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PCR primers for off-targets of CGCGGGCGACGATGCCCCCC 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.

NamePrimer Sequence Tm CFD Score
ontarget_mm0__chr7 5.53 Mbp_chr7_5529572_F TCGTCGGCAGCGTCCACGATGGAGGGGAAGACG 59.8 1.00
ontarget_mm0__chr7 5.53 Mbp_chr7_5529572_R GTCTCGTGGGCTCGGGCTATTCTCGCAGCTCACCA 60.1 1.00
mm1__chr2 131.63 Mbp_chr2_131626200_F TCGTCGGCAGCGTCGTGCTCGTCATTGACAACGG 59.8 1.00
mm1__chr2 131.63 Mbp_chr2_131626200_R GTCTCGTGGGCTCGGACTCCTTCTGATGCATGCCC 60.1 1.00
mm1__chr2 131.26 Mbp_chr2_131263617_F TCGTCGGCAGCGTCGTGCTCGTCATTGACAACGG 59.8 1.00
mm1__chr2 131.26 Mbp_chr2_131263617_R GTCTCGTGGGCTCGGCCCACGATGGAAGGGAAGAC 60.1 1.00
mm1__chr2 130.66 Mbp_chr2_130656811_F TCGTCGGCAGCGTCGTGCTCGTCATTGACAACGG 59.8 1.00
mm1__chr2 130.66 Mbp_chr2_130656811_R GTCTCGTGGGCTCGGCCCACGATGGAAGGGAAGAC 60.1 1.00
mm1__chr2 130.46 Mbp_chr2_130463858_F TCGTCGGCAGCGTCCCCACGATGGAAGGGAAGAC 60.1 1.00
mm1__chr2 130.46 Mbp_chr2_130463858_R GTCTCGTGGGCTCGGGTGCTCGTCATTGACAACGG 59.8 1.00
mm1__chr2 130.08 Mbp_chr2_130075286_F TCGTCGGCAGCGTCCCCACGATGGAAGGGAAGAC 60.1 1.00
mm1__chr2 130.08 Mbp_chr2_130075286_R GTCTCGTGGGCTCGGGTGCTCGTCATTGACAACGG 59.8 1.00
mm3__chr22 15.72 Mbp_chr22_15721548_F TCGTCGGCAGCGTCGTGCTCGTCATTGACAACGG 59.8 0.73
mm3__chr22 15.72 Mbp_chr22_15721548_R GTCTCGTGGGCTCGGATCATGTTCTGGTGCCTGGG 60.0 0.73
mm3__chr14 19.40 Mbp_chr14_19402823_F TCGTCGGCAGCGTCATCATGTTCTGGTGCCTGGG 60.0 0.73
mm3__chr14 19.40 Mbp_chr14_19402823_R GTCTCGTGGGCTCGGGTGCTCGTCATTGACAACGG 59.8 0.73
mm3__chr14 19.00 Mbp_chr14_18998929_F TCGTCGGCAGCGTCGTGCTCGTCATTGACAACGG 59.8 0.73
mm3__chr14 19.00 Mbp_chr14_18998929_R GTCTCGTGGGCTCGGATCATGTTCTGGTGCCTGGG 60.0 0.73
mm2__chr19 9.52 Mbp_chr19_9518211_F TCGTCGGCAGCGTCAGTTAACAATGGCTCCGGCA 59.9 0.68
mm2__chr19 9.52 Mbp_chr19_9518211_R GTCTCGTGGGCTCGGCACGATGGAGGGGAAGATGG 59.8 0.68
mm3__chr2 73.90 Mbp_chr2_73901376_F TCGTCGGCAGCGTCGTGTGAAGAGGAGACCACCG 60.0 0.63
mm3__chr2 73.90 Mbp_chr2_73901376_R GTCTCGTGGGCTCGGCCCACAATGGAGGGGAAGAC 60.0 0.63
mm4__chr6 131.81 Mbp_chr6_131808388_F TCGTCGGCAGCGTCGCACCGGAGAGAGGCATG 60.2 0.38
mm4__chr6 131.81 Mbp_chr6_131808388_R GTCTCGTGGGCTCGGGAGAGTGAACCATCCTGCCC 60.1 0.38
mm4__chr10 135.21 Kbp_chr10_135208_F TCGTCGGCAGCGTCGCCAGGGGAAGACGCGAG 62.8 0.31
mm4__chr10 135.21 Kbp_chr10_135208_R GTCTCGTGGGCTCGGTACTCCACCTCAGAGAACGC 58.8 0.31
mm4__chr2 131.04 Mbp_chr2_131040038_F TCGTCGGCAGCGTCTGCAGCTGAGGGTGAATCAG 60.0 0.29
