Ctdp1|Nfatc1_chr18_80582800_F TCGTCGGCAGCGTCCGTCAGGCAGAATGGCATCT 60.4 0.14
mm4_intergenic_Ctdp1|Nfatc1_chr18_80582800_R GTCTCGTGGGCTCGGATGTTCCTGAGCACCTTGGG 59.9 0.14
mm4_intergenic_Mir3962|Gm23885_chr1_194845089_F Primer3: not found at this Tm N.d. 0.13
mm4_intergenic_Mir3962|Gm23885_chr1_194845089_R Primer3: not found at this Tm N.d. 0.13
mm4_intergenic_Gm11655|Prkca_chr11_108213541_F TCGTCGGCAGCGTCGGGGAGAGACAGCAAAGCAT 60.0 0.13
mm4_intergenic_Gm11655|Prkca_chr11_108213541_R GTCTCGTGGGCTCGGAAGAGTTGACCCTCCCTGGA 59.8 0.13
mm4_intron_Bmper_chr9_23313562_F TCGTCGGCAGCGTCCTCAGCCCTGCAATTCAAGC 59.8 0.12
mm4_intron_Bmper_chr9_23313562_R GTCTCGTGGGCTCGGAGAGTCTTGGTAGTGGCTCT 57.3 0.12
mm4_intron_Tm6sf2_chr8_70077812_F Primer3: not found at this Tm N.d. 0.12
mm4_intron_Tm6sf2_chr8_70077812_R Primer3: not found at this Tm N.d. 0.12
mm4_intergenic_Dock2|Dock2/4930403D09Rik_chr11_34302982_F Primer3: not found at this Tm N.d. 0.12
mm4_intergenic_Dock2|Dock2/4930403D09Rik_chr11_34302982_R Primer3: not found at this Tm N.d. 0.12
mm4_intergenic_Tmem200a/Gm9767|Samd3_chr10_26203803_F Primer3: not found at this Tm N.d. 0.12
mm4_intergenic_Tmem200a/Gm9767|Samd3_chr10_26203803_R Primer3: not found at this Tm N.d. 0.12
mm4_intergenic_Gm23835|Fam84b/9930014A18Rik_chr15_60711142_F Primer3: not found at this Tm N.d. 0.11
mm4_intergenic_Gm23835|Fam84b/9930014A18Rik_chr15_60711142_R Primer3: not found at this Tm N.d. 0.11
mm4_intron_Hmgcll1_chr9_76058007_F Primer3: not found at this Tm N.d. 0.11
mm4_intron_Hmgcll1_chr9_76058007_R Primer3: not found at this Tm N.d. 0.11
mm4_intergenic_Tdrd3|Rps3a2_chr14_87695675_F Primer3: not found at this Tm N.d. 0.11
mm4_intergenic_Tdrd3|Rps3a2_chr14_87695675_R Primer3: not found at this Tm N.d. 0.11
mm4_intron_Pknox2_chr9_36930545_F Primer3: not found at this Tm N.d. 0.10
mm4_intron_Pknox2_chr9_36930545_R Primer3: not found at this Tm N.d. 0.10
mm4_intron_Sipa1l3_chr7_29479719_F TCGTCGGCAGCGTCAGAGTGTGCCCCTCTTCTCT 59.8 0.10
mm4_intron_Sipa1l3_chr7_29479719_R GTCTCGTGGGCTCGGGGTGTGACAGTGCCACAGTA 59.8 0.10
mm4_intron_Rere_chr4_150591801_F Primer3: not found at this Tm N.d. 0.10
mm4_intron_Rere_chr4_150591801_R Primer3: not found at this Tm N.d. 0.10
mm4_intergenic_F930017D23Rik|Gm9034_chr10_43665556_F Primer3: not found at this Tm N.d. 0.09
mm4_intergenic_F930017D23Rik|Gm9034_chr10_43665556_R Primer3: not found at this Tm N.d. 0.09
mm4_intergenic_5730508B09Rik|Gm10650_chr3_127898516_F Primer3: not found at this Tm N.d. 0.09
mm4_intergenic_5730508B09Rik|Gm10650_chr3_127898516_R Primer3: not found at this Tm N.d. 0.09
mm4_intergenic_Gm23891|1700018B24Rik_chr3_47274623_F Primer3: not found at this Tm N.d. 0.09
mm4_intergenic_Gm23891|1700018B24Rik_chr3_47274623_R Primer3: not found at this Tm N.d. 0.09
mm4_intergenic_Gm4791|Gm22286_chr9_47188834_F Primer3: not found at this Tm N.d. 0.09
mm4_intergenic_Gm4791|Gm22286_chr9_47188834_R Primer3: not found at this Tm N.d. 0.09
