CRISPOR

Contents:

PCR Primers
Amplicon sequences
Crispresso support

PCR primers for off-targets of CACGCTCCCGGGAAGTCGGA 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.

Name	Primer Sequence	Tm	CFD Score
ontarget_mm0_exon_5730457N03Rik/Evx1_chr6_52314002_F	`TCGTCGGCAGCGTCAACCGCCAGAGAAGATGGTG`	60.0	1.00
ontarget_mm0_exon_5730457N03Rik/Evx1_chr6_52314002_R	`GTCTCGTGGGCTCGGCTGCCTGCTAGTCCATCGAC`	60.2	1.00
mm4_intergenic_Prex1\|Gm24477_chr2_166714052_F	`Primer3: not found at this Tm`	N.d.	0.37
mm4_intergenic_Prex1\|Gm24477_chr2_166714052_R	`Primer3: not found at this Tm`	N.d.	0.37
mm3_intron_Ntmt1_chr2_30820795_F	`TCGTCGGCAGCGTCGTCCCATTGCTCTTCCCCAT`	59.7	0.36
mm3_intron_Ntmt1_chr2_30820795_R	`GTCTCGTGGGCTCGGTGGCTTCAGACACCTCTCCT`	60.1	0.36
mm4_intergenic_Nsmce2\|Trib1_chr15_59636197_F	`TCGTCGGCAGCGTCATCAAAGTGGGTTCAGGGCG`	60.6	0.29
mm4_intergenic_Nsmce2\|Trib1_chr15_59636197_R	`GTCTCGTGGGCTCGGCTGTCCCATGGCTTCCTCAG`	60.1	0.29
mm4_exon_1700021N21Rik_chr4_134449191_F	`TCGTCGGCAGCGTCCCCCTGTACCAGATGCTGTT`	59.3	0.28
mm4_exon_1700021N21Rik_chr4_134449191_R	`GTCTCGTGGGCTCGGCGACTCAAGACAAACAGGCC`	59.1	0.28
mm4_intron_Cdh23_chr10_60687645_F	`TCGTCGGCAGCGTCTCGTGATCTCGCAAAGGTCC`	60.1	0.27
mm4_intron_Cdh23_chr10_60687645_R	`GTCTCGTGGGCTCGGGCGCTTAAAGCCAACAGATG`	58.1	0.27
mm4_intergenic_Muc6\|Muc2_chr7_141694687_F	`TCGTCGGCAGCGTCCAGGAACCTGGATGGAGCTG`	60.1	0.27
mm4_intergenic_Muc6\|Muc2_chr7_141694687_R	`GTCTCGTGGGCTCGGGACCCCTCACTTTCCAACCC`	60.2	0.27
mm4_intron_Chmp7_chr14_69729665_F	`TCGTCGGCAGCGTCGGGCAGCAGGGAAAGAAAGA`	60.2	0.26
mm4_intron_Chmp7_chr14_69729665_R	`GTCTCGTGGGCTCGGAAGCTTTGGTTTCTCGCCCT`	60.1	0.26
mm3_intergenic_Rps19bp1\|Cacna1i_chr15_80285436_F	`TCGTCGGCAGCGTCAACTGGTTCCTGGGGCATTT`	59.8	0.25
mm3_intergenic_Rps19bp1\|Cacna1i_chr15_80285436_R	`GTCTCGTGGGCTCGGCAAGATGGGCCACCCTGTC`	60.3	0.25
mm4_intron_Dlgap2_chr8_14206229_F	`TCGTCGGCAGCGTCGAGTCTAGCCTGTGTCAGCG`	60.1	0.23
mm4_intron_Dlgap2_chr8_14206229_R	`GTCTCGTGGGCTCGGTGCCCAGCTGAGGATAATGG`	59.5	0.23
mm4_intron_Cdh13_chr8_118525554_F	`TCGTCGGCAGCGTCGGATTCTCACCAAAGGTTCAGC`	59.5	0.23
mm4_intron_Cdh13_chr8_118525554_R	`GTCTCGTGGGCTCGGTGCCATGCCACAAAACACTG`	59.8	0.23