mm4__chr2 131.04 Mbp_chr2_131040038_R GTCTCGTGGGCTCGGATCTGGTCCTTGCTGCTCTG 59.7 0.29
mm4__chr16 1.26 Mbp_chr16_1262928_F TCGTCGGCAGCGTCGCCCAGTGGTAGCTGTAGAC 59.8 0.28
mm4__chr16 1.26 Mbp_chr16_1262928_R GTCTCGTGGGCTCGGCCGTCCCAGAGAATGACCTG 59.8 0.28
mm4__chr5 36.88 Mbp_chr5_36876922_F TCGTCGGCAGCGTCCGCCGACAGGAGAATTGGTT 60.6 0.25
mm4__chr5 36.88 Mbp_chr5_36876922_R GTCTCGTGGGCTCGGACTCACAAACACCCGACCAC 60.4 0.25
mm4__chr17 4.74 Mbp_chr17_4739931_F TCGTCGGCAGCGTCGGCCCGGTGGAGAGAGTC 61.4 0.22
mm4__chr17 4.74 Mbp_chr17_4739931_R GTCTCGTGGGCTCGGGGTTGTGACGTCAGGGCTG 60.9 0.22
mm4__chr2 241.87 Mbp_chr2_241872904_F TCGTCGGCAGCGTCAAGAGAAGGAAGGTGGCCTG 59.3 0.18
mm4__chr2 241.87 Mbp_chr2_241872904_R GTCTCGTGGGCTCGGTGATGCAGCCCTCACTAACC 59.7 0.18
mm4__chr9 105.04 Mbp_chr9_105044568_F TCGTCGGCAGCGTCGCCAGTCCTAGCCTTGAGTG 60.1 0.17
mm4__chr9 105.04 Mbp_chr9_105044568_R GTCTCGTGGGCTCGGGACTGGCAGTCTGGCTTGAT 60.0 0.17
mm4__chr4 1.45 Mbp_chr4_1449103_F TCGTCGGCAGCGTCCATCACTGCAACGCCTCAAC 60.1 0.15
mm4__chr4 1.45 Mbp_chr4_1449103_R GTCTCGTGGGCTCGGCTAAGGATGGTGCCTCACGC 60.8 0.15
mm4__chr5 57.48 Mbp_chr5_57482619_F TCGTCGGCAGCGTCATCTCCCACGTAGCAGTCCT 60.0 0.14
mm4__chr5 57.48 Mbp_chr5_57482619_R GTCTCGTGGGCTCGGATGGGTCAGGGATGTGCAAG 60.0 0.14
mm4__chr13 21.02 Mbp_chr13_21023072_F TCGTCGGCAGCGTCCTAGTCCAGCCCAGCAATCC 60.1 0.14
mm4__chr13 21.02 Mbp_chr13_21023072_R GTCTCGTGGGCTCGGCTTTGGAAAGGAGTCCCCGG 60.3 0.14
mm4__chr9 8.86 Mbp_chr9_8857773_F Primer3: not found at this Tm N.d. 0.14
mm4__chr9 8.86 Mbp_chr9_8857773_R Primer3: not found at this Tm N.d. 0.14
mm4__chr17 76.14 Mbp_chr17_76140214_F TCGTCGGCAGCGTCCTGAACCTGGCACCTGGTG 60.6 0.14
mm4__chr17 76.14 Mbp_chr17_76140214_R GTCTCGTGGGCTCGGAGTGGCTGCAGGAATTCTCC 60.0 0.14
mm4__chr11 1.80 Mbp_chr11_1804010_F TCGTCGGCAGCGTCCGCCACCCACATAGAAGTCC 60.4 0.13
mm4__chr11 1.80 Mbp_chr11_1804010_R GTCTCGTGGGCTCGGAACACCTCTGGCATGTGCAA 60.4 0.13
mm4__chr5 179.70 Mbp_chr5_179702330_F Primer3: not found at this Tm N.d. 0.13
mm4__chr5 179.70 Mbp_chr5_179702330_R Primer3: not found at this Tm N.d. 0.13
mm4__chr1 12.58 Mbp_chr1_12584341_F TCGTCGGCAGCGTCCCCCAGCACTGTTGACCTAG 60.0 0.11
mm4__chr1 12.58 Mbp_chr1_12584341_R GTCTCGTGGGCTCGGAACAGCCAAGTGTTAGGGCC 60.5 0.11
mm4__chr3 19.15 Mbp_chr3_19148384_F TCGTCGGCAGCGTCCCACTGCGGGCTCTTTCC 60.7 0.09
mm4__chr3 19.15 Mbp_chr3_19148384_R GTCTCGTGGGCTCGGGCCAGCTGCTGAAACCCC 61.3 0.09
mm4__chr17 82.75 Mbp_chr17_82752592_F TCGTCGGCAGCGTCTTCCTAGGCGGGAGAGGG 59.7 0.09
mm4__chr17 82.75 Mbp_chr17_82752592_R GTCTCGTGGGCTCGGAGAGGCTTCACCCCGTGC 62.0 0.09