mm3_intergenic_Elovl5|Gm23609_chr9_78006128_F TCGTCGGCAGCGTCAACGCAGTATGAGCATGGCT 60.1 0.09
mm3_intergenic_Elovl5|Gm23609_chr9_78006128_R GTCTCGTGGGCTCGGGTCTTGGGTTCTGAAGGGAGG 59.9 0.09
mm4_intron_Kif13a_chr13_46771993_F Primer3: not found at this Tm N.d. 0.08
mm4_intron_Kif13a_chr13_46771993_R Primer3: not found at this Tm N.d. 0.08
mm4_intergenic_Gm22034|Gm23965_chr1_103126933_F Primer3: not found at this Tm N.d. 0.08
mm4_intergenic_Gm22034|Gm23965_chr1_103126933_R Primer3: not found at this Tm N.d. 0.08
mm4_intron_Cmya5_chr13_93084882_F Primer3: not found at this Tm N.d. 0.08
mm4_intron_Cmya5_chr13_93084882_R Primer3: not found at this Tm N.d. 0.08
mm4_intron_Chst11_chr10_82987548_F TCGTCGGCAGCGTCACCTGTGGTTGTGAAACTTGTG 59.5 0.08
mm4_intron_Chst11_chr10_82987548_R GTCTCGTGGGCTCGGTGGAGCTTGGCACTCTTGAG 59.9 0.08
mm4_intron_Lrfn5_chr12_61560861_F Primer3: not found at this Tm N.d. 0.08
mm4_intron_Lrfn5_chr12_61560861_R Primer3: not found at this Tm N.d. 0.08
mm4_intron_Tbc1d22a_chr15_86410433_F TCGTCGGCAGCGTCGGGGTTCTGATCACCTGCTT 59.6 0.07
mm4_intron_Tbc1d22a_chr15_86410433_R GTCTCGTGGGCTCGGCCTGCACCCTCAGTCAGAAG 60.0 0.07
mm4_intergenic_Gm5601|Acsm3_chr7_119745326_F Primer3: not found at this Tm N.d. 0.07
mm4_intergenic_Gm5601|Acsm3_chr7_119745326_R Primer3: not found at this Tm N.d. 0.07
mm4_intron_Ccdc18_chr5_108182417_F Primer3: not found at this Tm N.d. 0.07
mm4_intron_Ccdc18_chr5_108182417_R Primer3: not found at this Tm N.d. 0.07
mm4_intergenic_Plk2|Actbl2_chr13_110544175_F TCGTCGGCAGCGTCGCCTCTTCTCTTACCAGGCC 59.8 0.07
mm4_intergenic_Plk2|Actbl2_chr13_110544175_R GTCTCGTGGGCTCGGACCCAGAGTCATCTCAGTGC 59.0 0.07
mm4_intergenic_Arpc5|Ncf2_chr1_152784579_F Primer3: not found at this Tm N.d. 0.07
mm4_intergenic_Arpc5|Ncf2_chr1_152784579_R Primer3: not found at this Tm N.d. 0.07
mm4_intergenic_Gm13061|Zfp683_chr4_134048001_F TCGTCGGCAGCGTCTCCTTCCTCCAGGTCTGCTT 60.1 0.07
mm4_intergenic_Gm13061|Zfp683_chr4_134048001_R GTCTCGTGGGCTCGGTTTGAGGGTACTGAGCTGGC 59.6 0.07
mm4_intergenic_Caln1|Gm23761_chr5_130678067_F TCGTCGGCAGCGTCGGGATGGGCTAAGAAGTTGACA 60.0 0.07
mm4_intergenic_Caln1|Gm23761_chr5_130678067_R GTCTCGTGGGCTCGGTGGAAGTAACATATGCCCACTGT 59.7 0.07
mm4_intron_Mllt3_chr4_87931472_F Primer3: not found at this Tm N.d. 0.07
mm4_intron_Mllt3_chr4_87931472_R Primer3: not found at this Tm N.d. 0.07
mm4_intergenic_Dmrt2|Gm8825_chr19_25788629_F TCGTCGGCAGCGTCTTTCCCGATGATGGTCAGCT 59.0 0.07
mm4_intergenic_Dmrt2|Gm8825_chr19_25788629_R GTCTCGTGGGCTCGGAAGACCCAACACCAGTGAGC 60.1 0.07
mm3_intron_Gm14371_chr2_173844831_F Primer3: not found at this Tm N.d. 0.06
mm3_intron_Gm14371_chr2_173844831_R Primer3: not found at this Tm N.d. 0.06
mm4_intron_Eif4g3_chr4_138014184_F Primer3: not found at this Tm N.d. 0.06
mm4_intron_Eif4g3_chr4_138014184_R Primer3: not found at this Tm N.d. 0.06
mm4_intergenic_Cntn5|Gm25365_chr9_12515263_F Primer3: not found at this Tm N.d. 0.06