mm4_intron_Atxn1_chr13_45734131_F	`Primer3: not found at this Tm`	N.d.	0.20
mm4_intron_Atxn1_chr13_45734131_R	`Primer3: not found at this Tm`	N.d.	0.20
mm4_exon_Txlna_chr4_129640254_F	`Primer3: not found at this Tm`	N.d.	0.18
mm4_exon_Txlna_chr4_129640254_R	`Primer3: not found at this Tm`	N.d.	0.18
mm4_intergenic_Gm25672\|Barhl2_chr5_106119789_F	`TCGTCGGCAGCGTCCCTTCCTCCAAGCCACACTC`	60.3	0.17
mm4_intergenic_Gm25672\|Barhl2_chr5_106119789_R	`GTCTCGTGGGCTCGGTTCTCTGCACCAGTGTCTGC`	60.2	0.17
mm3_intergenic_Gm13065\|Gm13064_chr4_149798786_F	`TCGTCGGCAGCGTCTGTCTGCCTGTCTCACCAGA`	60.4	0.15
mm3_intergenic_Gm13065\|Gm13064_chr4_149798786_R	`GTCTCGTGGGCTCGGAACAAGAGTCCAGTGCCTCC`	59.6	0.15
mm4_intergenic_Gm6265\|Nkx2-1_chr12_56519826_F	`TCGTCGGCAGCGTCATCCCAACCAGCGAGGATTG`	60.1	0.14
mm4_intergenic_Gm6265\|Nkx2-1_chr12_56519826_R	`GTCTCGTGGGCTCGGAGAGGACCGGTTCTCACAGT`	60.1	0.14
mm4_exon_Gm26841/H13_chr2_152695462_F	`TCGTCGGCAGCGTCTGCAGCTTCAGTCTTTGCAG`	59.0	0.12
mm4_exon_Gm26841/H13_chr2_152695462_R	`GTCTCGTGGGCTCGGGACCCAGGCCGAAGATGTAG`	59.8	0.12
mm4_intergenic_Postn\|Gm5641_chr3_54426618_F	`TCGTCGGCAGCGTCCCTCGTTTCCAGGACAGGTG`	60.3	0.12
mm4_intergenic_Postn\|Gm5641_chr3_54426618_R	`GTCTCGTGGGCTCGGGTTCCAGAGAGAAAGGGGTCA`	59.0	0.12
mm3_intergenic_Gm26883\|Gm26883/Tshz2_chr2_169832172_F	`Primer3: not found at this Tm`	N.d.	0.10
mm3_intergenic_Gm26883\|Gm26883/Tshz2_chr2_169832172_R	`Primer3: not found at this Tm`	N.d.	0.10
mm4_intron_Jag2_chr12_112909749_F	`TCGTCGGCAGCGTCCTCTGGATCAGGCTGCTGTC`	60.1	0.10
mm4_intron_Jag2_chr12_112909749_R	`GTCTCGTGGGCTCGGCCGATCAGAGTTTGGGCAGT`	60.0	0.10
mm3_intergenic_Gm23239\|Ntrk3_chr7_78060683_F	`TCGTCGGCAGCGTCCATCCAACGCAGGCACATTC`	60.1	0.09
mm3_intergenic_Gm23239\|Ntrk3_chr7_78060683_R	`GTCTCGTGGGCTCGGTTTCCCTACTGTGTGGTGGC`	59.8	0.09
mm4_intergenic_Agpat2\|Fam69b_chr2_26609716_F	`TCGTCGGCAGCGTCGCCCTGTCTGGTAGGCATTT`	60.0	0.09
mm4_intergenic_Agpat2\|Fam69b_chr2_26609716_R	`GTCTCGTGGGCTCGGAGCTGTTGAAGGCACCAGTT`	60.1	0.09
mm4_intergenic_Apol7d\|Gm5528_chr1_71709956_F	`TCGTCGGCAGCGTCCGACGGGACCAAGTACTTCC`	60.1	0.08
mm4_intergenic_Apol7d\|Gm5528_chr1_71709956_R	`GTCTCGTGGGCTCGGTGGAACACAGATGCGTGGAA`	59.8	0.08