mm4__chr5 180.21 Mbp_chr5_180209282_F Primer3: not found at this Tm N.d. 0.09
mm4__chr5 180.21 Mbp_chr5_180209282_R Primer3: not found at this Tm N.d. 0.09
mm4__chr7 27.23 Mbp_chr7_27226023_F Primer3: not found at this Tm N.d. 0.08
mm4__chr7 27.23 Mbp_chr7_27226023_R Primer3: not found at this Tm N.d. 0.08
mm4__chr1 22.54 Mbp_chr1_22537708_F TCGTCGGCAGCGTCTACTGAGCATGCTGTCTGGG 59.4 0.07
mm4__chr1 22.54 Mbp_chr1_22537708_R GTCTCGTGGGCTCGGAGTTGTGAGAAAGCTGCAAAC 57.5 0.07
mm4__chr1 226.08 Mbp_chr1_226083817_F TCGTCGGCAGCGTCCAGCTCCTTTCCGTCCCG 60.1 0.07
mm4__chr1 226.08 Mbp_chr1_226083817_R GTCTCGTGGGCTCGGAGGATATGCGGCACCTTCAG 59.8 0.07
mm4__chr4 8.43 Mbp_chr4_8428550_F TCGTCGGCAGCGTCCCCTGACGTCATCGAACCG 60.5 0.07
mm4__chr4 8.43 Mbp_chr4_8428550_R GTCTCGTGGGCTCGGTGCCTAAAAGCAGAGAAGGCA 59.9 0.07
mm4__chrUn_GL000220v1 118.84 Kbp_chrUn_GL000220v1_118836_F Primer3: not found at this Tm N.d. 0.06
mm4__chrUn_GL000220v1 118.84 Kbp_chrUn_GL000220v1_118836_R Primer3: not found at this Tm N.d. 0.06
mm4__chr22_KI270733v1_random 135.70 Kbp_chr22_KI270733v1_random_135701_F Primer3: not found at this Tm N.d. 0.06
mm4__chr22_KI270733v1_random 135.70 Kbp_chr22_KI270733v1_random_135701_R Primer3: not found at this Tm N.d. 0.06
mm4__chr21 8.45 Mbp_chr21_8446628_F Primer3: not found at this Tm N.d. 0.06
mm4__chr21 8.45 Mbp_chr21_8446628_R Primer3: not found at this Tm N.d. 0.06
mm4__chr21 8.22 Mbp_chr21_8219358_F Primer3: not found at this Tm N.d. 0.06
mm4__chr21 8.22 Mbp_chr21_8219358_R Primer3: not found at this Tm N.d. 0.06
mm4__chr19 56.30 Mbp_chr19_56304338_F Primer3: not found at this Tm N.d. 0.06
mm4__chr19 56.30 Mbp_chr19_56304338_R Primer3: not found at this Tm N.d. 0.06
mm4__chr20 63.69 Mbp_chr20_63690635_F TCGTCGGCAGCGTCCCTCCCCTACAGGCAGAGAA 60.3 0.06
mm4__chr20 63.69 Mbp_chr20_63690635_R GTCTCGTGGGCTCGGGTGTCCTCCCTGCTATTGGG 59.8 0.06
mm4__chr6 32.85 Mbp_chr6_32853586_F TCGTCGGCAGCGTCGTAGCAGTACTGTCCCCAGC 59.8 0.05
mm4__chr6 32.85 Mbp_chr6_32853586_R GTCTCGTGGGCTCGGTGGCTAGCTCTAGGTGTCCC 60.3 0.05
mm4__chr12 130.42 Mbp_chr12_130424629_F TCGTCGGCAGCGTCCTGTGCTTCACCGGGAACC 60.9 0.05
mm4__chr12 130.42 Mbp_chr12_130424629_R GTCTCGTGGGCTCGGGCTGTGGGCTGCTACACAAG 61.5 0.05
mm4__chr4 74.67 Mbp_chr4_74671272_F TCGTCGGCAGCGTCGCCTATTTACAGACACGGATGG 58.8 0.05
mm4__chr4 74.67 Mbp_chr4_74671272_R GTCTCGTGGGCTCGGTCCAAGCTCCTGCCTTTAGC 60.0 0.05
mm3__chr5 77.78 Mbp_chr5_77784948_F TCGTCGGCAGCGTCATATCACCGCGCTCGTCATT 59.9 0.05