mm4_intergenic_Cntn5|Gm25365_chr9_12515263_R Primer3: not found at this Tm N.d. 0.06
mm4_intergenic_Hk2|Sema4f_chr6_82863343_F Primer3: not found at this Tm N.d. 0.06
mm4_intergenic_Hk2|Sema4f_chr6_82863343_R Primer3: not found at this Tm N.d. 0.06
mm4_intergenic_Fam166b|Tesk1_chr4_43430326_F Primer3: not found at this Tm N.d. 0.06
mm4_intergenic_Fam166b|Tesk1_chr4_43430326_R Primer3: not found at this Tm N.d. 0.06
mm4_intron_Piezo2_chr18_63290957_F Primer3: not found at this Tm N.d. 0.06
mm4_intron_Piezo2_chr18_63290957_R Primer3: not found at this Tm N.d. 0.06
mm3_intergenic_Gm26258|Zfp516_chr18_82976546_F TCGTCGGCAGCGTCAGTCACATTCATGCTGAGCT 57.2 0.06
mm3_intergenic_Gm26258|Zfp516_chr18_82976546_R GTCTCGTGGGCTCGGAACTCAAGGAGAGGTGCTGC 59.9 0.06
mm4_intron_Slc16a10_chr10_40079985_F TCGTCGGCAGCGTCTCTTTGGGCTTCTCCTTGCT 59.2 0.06
mm4_intron_Slc16a10_chr10_40079985_R GTCTCGTGGGCTCGGACAGGACACGCTGTGATGTT 59.8 0.06
mm4_intergenic_Fbxl17|4930405O22Rik_chr17_63243161_F Primer3: not found at this Tm N.d. 0.05
mm4_intergenic_Fbxl17|4930405O22Rik_chr17_63243161_R Primer3: not found at this Tm N.d. 0.05
mm4_intron_Prss12_chr3_123486662_F Primer3: not found at this Tm N.d. 0.05
mm4_intron_Prss12_chr3_123486662_R Primer3: not found at this Tm N.d. 0.05
mm4_intergenic_Gm8061|D330045A20Rik_chrX_139377766_F Primer3: not found at this Tm N.d. 0.05
mm4_intergenic_Gm8061|D330045A20Rik_chrX_139377766_R Primer3: not found at this Tm N.d. 0.05
mm4_exon_Dmd_chrX_84974731_F Primer3: not found at this Tm N.d. 0.05
mm4_exon_Dmd_chrX_84974731_R Primer3: not found at this Tm N.d. 0.05
mm3_exon_Tbrg1_chr9_37649439_F TCGTCGGCAGCGTCTCAACCAAGGGTTCGTGTGT 59.7 0.05
mm3_exon_Tbrg1_chr9_37649439_R GTCTCGTGGGCTCGGAGGCCTGAGATTCCCAGACA 60.2 0.05
mm4_intergenic_Gm21614|Gm23249_chr12_92608625_F Primer3: not found at this Tm N.d. 0.05
mm4_intergenic_Gm21614|Gm23249_chr12_92608625_R Primer3: not found at this Tm N.d. 0.05
mm4_intron_Ggta1_chr2_35429499_F Primer3: not found at this Tm N.d. 0.05
mm4_intron_Ggta1_chr2_35429499_R Primer3: not found at this Tm N.d. 0.05
mm4_intergenic_Gm8604|MALAT1_chr3_71860273_F Primer3: not found at this Tm N.d. 0.05
mm4_intergenic_Gm8604|MALAT1_chr3_71860273_R Primer3: not found at this Tm N.d. 0.05
mm4_intergenic_Gm13218|Gata3_chr2_9618588_F TCGTCGGCAGCGTCACAGACTTATTGTGAGGCCCG 60.0 0.05
mm4_intergenic_Gm13218|Gata3_chr2_9618588_R GTCTCGTGGGCTCGGAGGTCAGTCAACGCTCTGAC 59.6 0.05
mm4_intergenic_Gm22967|Dlgap1_chr17_69852023_F Primer3: not found at this Tm N.d. 0.04
mm4_intergenic_Gm22967|Dlgap1_chr17_69852023_R Primer3: not found at this Tm N.d. 0.04
mm4_intergenic_Gm5742|Gm22223_chr8_101222580_F Primer3: not found at this Tm N.d. 0.04
mm4_intergenic_Gm5742|Gm22223_chr8_101222580_R Primer3: not found at this Tm N.d. 0.04
mm4_intergenic_Gm13636|Gm13637_chr2_72560200_F TCGTCGGCAGCGTCAGGAGCCACACTCTCTCCAA 60.1 0.04
mm4_intergenic_Gm13636|Gm13637_chr2_72560200_R GTCTCGTGGGCTCGGGAGCTAGGCAACAGGGCATC 60.8 0.04