mm4_intergenic_Spata18\|Usp46_chr5_73855147_F	`TCGTCGGCAGCGTCGCAACTGTGGTCCAGATGGA`	59.9	0.08
mm4_intergenic_Spata18\|Usp46_chr5_73855147_R	`GTCTCGTGGGCTCGGTGTTTCAAGAGTTGGCGGGA`	59.8	0.08
mm4_intron_Ppfia3_chr7_45341878_F	`Primer3: not found at this Tm`	N.d.	0.06
mm4_intron_Ppfia3_chr7_45341878_R	`Primer3: not found at this Tm`	N.d.	0.06
mm4_intergenic_Gm10476\|Gm17391_chr12_22541921_F	`TCGTCGGCAGCGTCAGCTGAGTCATGGGCAGAAC`	60.0	0.05
mm4_intergenic_Gm10476\|Gm17391_chr12_22541921_R	`GTCTCGTGGGCTCGGTCTTCAGAGGTTGCCTTGCC`	60.2	0.05
mm4_intergenic_Gm10330\|Gm17330_chr12_23886110_F	`TCGTCGGCAGCGTCAGCTGAGTCATGGGCAGAAC`	60.0	0.05
mm4_intergenic_Gm10330\|Gm17330_chr12_23886110_R	`GTCTCGTGGGCTCGGTCTTCAGAGGTTGCCTTGCC`	60.2	0.05
mm4_intron_Sorcs3_chr19_48493406_F	`TCGTCGGCAGCGTCGTTGAGCCTTTTGCACAGGG`	59.9	0.05
mm4_intron_Sorcs3_chr19_48493406_R	`GTCTCGTGGGCTCGGTCTCTCCATCAGCCCAGTGA`	59.9	0.05
mm4_exon_Tbc1d10b_chr7_127198984_F	`Primer3: not found at this Tm`	N.d.	0.04
mm4_exon_Tbc1d10b_chr7_127198984_R	`Primer3: not found at this Tm`	N.d.	0.04
mm4_intergenic_Tug1/TUG1_2/TUG1_1\|Tug1_chr11_3648645_F	`TCGTCGGCAGCGTCCTCCAACTGGGTCCTAGCAG`	59.4	0.04
mm4_intergenic_Tug1/TUG1_2/TUG1_1\|Tug1_chr11_3648645_R	`GTCTCGTGGGCTCGGGGTCGTCCGGGTGGTTGG`	62.6	0.04
mm4_intron_Ppapdc1a_chr7_129278455_F	`TCGTCGGCAGCGTCGGGTAACGACCTCACCCAAG`	60.0	0.03
mm4_intron_Ppapdc1a_chr7_129278455_R	`GTCTCGTGGGCTCGGTGCCCAATCTCGAATCTCGT`	59.1	0.03
mm4_intergenic_Gm23234\|Shq1_chr6_100567306_F	`Primer3: not found at this Tm`	N.d.	0.03
mm4_intergenic_Gm23234\|Shq1_chr6_100567306_R	`Primer3: not found at this Tm`	N.d.	0.03
mm4_intergenic_Gm23950\|Gm11218_chr4_64582838_F	`TCGTCGGCAGCGTCCCACCTGTTCCTGTTCAACA`	57.9	0.03
mm4_intergenic_Gm23950\|Gm11218_chr4_64582838_R	`GTCTCGTGGGCTCGGACGAAAATAAGACAGAGAACGTGA`	58.4	0.03
mm4_intron_Prima1_chr12_103226807_F	`TCGTCGGCAGCGTCATTTGCATCTGGGAGCCTGT`	59.6	0.02
mm4_intron_Prima1_chr12_103226807_R	`GTCTCGTGGGCTCGGCTGTGGCTATGAAAACGGCC`	59.5	0.02
mm4_exon_Nbl1_chr4_139083273_F	`TCGTCGGCAGCGTCTTCCAAGTCCATCCAGTGCC`	59.9	0.02
mm4_exon_Nbl1_chr4_139083273_R	`GTCTCGTGGGCTCGGTTCCTCCCCTCTTGTTCCCT`	59.8	0.02