mm3__chr5 77.78 Mbp_chr5_77784948_R GTCTCGTGGGCTCGGAACGATGGAGGGGAAGACTG 59.0 0.05
mm4__chr6 22.57 Mbp_chr6_22570261_F TCGTCGGCAGCGTCCTCAGCCAGAGGAGGAGGAG 60.7 0.04
mm4__chr6 22.57 Mbp_chr6_22570261_R GTCTCGTGGGCTCGGGTAACTACAGGCTGTCGCGA 59.8 0.04
mm3__chr1 237.93 Mbp_chr1_237926892_F TCGTCGGCAGCGTCTGACAATGGCTCCAGCATGT 59.9 0.04
mm3__chr1 237.93 Mbp_chr1_237926892_R GTCTCGTGGGCTCGGCACGTAGGAGTCCTTCTGGC 59.8 0.04
mm4__chr2 175.00 Mbp_chr2_175004806_F Primer3: not found at this Tm N.d. 0.04
mm4__chr2 175.00 Mbp_chr2_175004806_R Primer3: not found at this Tm N.d. 0.04
mm4__chr22 37.05 Mbp_chr22_37051773_F TCGTCGGCAGCGTCGAGGAGGATGCAGACGCC 59.8 0.04
mm4__chr22 37.05 Mbp_chr22_37051773_R GTCTCGTGGGCTCGGTGGTCAGGAACACCGTGC 59.8 0.04
mm4__chr9 134.81 Mbp_chr9_134810346_F TCGTCGGCAGCGTCAGGTAAGTATTGGCACGGGG 59.4 0.04
mm4__chr9 134.81 Mbp_chr9_134810346_R GTCTCGTGGGCTCGGCAGCATGTCCCGCTAGTCAT 59.8 0.04
mm4__chr17 10.20 Mbp_chr17_10198033_F Primer3: not found at this Tm N.d. 0.03
mm4__chr17 10.20 Mbp_chr17_10198033_R Primer3: not found at this Tm N.d. 0.03
mm4__chrX 48.83 Mbp_chrX_48826477_F TCGTCGGCAGCGTCCTGCGCATGTCCACTCCC 60.8 0.03
mm4__chrX 48.83 Mbp_chrX_48826477_R GTCTCGTGGGCTCGGGACGCTCTGACAGGCCTG 60.1 0.03
mm4__chr7 6.85 Mbp_chr7_6854999_F TCGTCGGCAGCGTCTAGGTCAGGGCCTCTCACC 59.9 0.03
mm4__chr7 6.85 Mbp_chr7_6854999_R GTCTCGTGGGCTCGGAGATTTTGTACTGTCCTGACTGGA 59.4 0.03
mm4__chr3 75.62 Mbp_chr3_75618996_F Primer3: not found at this Tm N.d. 0.03
mm4__chr3 75.62 Mbp_chr3_75618996_R Primer3: not found at this Tm N.d. 0.03
mm4__chr11 71.61 Mbp_chr11_71608060_F TCGTCGGCAGCGTCTGTACTGTCCTGACTGGGGA 59.5 0.03
mm4__chr11 71.61 Mbp_chr11_71608060_R GTCTCGTGGGCTCGGTAGGTCAGGGCCTGTCACC 60.6 0.03
mm4__chr11 67.71 Mbp_chr11_67711211_F TCGTCGGCAGCGTCCCTAGGTCAGGGCCTGTCA 60.3 0.03
mm4__chr11 67.71 Mbp_chr11_67711211_R GTCTCGTGGGCTCGGCTGTCCTTACTGGGGAGTCC 58.8 0.03
mm4__chr9 87.65 Mbp_chr9_87650719_F Primer3: not found at this Tm N.d. 0.03
mm4__chr9 87.65 Mbp_chr9_87650719_R Primer3: not found at this Tm N.d. 0.03
mm4__chr17 75.63 Mbp_chr17_75634103_F TCGTCGGCAGCGTCCTCCAGGACGACCAACAACA 59.8 0.03
mm4__chr17 75.63 Mbp_chr17_75634103_R GTCTCGTGGGCTCGGCACGTGCTGTCCTCGTACTT 60.0 0.03
mm4__chr10 69.02 Mbp_chr10_69022815_F Primer3: not found at this Tm N.d. 0.02
mm4__chr10 69.02 Mbp_chr10_69022815_R Primer3: not found at this Tm N.d. 0.02
mm4__chr15 61.07 Mbp_chr15_61066706_F Primer3: not found at this Tm N.d. 0.02
mm4__chr15 61.07 Mbp_chr15_61066706_R Primer3: not found at this Tm N.d. 0.02