mm4_intron_Hsd3b1_chr3_98858987_F Primer3: not found at this Tm N.d. 0.04
mm4_intron_Hsd3b1_chr3_98858987_R Primer3: not found at this Tm N.d. 0.04
mm4_intergenic_Ntm|Gm26435_chr9_30286336_F TCGTCGGCAGCGTCCCATCTGCTGCTGAGATGCA 60.4 0.04
mm4_intergenic_Ntm|Gm26435_chr9_30286336_R GTCTCGTGGGCTCGGAGTTGGAGCAAACCTTTGGA 57.5 0.04
mm4_intergenic_Gm22122|Gm16630_chr6_48352358_F Primer3: not found at this Tm N.d. 0.04
mm4_intergenic_Gm22122|Gm16630_chr6_48352358_R Primer3: not found at this Tm N.d. 0.04
mm4_intergenic_Gm22122|Gm16630_chr6_48335439_F TCGTCGGCAGCGTCTGAGAAGCTCAGCACAGTGG 59.9 0.04
mm4_intergenic_Gm22122|Gm16630_chr6_48335439_R GTCTCGTGGGCTCGGGGCCAAGAAAAGCCTCATCC 59.1 0.04
mm4_intergenic_Gm22122|Gm16630_chr6_48308060_F Primer3: not found at this Tm N.d. 0.04
mm4_intergenic_Gm22122|Gm16630_chr6_48308060_R Primer3: not found at this Tm N.d. 0.04
mm4_intron_Lrp4_chr2_91492436_F TCGTCGGCAGCGTCTCACAGCATGAGGACATCATCA 59.4 0.04
mm4_intron_Lrp4_chr2_91492436_R GTCTCGTGGGCTCGGTGTCGGAAGAGCACACTGAC 59.9 0.04
mm4_intergenic_Usb1|Mmp15_chr8_95348835_F Primer3: not found at this Tm N.d. 0.04
mm4_intergenic_Usb1|Mmp15_chr8_95348835_R Primer3: not found at this Tm N.d. 0.04
mm4_intron_Clk3_chr9_57762592_F Primer3: not found at this Tm N.d. 0.04
mm4_intron_Clk3_chr9_57762592_R Primer3: not found at this Tm N.d. 0.04
mm4_intergenic_Syt3|Lrrc4b_chr7_44409991_F TCGTCGGCAGCGTCACGAAGACAGGAAGATGGCC 59.7 0.04
mm4_intergenic_Syt3|Lrrc4b_chr7_44409991_R GTCTCGTGGGCTCGGAGCTGAGAAGGAGTGTGTGC 59.9 0.04
mm4_intergenic_Thrb|Gm24140_chr14_17867110_F TCGTCGGCAGCGTCGTTCCCAGGCACAGCAGT 59.8 0.03
mm4_intergenic_Thrb|Gm24140_chr14_17867110_R GTCTCGTGGGCTCGGGGGCCTCGACAAACAGTGT 60.2 0.03
mm4_intron_Dlc1_chr8_36675671_F Primer3: not found at this Tm N.d. 0.03
mm4_intron_Dlc1_chr8_36675671_R Primer3: not found at this Tm N.d. 0.03
mm4_intergenic_Gm5093|Ttbk1_chr17_46441550_F Primer3: not found at this Tm N.d. 0.03
mm4_intergenic_Gm5093|Ttbk1_chr17_46441550_R Primer3: not found at this Tm N.d. 0.03
mm4_intron_Msra_chr14_64235645_F TCGTCGGCAGCGTCAGAGTGTCCGCTTGCATGAG 60.3 0.03
mm4_intron_Msra_chr14_64235645_R GTCTCGTGGGCTCGGGGAGTCAGCGGGCATATGTT 60.1 0.03
mm4_intron_Rp9_chr9_22450067_F Primer3: not found at this Tm N.d. 0.03
mm4_intron_Rp9_chr9_22450067_R Primer3: not found at this Tm N.d. 0.03
mm4_intergenic_Gm8079|Otud4_chr8_79575061_F TCGTCGGCAGCGTCAAAGAAGAGAGTGGCAGTGC 58.1 0.03
mm4_intergenic_Gm8079|Otud4_chr8_79575061_R GTCTCGTGGGCTCGGGGCTCTTGCTCATTCCTGGT 60.0 0.03
mm3_intron_Oaf_chr9_43225798_F Primer3: not found at this Tm N.d. 0.02
mm3_intron_Oaf_chr9_43225798_R Primer3: not found at this Tm N.d. 0.02
mm4_intergenic_Egfem1|mmu-mir-21b_chr3_29634597_F Primer3: not found at this Tm N.d. 0.02
mm4_intergenic_Egfem1|mmu-mir-21b_chr3_29634597_R Primer3: not found at this Tm N.d. 0.02
mm4_intergenic_Lmod1|Gm22796_chr1_135349508_F TCGTCGGCAGCGTCTGTATGGCGGAGATGAGGGA 60.1 0.02