mm3_intron_Gon4l_chr3_88901728_F	`Primer3: not found at this Tm`	N.d.	0.02
mm3_intron_Gon4l_chr3_88901728_R	`Primer3: not found at this Tm`	N.d.	0.02
mm4_exon_Gm11491_chr11_87126815_F	`TCGTCGGCAGCGTCGCTCCAGGGTCTCCTTAGGT`	60.3	0.02
mm4_exon_Gm11491_chr11_87126815_R	`GTCTCGTGGGCTCGGTCGCAGATTTTACCGCCAGT`	60.0	0.02
mm4_intron_Tns1_chr1_74090592_F	`TCGTCGGCAGCGTCCCGGCAGCATCAAGTTGTTT`	59.6	0.01
mm4_intron_Tns1_chr1_74090592_R	`GTCTCGTGGGCTCGGGAAGAGGTGTGCAGGGCTAG`	60.1	0.01
mm4_intergenic_Opn3\|Wdr64_chr1_175693054_F	`TCGTCGGCAGCGTCGCATACAGCTCCGCCTTCTT`	60.4	0.01
mm4_intergenic_Opn3\|Wdr64_chr1_175693054_R	`GTCTCGTGGGCTCGGTGAAACTCACCTCTGCTGGG`	59.6	0.01
mm4_intergenic_Eya2\|Zmynd8_chr2_165783910_F	`TCGTCGGCAGCGTCCATGAAGCCTGGCCTCAGAA`	60.0	0.00
mm4_intergenic_Eya2\|Zmynd8_chr2_165783910_R	`GTCTCGTGGGCTCGGTGTGGCTGTGTCAGGTTTGA`	59.7	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_52314002	`AACCGCCAGAGAAGATGGTGCCCCACGGTTGCCTGAGCCCGCGAGCCGGCCCTCCGACTTCCCGGGAGCGTGGCGGGGGA GGCCAGGAGGAGGAGCCGGTCGATGGACTAGCAGGCAG`
mm3_intron_Ntmt1_chr2_30820795	`GTCCCATTGCTCTTCCCCATACGCACCGTGCTCTCTGCCACTCAGGTGCTCCACCAGCCCTGTTGAGCTGGCCAGCCGAG ATGCAGCTCCCTCCGACTTCCCAGGACCATGAGGAGAGGTGTCTGAAGCCA`
mm4_intergenic_Nsmce2\|Trib1_chr15_59636197	`ATCAAAGTGGGTTCAGGGCGCATACCTGTAGCCCTCCGTCTTCCTGGGCCCGTGGAGGGATCTCCTGCCAACCTTGTAGT CTGAGGAAGCCATGGGACAG`
mm4_exon_1700021N21Rik_chr4_134449191	`CCCCTGTACCAGATGCTGTTATTTTCTCAGAGACTGAGGATACCCACAGGCTCCTGGGAAATCAGAGGGAGGAGGGAGCA AGTCTAAATAAACAATAATTATGATGACTAGATATGAGGCCTGTTTGTCTTGAGTCG`
mm4_intron_Cdh23_chr10_60687645	`TCGTGATCTCGCAAAGGTCCGGGATCCAACCGCAGCCTCCCGCTTGCTCCGAGCCGAGGCCTGAGGCTGCAACGCTCTCG GGAAGCAGGAAGGCGCACCGCCTAGGTGAGGCCGCGCCATCTGTTGGCTTTAAGCGC`
mm4_intergenic_Muc6\|Muc2_chr7_141694687	`CAGGAACCTGGATGGAGCTGGGGACCCTCTGTCTTCCAGGGAGGGTGGAAAAAATGATTCTGGAGAAGGCTGTCCTTGGG GTGGTGGGTAATGCTGTTCTTAGAAATGGGTTGGAAAGTGAGGGGTC`
mm4_intron_Chmp7_chr14_69729665	`GGGCAGCAGGGAAAGAAAGAAGGGATGGTGCCTGCTGGTCTCATCCAGGCAAAAGACAGGGAACATTGACAAGCAAGCTA CTGGGAAGTTGGAGGGGAAAAAAGTAATCAGAGGGCGAGAAACCAAAGCTT`