mm3__chr3 175.98 Mbp_chr3_175978494_F TCGTCGGCAGCGTCGAGTCCTTCTGACCCATGCC 60.1 0.02
mm3__chr3 175.98 Mbp_chr3_175978494_R GTCTCGTGGGCTCGGGCAAAGGCTCCTGTATGTGC 59.5 0.02
mm4__chr4 1.37 Mbp_chr4_1365978_F Primer3: not found at this Tm N.d. 0.02
mm4__chr4 1.37 Mbp_chr4_1365978_R Primer3: not found at this Tm N.d. 0.02
mm4__chr11 124.76 Mbp_chr11_124762905_F Primer3: not found at this Tm N.d. 0.02
mm4__chr11 124.76 Mbp_chr11_124762905_R Primer3: not found at this Tm N.d. 0.02
mm4__chr22 19.45 Mbp_chr22_19447974_F TCGTCGGCAGCGTCGGGGTCGCAGGGTAAATCC 60.1 0.02
mm4__chr22 19.45 Mbp_chr22_19447974_R GTCTCGTGGGCTCGGTGATTTGAGAGGCGGCTGAC 60.3 0.02
mm4__chr22 20.36 Mbp_chr22_20359162_F TCGTCGGCAGCGTCCTAACGAGGTCGCTGCCC 60.2 0.02
mm4__chr22 20.36 Mbp_chr22_20359162_R GTCTCGTGGGCTCGGGTCCTCGTTAGCGATGCCC 60.5 0.02
mm4__chr22 20.35 Mbp_chr22_20354934_F Primer3: not found at this Tm N.d. 0.02
mm4__chr22 20.35 Mbp_chr22_20354934_R Primer3: not found at this Tm N.d. 0.02
mm4__chr17 29.59 Mbp_chr17_29589797_F Primer3: not found at this Tm N.d. 0.01
mm4__chr17 29.59 Mbp_chr17_29589797_R Primer3: not found at this Tm N.d. 0.01
mm4__chr22 38.46 Mbp_chr22_38455304_F Primer3: not found at this Tm N.d. 0.01
mm4__chr22 38.46 Mbp_chr22_38455304_R Primer3: not found at this Tm N.d. 0.01
mm4__chr6 131.63 Mbp_chr6_131628374_F TCGTCGGCAGCGTCGTTCCGTCTGTGGAGAAGGG 60.0 0.01
mm4__chr6 131.63 Mbp_chr6_131628374_R GTCTCGTGGGCTCGGAAGCAACTCCTTCTCCAGCC 59.9 0.01
mm4__chrY 345.05 Kbp_chrY_345052_F TCGTCGGCAGCGTCGATGACTCTTAGAGGGGCCG 59.3 0.01
mm4__chrY 345.05 Kbp_chrY_345052_R GTCTCGTGGGCTCGGAGTTTCCATCCAATCCCGGG 59.7 0.01
mm4__chr16 1.26 Mbp_chr16_1263519_F Primer3: not found at this Tm N.d. 0.01
mm4__chr16 1.26 Mbp_chr16_1263519_R Primer3: not found at this Tm N.d. 0.01
mm3__chr22 41.08 Mbp_chr22_41075154_F TCGTCGGCAGCGTCGGAGTCCTTCTGACCCATGC 60.1 0.01
mm3__chr22 41.08 Mbp_chr22_41075154_R GTCTCGTGGGCTCGGTGTTGACAACAGCTCTGGCA 60.1 0.01
mm4__chr6 100.88 Mbp_chr6_100881496_F TCGTCGGCAGCGTCCTGGGTTCGGAGGAGCAGA 60.9 0.01
mm4__chr6 100.88 Mbp_chr6_100881496_R GTCTCGTGGGCTCGGAGAGAGGTAGAGACGGCAGG 60.1 0.01
mm4__chr11 66.70 Mbp_chr11_66701055_F TCGTCGGCAGCGTCTTGCCTCTCGAGTCAGTTCG 59.7 0.01
mm4__chr11 66.70 Mbp_chr11_66701055_R GTCTCGTGGGCTCGGAAGTCATCGAGTCCACCCAG 59.1 0.01
mm4__chr20 4.25 Mbp_chr20_4248842_F Primer3: not found at this Tm N.d. 0.01
mm4__chr20 4.25 Mbp_chr20_4248842_R Primer3: not found at this Tm N.d. 0.01