mm4_intergenic_Lmod1|Gm22796_chr1_135349508_R GTCTCGTGGGCTCGGGGTGGTCATGTGGGTCTCTG 60.0 0.02
mm4_intron_Tpbpa_chr13_60940549_F TCGTCGGCAGCGTCAGCAAGCACTATTCTCCTTGAGA 59.4 0.02
mm4_intron_Tpbpa_chr13_60940549_R GTCTCGTGGGCTCGGTAGTCCCTGAAGCGCAGTTG 60.0 0.02
mm4_intron_Auts2_chr5_132239695_F TCGTCGGCAGCGTCACTACAAAGTATCCCATTGTCTGT 57.6 0.02
mm4_intron_Auts2_chr5_132239695_R GTCTCGTGGGCTCGGCCAGAGGTCCCTTATGGAGAC 58.9 0.02
mm4_intron_Ptpre_chr7_135659344_F Primer3: not found at this Tm N.d. 0.02
mm4_intron_Ptpre_chr7_135659344_R Primer3: not found at this Tm N.d. 0.02
mm4_exon_Trpc2_chr7_102082315_F Primer3: not found at this Tm N.d. 0.02
mm4_exon_Trpc2_chr7_102082315_R Primer3: not found at this Tm N.d. 0.02
mm4_intron_Ak8_chr2_28746849_F Primer3: not found at this Tm N.d. 0.02
mm4_intron_Ak8_chr2_28746849_R Primer3: not found at this Tm N.d. 0.02
mm4_intron_Rab10_chr12_3265939_F Primer3: not found at this Tm N.d. 0.01
mm4_intron_Rab10_chr12_3265939_R Primer3: not found at this Tm N.d. 0.01
mm4_intergenic_Gm25061|Gm5403_chrX_128046606_F Primer3: not found at this Tm N.d. 0.01
mm4_intergenic_Gm25061|Gm5403_chrX_128046606_R Primer3: not found at this Tm N.d. 0.01
mm4_intron_Gm12866_chr4_119064002_F TCGTCGGCAGCGTCTGTCAAAGACAAAGTCCCCTCA 59.4 0.01
mm4_intron_Gm12866_chr4_119064002_R GTCTCGTGGGCTCGGCTGAGTGCAGGATACAGGGC 60.1 0.01
mm4_intron_Dapk2_chr9_66162714_F TCGTCGGCAGCGTCGGGTCTCAAGGGTCTGTGTG 59.9 0.01
mm4_intron_Dapk2_chr9_66162714_R GTCTCGTGGGCTCGGGGGGCTCTTGCAGATGTCAA 60.3 0.01
mm3_intergenic_AY512915|Suclg2_chr6_95351545_F Primer3: not found at this Tm N.d. 0.01
mm3_intergenic_AY512915|Suclg2_chr6_95351545_R Primer3: not found at this Tm N.d. 0.01
mm4_intron_Clmn_chr12_104833734_F TCGTCGGCAGCGTCTCCCAAACAGAAGCCAAGCA 60.1 0.01
mm4_intron_Clmn_chr12_104833734_R GTCTCGTGGGCTCGGGCTGGAAAGACCACTCTGCT 59.9 0.01
mm4_intron_Lamb1_chr12_31317737_F Primer3: not found at this Tm N.d. 0.01
mm4_intron_Lamb1_chr12_31317737_R Primer3: not found at this Tm N.d. 0.01
mm4_intron_Padi2_chr4_140931577_F TCGTCGGCAGCGTCGCTAGGAGTTTGACAGGGCA 59.6 0.01
mm4_intron_Padi2_chr4_140931577_R GTCTCGTGGGCTCGGACAGGCATGCCTTTGGTTTG 59.6 0.01
mm4_intron_Slc22a23_chr13_34206586_F TCGTCGGCAGCGTCTGCCCAGTGAAATCAGCAGT 59.8 0.01
mm4_intron_Slc22a23_chr13_34206586_R GTCTCGTGGGCTCGGCTTCTGTCCTGGGCCTGATG 60.1 0.01
mm3_intergenic_Gm24246|Pik3c3_chr18_30060891_F TCGTCGGCAGCGTCGTGCTCATCTAGGGCAGTCC 59.8 0.00
mm3_intergenic_Gm24246|Pik3c3_chr18_30060891_R GTCTCGTGGGCTCGGGGCATCACCATTTTCATTTGTGG 59.3 0.00
mm4_intergenic_Galnt1|Mir187_chr18_24420664_F TCGTCGGCAGCGTCGTACCATGTCCCCTGCAGTT 59.6 0.00
mm4_intergenic_Galnt1|Mir187_chr18_24420664_R GTCTCGTGGGCTCGGCAAACACATCTGCACGGTGT 59.3 0.00
mm4_intergenic_Cep112|Axin2_chr11_108875922_F TCGTCGGCAGCGTCGGAATCTGTCCCTTGCCACA 59.9 0.00
mm4_intergenic_Cep112|Axin2_chr11_108875922_R GTCTCGTGGGCTCGGCAGGCTCAGGATGTGGTGAG 60.1 0.00
mm4_intergenic_Csmd1|Gm25665_chr8_17742413_F Primer3: not found at this Tm N.d. 0.00