mm3_intergenic_Rps19bp1\|Cacna1i_chr15_80285436	`AACTGGTTCCTGGGGCATTTGCTACATTTTTTCCTCCTGGAGCCCAAGCCTCATGAAGAGACCCCACCACACACTCTCCA TGGAAGTCGGAAGGGCCAGACAGGGTGGCCCATCTTG`
mm4_intron_Dlgap2_chr8_14206229	`GAGTCTAGCCTGTGTCAGCGACACTTCTGAATTTGTAACAAGCTGTTCAGACCTTCTGACTTCCAGGGAGGGGGGCAGAG TGAGTGTCTAACCCTGCTTCCTCCTGTCCATTATCCTCAGCTGGGCA`
mm4_intron_Cdh13_chr8_118525554	`GGATTCTCACCAAAGGTTCAGCCAAGCTCCAGGGAGGTCTGAAGGTGGGGCAACCCTCTGGGGGTAGGTAGTTCTGAGTT GGGACACTGGAGCCAGACTTTCATAATGGTATGCCAGTGTTTTGTGGCATGGCA`
mm4_intergenic_Gm25672\|Barhl2_chr5_106119789	`CCTTCCTCCAAGCCACACTCTGCAGTCCTGGGGACCACACACTCTCTCTGGAAGCCGGATGGTGGTGTCTTTGTGAGAGA TAACAGATGCTGGCACTCAGAACTTGCAGACACTGGTGCAGAGAA`
mm3_intergenic_Gm13065\|Gm13064_chr4_149798786	`TGTCTGCCTGTCTCACCAGAATAAACAAACAGGCTCCCGGGAAGTCACATGGGGCTGCCTCTCTCTGCTCCCAGCCTTCC TCCCAGCTAGCCTGGGAGCCATCAGTCCCTTGGGGGTGGGGGAGGCACTGGACTCTTGTT`
mm4_intergenic_Gm6265\|Nkx2-1_chr12_56519826	`ATCCCAACCAGCGAGGATTGCCCCACCCCATCCGACCTCCAGGGAGCCGGGTTAGCCTGAAGGCAACATCCCATCAGGCT CCGGGACTGTGAGAACCGGTCCTCT`
mm4_exon_Gm26841/H13_chr2_152695462	`TGCAGCTTCAGTCTTTGCAGAAAGGATGTTACTCGTCTAACCTCTTCCTTCCGCCTTCCCTGCAGCTTGAAGAAGAACAC GCACACCTACTTCTACACCAGCTTCGCCGCCTACATCTTCGGCCTGGGTC`
mm4_intergenic_Postn\|Gm5641_chr3_54426618	`CCTCGTTTCCAGGACAGGTGTTTGGTCCTCTCTAGTAGACAGGTTGTTCTCTCTCCGACTTCCTGGGAATTTGTGGATAC CCCCTTAAAGGAAGGCATCTTAAATGTTTTCTGTTCATGACCCCTTTCTCTCTGGAAC`
mm4_intron_Jag2_chr12_112909749	`CTCTGGATCAGGCTGCTGTCAGGCAGGTCCCTTGCAGGGCTGAAAGACTGTGGCAGAGGATGACACTGGGGGACGGCCCA AAGGTACCCTTCCTACATCCCAGGAGCCTGTTATAGCCACTGCCCAAACTCTGATCGG`
mm3_intergenic_Gm23239\|Ntrk3_chr7_78060683	`CATCCAACGCAGGCACATTCTCCTCAGCTACCACCTTTCCGACTTCCCAGCAGTGTGGACAAGGGAAGGATGGAGGTAGG GAGATTGAGAGGGGTCTAGCCACCACACAGTAGGGAAA`
mm4_intergenic_Agpat2\|Fam69b_chr2_26609716	`GCCCTGTCTGGTAGGCATTTAAGCATGTGGCTGTTGTCCTCCAATCCCCTCCAACTTCCCTGCAGCCTGGTCTGGGACAG ACAGCAGGCTGTTTCCCAACCTCTAGCTATAACTGGTGCCTTCAACAGCT`
mm4_intergenic_Apol7d\|Gm5528_chr1_71709956	`CGACGGGACCAAGTACTTCCTCCTGTTAATGTCAACAATCTGAGAGCCGGAGACTTTTTCCACGATCACCGGAAGTCGGT CGGGGTACTTCGCTCTGATCTTCGCGGATTCCACGCATCTGTGTTCCA`
mm4_intergenic_Spata18\|Usp46_chr5_73855147	`GCAACTGTGGTCCAGATGGAGCTGGAAGCTCCTCTCTCCGGCTCCCGGGAAGTCCCACGGGGTTTACTCAGACCTCCCGG AGTTTTCCAGGCGTCCCGCCAACTCTTGAAACA`