mm4__chr19 5.11 Mbp_chr19_5109759_F Primer3: not found at this Tm N.d. 0.01
mm4__chr19 5.11 Mbp_chr19_5109759_R Primer3: not found at this Tm N.d. 0.01
mm4__chr1 227.45 Mbp_chr1_227447817_F TCGTCGGCAGCGTCCAGTTCCAAAAGGCTGGGGA 60.1 0.01
mm4__chr1 227.45 Mbp_chr1_227447817_R GTCTCGTGGGCTCGGGAGGTGGCAGAGCAGGAAAA 60.2 0.01
mm4__chr16 75.15 Mbp_chr16_75148974_F TCGTCGGCAGCGTCTCTTTGTCAGGAGATGCGCC 60.3 0.01
mm4__chr16 75.15 Mbp_chr16_75148974_R GTCTCGTGGGCTCGGCAGGTGTGTCAGGCCACG 60.6 0.01
mm4__chr22 18.19 Mbp_chr22_18186220_F Primer3: not found at this Tm N.d. 0.01
mm4__chr22 18.19 Mbp_chr22_18186220_R Primer3: not found at this Tm N.d. 0.01
mm4__chr3 14.51 Mbp_chr3_14514349_F TCGTCGGCAGCGTCACTGTCAGGCTCGATGAAGC 60.1 0.00
mm4__chr3 14.51 Mbp_chr3_14514349_R GTCTCGTGGGCTCGGAGATTGTGCACACGGAGACC 60.3 0.00
mm4__chr1 11.48 Mbp_chr1_11480505_F Primer3: not found at this Tm N.d. 0.00
mm4__chr1 11.48 Mbp_chr1_11480505_R Primer3: not found at this Tm N.d. 0.00
mm4__chr16 75.27 Mbp_chr16_75265856_F Primer3: not found at this Tm N.d. 0.00
mm4__chr16 75.27 Mbp_chr16_75265856_R Primer3: not found at this Tm N.d. 0.00
mm4__chr1 185.32 Mbp_chr1_185316570_F TCGTCGGCAGCGTCTTCCTGACAGCAAGAACGGG 60.2 0.00
mm4__chr1 185.32 Mbp_chr1_185316570_R GTCTCGTGGGCTCGGGGCTGGGAGGAACAAGAGTT 59.5 0.00
mm4__chr7 116.67 Mbp_chr7_116672397_F Primer3: not found at this Tm N.d. 0.00
mm4__chr7 116.67 Mbp_chr7_116672397_R Primer3: not found at this Tm N.d. 0.00
mm4__chr15 30.22 Mbp_chr15_30223283_F TCGTCGGCAGCGTCCCAAGGTGTAGTTCTTGTGCC 59.1 0.00
mm4__chr15 30.22 Mbp_chr15_30223283_R GTCTCGTGGGCTCGGGGCGCTGCATGAAGCTGG 62.1 0.00
mm4__chr6 26.12 Mbp_chr6_26123660_F TCGTCGGCAGCGTCGTCTGGATCTCCCTGGAGGT 60.0 0.00
mm4__chr6 26.12 Mbp_chr6_26123660_R GTCTCGTGGGCTCGGACTGGCATCTCTTCCAAGGC 60.0 0.00
mm4__chr3 114.10 Mbp_chr3_114103385_F TCGTCGGCAGCGTCGTCTGGATCTCCCTGGAGGT 60.0 0.00
mm4__chr3 114.10 Mbp_chr3_114103385_R GTCTCGTGGGCTCGGTGACACCGGCATCTCCTCTA 60.0 0.00
mm4__chr2 45.01 Mbp_chr2_45009203_F Primer3: not found at this Tm N.d. 0.00
mm4__chr2 45.01 Mbp_chr2_45009203_R Primer3: not found at this Tm N.d. 0.00
mm4__chr14 100.21 Mbp_chr14_100214630_F TCGTCGGCAGCGTCGCTCTCAGGGCCCTCGTG 62.1 0.00
mm4__chr14 100.21 Mbp_chr14_100214630_R GTCTCGTGGGCTCGGCGTCGAGGATCCAGCACAG 60.2 0.00
mm4__chr5 175.80 Mbp_chr5_175796739_F TCGTCGGCAGCGTCCGGAGGAGTCAAGGAAGAGG 59.1 0.00
mm4__chr5 175.80 Mbp_chr5_175796739_R GTCTCGTGGGCTCGGCGCGTTCTACGAACCTGTTG 59.5 0.00

Off-target amplicon sequences

Primers underlined, off-targets in bold.