mm4_intergenic_Csmd1|Gm25665_chr8_17742413_R Primer3: not found at this Tm N.d. 0.00
mm3_intergenic_Nrxn3|Dio2_chr12_90386007_F Primer3: not found at this Tm N.d. 0.00
mm3_intergenic_Nrxn3|Dio2_chr12_90386007_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_52313891 GAGAGTCCGGGGATGGAGAGCCGAAAGGACATGGTTATGTTTCTGGATGGGGGTCAGCTTGGCACTCTGGTTGGTAAGAG
GGTCTCTAATTTGTCCGAAGCCGTGAGCAGCCCGCTGCCTGAACCGCCAGAGAAGATGG
mm3_intergenic_Gm7627|Gm24120_chr7_69751823 TCCCTTGTGAAAAGAATGTGGTTTTAAGTTTGAGTGGCACTCTGGCTAATAAGATGGATGGGAAAGGACTATTCTGGATT
TGTGGGTCTTACATTGTGGTAGGGG
mm4_intergenic_Gm26288|Atp10a_chr7_58495328 AAAGGTTCCATCCCACCTGGAAACTACAGGTGAGGAGTATTCTGGTTGGTAAGAGGGCCCTTAGTGTTCAAAACCCTTGA
CTACATTACCTGTGCTAAGCAATGCCACCCAGCTTCTTCAAGTGCGTGTTTCAGTGTGC
mm4_intron_BC089491_chr7_28288645 CCACTCCCTTGGTACCTTGCGGGGGGGGGGGGGGGGGAATCCTCCTCCTTCTTACCTTCCTGAGTGCCCACATAACCGTG
CCCATTATTCCTCACCCTTTATCCCCCACCTTGCCCAGCTACAAA
mm4_intron_Mb21d2_chr16_28874579 CTCTGGCTCGCCCTTAAGAGTTTCCTGCTGGGCATGGTTTTTGACTAGGCATCACAATCACCAATTAGACCATGCCTTCT
TACCAACCAGTATCCCTGCCTGAGCCCCACCATGAACCCCTGTCCCCAGATCGAGGGATA
mm3_intergenic_Gm25682|Adgb_chr10_10190652 TGTGAACACATTCCCTCAAGAGATGACATATCTATCATAGACTATATATTTGTTTTCTATGTGAACAGATCATTGGGATG
TTATCTTCTCTGGGACTCTGGTAGATAAGAAGGGCAGGGAGACTAGGAATGAGG
mm2_intergenic_Myl10|Col26a1_chr5_136701117 GCGTCTGAGTGATGTTTGCGTGGTTAGCACTCTGGTTGGGAAGATGGTGAAACATTCCCTTCCACGCTAGTTTTTCCAAA
ACTCTTGGTTCCCTTGCTCTGCTCAGCTGTTCC
mm4_intergenic_Gm22021|Gm25724_chr14_104611204 GTTAGTTATGATAGCTCCTTTTGGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNGTGTTTTGCATTGATGTTTGCATCTCCCCTGTTT
mm4_intergenic_Capn10|Gpr35_chr1_92958318 GGTGTAGGTAGGAGAGGTCACTCTGAATTGGCAAATTTTAGGGAAAATTGGCATTTGGGGTGGTAAGAGGGGTAGATGAG
GAAGTCATCTAGACACAAACTGATTGTAAAGTACTTTGGAGGCATCTGACAGAAGACACC
mm4_intergenic_Gm23352|Wdr27_chr17_14795969 TCCACCCTATCTCACACCTGTCTACTAAAGCCTCACTCTGTTGTTTTTCTGATTATAGAGACCCACTTATCTCTGTACTC
CATGTTACCAACCAGCATGCCCAGAGTAATATGTATTACAGTTCTCACAGCCAATAAGC
mm4_intron_Megf11_chr9_64571503 TGCGACTCTACTCCTGACTGTTGCCAAAACCTGTCACACTAGGTGGTAAGATGGATGGAAAGGCACATTATGATGGGTAA
TGGGGTTCTCGACTCCCTTACCATAGCAATGCTCATGTCTGCTCTCACC
mm4_intergenic_Gm22527|Rnf144a_chr12_25732364 CCCTGCTGACGGAACTGTTCCAGAGTTTAGAAGACATAGAAGTGTTTACACTGGGAACTTTGGTGGGTAAGATGGGAAAT
GGAACAAGATCTCGATGAACCATGGAATGGGAGGGGCACAGGCCGAAGGATCCCTTA
mm4_intron_Gm765_chr6_98267716 TAAGTGTCTCACTCTGCCGCTGCCCTCTTGCCACCACGAGTGCCAGAGGCAGTAATGGGGTCAGTGCGAACACTTCTCCA
ACACTCAGGATCCACCCTCTGAGACC
mm4_intron_Efna1_chr3_89275963 CCTTCCCAGCTTCCTCAAGGACAGGGGCTAGGAGTGTTTTTGACCTTTGTTCCCATTTACCAAACAGAGTGCCTAAGACA
CCTGAAGCTCACACCACATCCCTGATGC
mm4_intergenic_Gm24490|Abcc12_chr8_86461793 TGTGTAGGGTGGGAACAGGAAGTGGGGGACAACTTCATTCTCCCTTCTTTCCACCCAGAGCCCCATTCTGCTGGTCAGAC
AGCCGTAGGAAG
mm4_intron_Dennd2a_chr6_39495410 GACAAAGGGAAAGGGGAGGGGACACACTTCCACTGCCTCGTGTCCTCTGATCCTTCTTGCCAACCATACTGTCAAAACAC
TGAAGGTGGCTGTCC
mm4_intron_Ankrd27_chr7_35603502 ATGTGCATATGCCCGAGAGCCCGTCACTCTGGGTAGTAAGAGGGGTCTCCTCTCTCTGTTCTTGGTTGCATAGGACTCCG