mm4_intergenic_Gm10476\|Gm17391_chr12_22541921	`AGCTGAGTCATGGGCAGAACAGACACGCTCATGGGAATTCAGAAGGGAAAACTGTTAGCAGTGAGATGGGTTCTATCCTT CTTGAGGGAGCTGTTCACAATATTCAGGCAAGGCAACCTCTGAAGA`
mm4_intergenic_Gm10330\|Gm17330_chr12_23886110	`AGCTGAGTCATGGGCAGAACAGACACGCTCATGGGAATTCAGAAGGGAAAACTGTTAGCAGTGAGATGGGTTCTATCCTT CTTGAGGGAGCTGTTCACAATATTCAGGCAAGGCAACCTCTGAAGA`
mm4_intron_Sorcs3_chr19_48493406	`GTTGAGCCTTTTGCACAGGGTACACCATCGCCTTCTCCCCAGACTCTTAAAACCAAACCAGCCGACTTCCCGAGAGAGAG ATTGATCACTGGGCTGATGGAGAGA`
mm4_intergenic_Tug1/TUG1_2/TUG1_1\|Tug1_chr11_3648645	`CTCCAACTGGGTCCTAGCAGGCCCCGAGGGGTGGCGCCAGGCCTCCAGGCCAGCCCCGGCCACCCCAGCTTCCCCCGCCG CCTCCCCGGGAGCGGGGCGGAGTTGCCCGCCGCCGCCAACCACCCGGACGACC`
mm4_intron_Ppapdc1a_chr7_129278455	`GGGTAACGACCTCACCCAAGAGCACACTCCCAGGAAGTGAGATGGCCAGTGCTTGGCAAGAAATTTGAAAGCAAATGTTT TCTAAGTTGGGACAATTTACACGAGATTCGAGATTGGGCA`
mm4_intergenic_Gm23950\|Gm11218_chr4_64582838	`CCACCTGTTCCTGTTCAACACACCCTCCAGGGAATTTGGATGGGATTCCTCCTCTTTCTCTCATATATAGCAGTGATGCA TCCATTTGCTTAAAATTAATTTGAAAACTTATTTAATCACGTTCTCTGTCTTATTTTCGT`
mm4_intron_Prima1_chr12_103226807	`ATTTGCATCTGGGAGCCTGTGTTTTCCTTCACACTTCCCGGAAGTGTGTAAAGAGGGAACTGGGCCGTTTTCATAGCCAC AG`
mm4_exon_Nbl1_chr4_139083273	`TTCCAAGTCCATCCAGTGCCAAAGGGGGAGGGGGGCTTCTGCCTATCCCCTCCCTCTTCCCTGGAGGGTGGGACCGACAT TCCACAGGGAACAAGAGGGGAGGAA`
mm4_exon_Gm11491_chr11_87126815	`GCTCCAGGGTCTCCTTAGGTGACCCACAAACAATGGGAACGCAAATAAGACTCTCCGTCCCTTCCTAATACTCGGGAGCG TGGCTTCTTCCAATTAGGACGCACCAAGGAGCCTACATCACTGGCGGTAAAATCTGCGA`
mm4_intron_Tns1_chr1_74090592	`CCGGCAGCATCAAGTTGTTTCCCATCCCCCTTCCTGGGAGCGTCTACCCACCCGCTCCTTCTAGATAGACTCCCACGTGG GCCCCAGACCTGTCGCAGACCCCTAGCCCTGCACACCTCTTC`
mm4_intergenic_Opn3\|Wdr64_chr1_175693054	`GCATACAGCTCCGCCTTCTTAGAACCTCTGACCGCGCCTCTGAGCTGTGGCCCCGCCCTACTGCTTTAGCGGCCCGCCCC TTTTCCCCCCTCCCACCTCCCGGGCGCGTTCCCGCCCAGCAGAGGTGAGTTTCA`
mm4_intergenic_Eya2\|Zmynd8_chr2_165783910	`CATGAAGCCTGGCCTCAGAAGACTGCAGCTACCATGGGAGGTAAGAAAGTCCCAGTCCAGCCCACGTCCCGGGAGGGTGC CCGGGACCTCAGGAGACCTGTCTCTTGTGGCCATTCAAACCTGACACAGCCACA`

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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