ontarget_mm0__chr7 5.53 Mbp_chr7_5529572 CACGATGGAGGGGAAGACGGCCCGGGGGGCATCGTCGCCCGCGAAGCCGGCCTTGCACATGCCGGAGCCGTTGTCGACGA
CGAGCGCGGCGATATCATCATCCATGGTGAGCTGCGAGAATAGC
mm1__chr2 131.63 Mbp_chr2_131626200 GTGCTCGTCATTGACAACGGCTCTGGCATGTGCAAGGCCGGCTTTGCGGGCGACGATGCCCCCCAGGCTGTCTTCCCTTC
TATCGTGGGGCGCCCCAGGCACCAGGGCATGATGGAGGGCATGCATCAGAAGGAGT
mm1__chr2 131.26 Mbp_chr2_131263617 GTGCTCGTCATTGACAACGGCTCTGGCATGTGCAAGGCCGGCTTTGCGGGCGACGATGCCCCCCGGGCTGTCTTCCCTTC
CATCGTGGG
mm1__chr2 130.66 Mbp_chr2_130656811 GTGCTCGTCATTGACAACGGCTCTGGCATGTGCAAGGCCGGCTTTGCGGGCGACGATGCCCCCCGGGCTGTCTTCCCTTC
CATCGTGGG
mm1__chr2 130.46 Mbp_chr2_130463858 CCCACGATGGAAGGGAAGACAGCCCGGGGGGCATCGTCGCCCGCAAAGCCGGCCTTGCACATGCCAGAGCCGTTGTCAAT
GACGAGCAC
mm1__chr2 130.08 Mbp_chr2_130075286 CCCACGATGGAAGGGAAGACAGCCCGGGGGGCATCGTCGCCCGCAAAGCCGGCCTTGCACATGCCAGAGCCGTTGTCAAT
GACGAGCAC
mm3__chr22 15.72 Mbp_chr22_15721548 GTGCTCGTCATTGACAACGGCTCTGGCATGTGCAAGGCCGGCTTTGCAGGTGACGATGCCCCCCGGGCTGTCTTCCCTTC
CATCGTGGGGTGCCCCAGGCACCAGAACATGAT
mm3__chr14 19.40 Mbp_chr14_19402823 ATCATGTTCTGGTGCCTGGGGCACCCCACGATGGAAGGGAAGACAGCCCGGGGGGCATCGTCACCTGCAAAGCCGGCCTT
GCACATGCCAGAGCCGTTGTCAATGACGAGCAC
mm3__chr14 19.00 Mbp_chr14_18998929 GTGCTCGTCATTGACAACGGCTCTGGCATGTGCAAGGCCGGCTTTGCAGGTGACGATGCCCCCCGGGCTGTCTTCCCTTC
CATCGTGGGGTGCCCCAGGCACCAGAACATGAT
mm2__chr19 9.52 Mbp_chr19_9518211 AGTTAACAATGGCTCCGGCATGTGCAAGGTCAACTTCGTGGGCGACAATGCCCCCCGGGCCATCTTCCCCTCCATCGTG
mm3__chr2 73.90 Mbp_chr2_73901376 GTGTGAAGAGGAGACCACCGCGCTCGTGTGTGACAATGGCTCTGGCCTGTGCAAGGCAGGCTTCGCAGGAGATGATGCCC
CCCGGG
CTGTCTTCCCCTCCATTGTGGG
mm4__chr6 131.81 Mbp_chr6_131808388 GCACCGGAGAGAGGCATGGTCCGGGAGTGCTTCTTCGCCCGCGCGCTCTCCTCCGCAGCCTTTGCAAGTGCCCTACACAG
CCGCCCCTGCCAGGTACCTTGCCAGGGCAGGATGGTTCACTCTC
mm4__chr10 135.21 Kbp_chr10_135208 GCCAGGGGAAGACGCGAGTAAGTGCGGGCGGCGGTGCCCTCCCGGCCCTCACCCCGCACGCGGCGACCCGGCCGCCTAGC
CTCCCTCGCTCAGGCGCGACCGCGGCGTTCTCTGAGGTGGAGTA
mm4__chr2 131.04 Mbp_chr2_131040038 TGCAGCTGAGGGTGAATCAGGACGAGCCCGCGGATGACGACGCCCCTCTGGCCGGGAACAGCGGAGCGGAGGACGGCGGG
GCGGAGGCGCAGAGCAGCAAGGACCAGAT
mm4__chr16 1.26 Mbp_chr16_1262928 GCCCAGTGGTAGCTGTAGACCCTCAGGCTGACCTGCCACGGCCACTTCCCCGGGGGGGCATTGTGGCCCCCCACAATGCC
CACCAGGTCATTCTCTGGGACGG
mm4__chr5 36.88 Mbp_chr5_36876922 CGCCGACAGGAGAATTGGTTCCCGGGCCCGCGGCGATGCCCCCCCGGTAGCTCGGGCCCGTGGTCGGGTGTTTGTGAGT