TAAATGCTCTCTACACCAAATGCCTCCAGCAGCTTCTCCGAGACTCTCACCTGG
mm4_intergenic_Gm27039|Adcyap1_chr17_92846542 TGCACCACTTTCAAGGGTTGAAATATCGGCACTGTGGTTGGGAAGGGGGCATACAAATAAAAAGTACAAAAATTAGAAAC
AAACCAGTGCAGAGATGA
mm4_intergenic_Ctdp1|Nfatc1_chr18_80582800 CGTCAGGCAGAATGGCATCTTACCTAGCATCTTCCATGTTACCATCCAGAGGACCAGTGGTGGCTCCCAAGGTGCTCAGG
AACAT
mm4_intergenic_Gm11655|Prkca_chr11_108213541 GGGGAGAGACAGCAAAGCATTGGAGGAATCTGGAAAACAGAGAAATGGTCCTCTGGGAGGTAAGAGGGAGCAGTGAGTGG
GATACCCGCTGGTCCCCACTCTTCTGGACTCCAGGGAGGGTCAACTCTT
mm4_intron_Bmper_chr9_23313562 CTCAGCCCTGCAATTCAAGCAAATGAATGCAACTCTGAGTCTCACATTCTGGTTTGTAAGATGGAGAGCCACTACCAAGA
CTCT
mm4_intron_Sipa1l3_chr7_29479719 AGAGTGTGCCCCTCTTCTCTTCCATCTCACCAGCCAGAGTGCACAGTTGGACTCACATGCAATGAAGGCATCAACCAAGG
TGAGATAAGAAAGCAGGGGCCAGGTCCCCAGTACTGTGGCACTGTCACACC
mm3_intergenic_Elovl5|Gm23609_chr9_78006128 AACGCAGTATGAGCATGGCTCTTCGAATTCCCTCCGTCTGCACCCTAAATTTGTCAGCCACCGAGGCCACCGAGTTTCAC
CTCTCTTACCTACCAGAGTGACTTTCCTCCCTTCAGAACCCAAGAC
mm4_intron_Chst11_chr10_82987548 ACCTGTGGTTGTGAAACTTGTGAGAGAATTTAAAAATGGACTTTGCTGGCATTCTGGGTTGCAAGAGGGTGGGACCAGAC
ACACGGGCATCTCAAGAGTGCCAAGCTCCA
mm4_intron_Tbc1d22a_chr15_86410433 GGGGTTCTGATCACCTGCTTCAGGTGCTCTGGTCCCTGGCACTCTGTGTGGAAACATGGCTGGTACATGTGGGTAGAAGA
GCTGCCCCACCCTGACTTCAGTCTTCTGACTGAGGGTGCAGG
mm4_intergenic_Plk2|Actbl2_chr13_110544175 GCCTCTTCTCTTACCAGGCCTGTGGCTAGATAATGAGATATAAATAAACGTTCTGTCTAGAACTGTGGCCTTCTTACCCA
CCGGAGTAGCAATTCCATGTCTTGCTGATTTGAGAGCACTGAGATGACTCTGGGT
mm4_intergenic_Gm13061|Zfp683_chr4_134048001 TCCTTCCTCCAGGTCTGCTTTTCCTTCTGGCCAGCCACAGTGCCAGGCCCTCTCCTGACCTGGAGTGCCAGCTCAGTACC
CTCAAA
mm4_intergenic_Caln1|Gm23761_chr5_130678067 GGGATGGGCTAAGAAGTTGACAGTGGCATTCTGTGTGGTAGGAGGGTGGAGGTGTTGTCTAAAATCTCAACAGTGGGCAT
ATGTTACTTCCA
mm4_intergenic_Dmrt2|Gm8825_chr19_25788629 TTTCCCGATGATGGTCAGCTACTATTTCGACATCTCTTTCACAGCCGTCTCACCATCCAGAGTCCCTTAAATAACTGCTC
ACTGGTGTTGGGTCTT
mm3_intergenic_Gm26258|Zfp516_chr18_82976546 AGTCACATTCATGCTGAGCTACATGTATGTCACCCTGGTTGGTCAGAAGGCACAGCAGCACCTCTCCTTGAGTT
mm4_intron_Slc16a10_chr10_40079985 TCTTTGGGCTTCTCCTTGCTAATGGCCCCTGCTACCAACCAGTGTGGCAGAGTACACCAGTGTTCCTCTAACTGAAATTC
TCAGAGCCACAAAGAGAACTGAGGACAAGAGCTCTGAACATCACAGCGTGTCCTGT
mm3_exon_Tbrg1_chr9_37649439 TCAACCAAGGGTTCGTGTGTCAGGAACTCTGGCTGGTAAGATGACACAAAGGCTTCATGCTGAAGCTCAGGGAGGTCCAG
GGAGCCTGGAAAAAGAGAATTCTTTAATGGAACCATTGTCTGGGAATCTCAGGCCT
mm4_intergenic_Gm13218|Gata3_chr2_9618588 ACAGACTTATTGTGAGGCCCGCCCTCCAACCAATCAGAATGCCAGAGAACTCCCGGTCAGAGCGTTGACTGACCT
mm4_intergenic_Gm13636|Gm13637_chr2_72560200 AGGAGCCACACTCTCTCCAATCTGTCAGCACGACTGTGTTGTGCATCACAGTATAATACAGATAACAGTACATTAGAATT
ACATGTTCCTCATCCATCTTCCCCACCAGAGGGCCTCTGGGATGCCCTGTTGCCTAGCTC
mm4_intergenic_Ntm|Gm26435_chr9_30286336 CCATCTGCTGCTGAGATGCAGCAGTGTTGTTTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNTTTCATCAGTTTTATAGATCCAAAGGTTTGCTCCAACT
mm4_intergenic_Gm22122|Gm16630_chr6_48335439 TGAGAAGCTCAGCACAGTGGGGGACAGTGGGGGTCTGCATGTTCCCTGTGTCTTCAGTAAATGGACAGGTAGAGGAGCTG
TCCATGTTACAAAGCAGAGTTCCACCAGGATGAGGCTTTTCTTGGCC
mm4_intron_Lrp4_chr2_91492436 TCACAGCATGAGGACATCATCACTACAGGTGAGCCTTCCTCCCAACCCGAGGGCCACCTGTCTGGCTAAAGAGCTGGGAA
ATATCCCATCTGTCTTAAGGCAGGAGTCAGTGTGCTCTTCCGACA
mm4_intergenic_Syt3|Lrrc4b_chr7_44409991 ACGAAGACAGGAAGATGGCCTTCTTCCCTCATAGCAACCAGAGAACCAAGGCAACACGGCCTCCCTGGTAACCAGGAAAG
GCTCAGAGGATGAGTTCTAGGCCTGGGCCCTGCACACACTCCTTCTCAGCT
mm4_intergenic_Thrb|Gm24140_chr14_17867110 GTTCCCAGGCACAGCAGTGAGCCCTGTGGCACTATGGCTGGGGAGAGGGAAGGAGCTGCTATTCTCAATAGCATATGAAC
CCAGGGAATAGTTATTTGCCTTCAGCTAATTCATCAGCTTGACACTGTTTGTCGAGGCCC
mm4_intron_Msra_chr14_64235645 AGAGTGTCCGCTTGCATGAGGGCTTTCTCACTTCAGTTGTGTCTGACAGCAACTCCCTTTTACAAACCAGACAGCCAAGA
TACACAGAAGCTTAAAAACATATGCCCGCTGACTCC
mm4_intergenic_Gm8079|Otud4_chr8_79575061 AAAGAAGAGAGTGGCAGTGCCTGGCACTGTGGCTGTGAAGAAGGGAGGCTGGACCCTGCTTCCAGGCTGAGCACCAGGAA
TGAGCAAGAGCC
mm4_intergenic_Lmod1|Gm22796_chr1_135349508 TGTATGGCGGAGATGAGGGAATACAGAACTTTGGTATGAAATAGGATGGTTTTCCAGTCTCCTGCCTTTGGACCTCTGGT
TGGGCAGAAGGGAAAATGACTACAGAGACCCACATGACCACC
mm4_intron_Tpbpa_chr13_60940549 AGCAAGCACTATTCTCCTTGAGATCTCTTTGGACAGTTCCCATGTGACCAACCAGCCTGCCAGTTTCCTCATATGTTACC
TTCTGCTCTTGCAGTTCAGCATCCAACTGCGCTTCAGGGACTA
mm4_intron_Auts2_chr5_132239695 ACTACAAAGTATCCCATTGTCTGTAAGTATCTCTACAAATGAGTTTAAAGTAGTCTCTATAGAACATGCCCTAGTACCAA
CCAGAGAGACAGTCTCCATAAGGGACCTCTGG
mm4_intron_Gm12866_chr4_119064002 TGTCAAAGACAAAGTCCCCTCAGTAACTGTTTAGTGAATTCAGTTTTTCTGACACTCTGCTTGGTTGGATGGTTGGGGGA
GTAATTGAAGGCATATAGAATTCCACCTGGCCCTGTATCCTGCACTCAG
mm4_intron_Dapk2_chr9_66162714 GGGTCTCAAGGGTCTGTGTGCTTTGGCAGAAGAATTGAAGGAGTGGACATTTTGGTAATGGGGCTCTGGTTTGTGAGAAG
GAGAAATGTATATATCCATTGACATCTGCAAGAGCCCC
mm4_intron_Clmn_chr12_104833734 TCCCAAACAGAAGCCAAGCAAATAAACCCATCCTAACCACTAGAGTGCCACACAGCAAAAGCTGGGCTGGAAGACCAGCT
AGAATGAGCAGAGTGGTCTTTCCAGC
mm4_intron_Padi2_chr4_140931577 GCTAGGAGTTTGACAGGGCAGGATTGAATGCCTTCCTCCCCACCAGAGAGCCACACAGCATGGCTTCCAAGATACAGATA
AGAATGTCTCAAACCAAAGGCATGCCTGT
mm4_intron_Slc22a23_chr13_34206586 TGCCCAGTGAAATCAGCAGTTAAAAATGAGTACAAAGGAACACGTTTCCTTCTCCCCCACCAGAGTGTCAGCATCAGGCC
CAGGACAGAAG
mm3_intergenic_Gm24246|Pik3c3_chr18_30060891 GTGCTCATCTAGGGCAGTCCGAGAGGCTCCTCTGAAACTTCCCTGACAACAAGGAAAGAATCTGGACCATCTTCTCACCA
ACCAAAGTTCCACTTCAAGCTTTTCCACAAATGAAAATGGTGATGCC
mm4_intergenic_Galnt1|Mir187_chr18_24420664 GTACCATGTCCCCTGCAGTTATTGAAATGTCACTCTGGTAGTTCAGAAGGCTGGCACATGGAGATTTAGCTTGATGACAC
AATATTAAAATAACACCGTGCAGATGTGTTTG
mm4_intergenic_Cep112|Axin2_chr11_108875922 GGAATCTGTCCCTTGCCACAAGCCTTCAAGGACACTTCTGGCCCCCATCCTTTGTGGAATGGAACTCTGGGTGTTTAGAT
GGGCCGTCCTAGTCCATAGGATAATTTCCCTCTCTCACCACATCCTGAGCCTG

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

Version 5.01 - Documentation  - Contact us - Downloads/local installation - Citation - License
CRISPR/Cas9 Guide Designer for chordate vertebrate ecdysozoans lophotrochozoans protostomes spongi corals plants butterflies metazoans genomes fruitflies insects nematodes mammals.