mm4__chr17 4.74 Mbp_chr17_4739931 GGCCCGGTGGAGAGAGTCGCCGCCAGCCCCGGCCGCGCGCACCTGCGGGGCAGCCACCCGCGGACGCACCGAGCCCGGGG
GGCGTGGCCGCCCGCT
GAGCCGGCGAGGGCTCGGGCAGCCCTGACGTCACAACC
mm4__chr2 241.87 Mbp_chr2_241872904 AAGAGAAGGAAGGTGGCCTGGTCACCGCGGGTCACGACGCCCCTCTGGAGGCCAATGCCGAGGGCCCCATCACGGTTAGT
GAGGGCTGCATCA
mm4__chr9 105.04 Mbp_chr9_105044568 GCCAGTCCTAGCCTTGAGTGTGAAGGGTCACCAGTGGGGCATCATCCCCTGCGTTCTGGAGTGTGCTGAATGCCAACTCC
CATTACATGGGGACCAAAATGAGCTCAGGAGCATTGGTATCAAGCCAGACTGCCAGTC
mm4__chr4 1.45 Mbp_chr4_1449103 CATCACTGCAACGCCTCAACCCGTCTGCTCGGTGCGTGTGGGTCAGGTGCCCAGAACGCGGGTCCCCAGGAGCCCCAGCC
AGGGGGGCTTGGTAGCCCGTG
GCGCCTGCTGCTGGGGCGTGAGGCACCATCCTTAG
mm4__chr5 57.48 Mbp_chr5_57482619 ATCTCCCACGTAGCAGTCCTTCTGGCCCATGCCTACCATAACGCCCTGGTGTCGAGGACGCCCTATCATGGAGGGGAACA
CAGCCCGGGGGGCATCGTCACCACCAAAGCCTGCCTTGCACATCCCTGACCCAT
mm4__chr13 21.02 Mbp_chr13_21023072 CTAGTCCAGCCCAGCAATCCCACTGCATGCACCTGCAGAGCCCCAGGGGGGCAGTGTCGCTCGAGCCGGGGACTCCTTTC
CAAAG
mm4__chr17 76.14 Mbp_chr17_76140214 CTGAACCTGGCACCTGGTGGTAGCCGTGGGGGTCGGTGCCCCCCGGGGGCAGGGCGGGGGCCTTGGCGTTGAGAATGGAG
AATTCCTGCAGCCACT
mm4__chr11 1.80 Mbp_chr11_1804010 CGCCACCCACATAGAAGTCCTTCTGACCCATGCCCACCGTCATGCCCTGGTGTCTGGGGCACCCCACGATGGAGGGGAAG
ACGGCCCAGGGGGCATCGTCGTCGGTGAAGCTGGCCTTGCACATGCCAGAGGTGTT
mm4__chr1 12.58 Mbp_chr1_12584341 CCCCAGCACTGTTGACCTAGCTGGAAGACCACCCTGGAGAGGAAGTGGAGCAGGGCTGAGGGAGAAGGAATGAAGGCTGT
CTCCCACTGTCTTCCGTGGGCCAGGAAGCCCCCCAGGCAGGGCCCTAACACTTGGCTGTT
mm4__chr3 19.15 Mbp_chr3_19148384 CCACTGCGGGCTCTTTCCGGGCGGGCGACGTGGGGGGCGAGGCACCGCGCGGCGGCGCCTGGCGGGCACTGTTGCCCGCG
GAGGGACGGTGGGGGGGTTTCAGCAGCTGGC
mm4__chr17 82.75 Mbp_chr17_82752592 TTCCTAGGCGGGAGAGGGCCACCCCGGCGCGGCGTTAGGTGCACGGGGCAGACGCGCGCCTCCCTTGGGGGGACCGTGGC
CCGCG
GAGCGCCTGCTCTCGCACGGGGTGAAGCCTCT
mm4__chr1 22.54 Mbp_chr1_22537708 TACTGAGCATGCTGTCTGGGCACAGCCACTGCTCCCAGAGAGTGGGCAGAGGGCCAGGCACGCCACTCCTGGGGGGCAGC
CTCGCCTGTG
TGTTTGCAGCTTTCTCACAACT
mm4__chr1 226.08 Mbp_chr1_226083817 CAGCTCCTTTCCGTCCCGGGGCCTGGGGGGCACCGTCCCACGGGTGAGGGCCGCCTCCAGCGCCTGGCCCAGCCATGCGA
ACGCCTGGAGCCCGCGAGCTGCAGCTGCGGCCCTGAAGGTGCCGCATATCCT
mm4__chr4 8.43 Mbp_chr4_8428550 CCCTGACGTCATCGAACCGCGCCACCCTCGTTGCCCTGGAAACGCGGACGCCGCTGCCACCCGGGCGGGCTGGAAGCCAC
GAAGCTTCGCCAGGCGCTCCCGGGCACTCTTGCCTTCTCTGCTTTTAGGCA
mm4__chr20 63.69 Mbp_chr20_63690635 CCTCCCCTACAGGCAGAGAACGCCCCAGGCAAGGATGCCCCCCGAGGCTGAGACTCCCCCCAATAGCAGGGAGGACAC
mm4__chr6 32.85 Mbp_chr6_32853586 GTAGCAGTACTGTCCCCAGCCATGCGAGAGAAGCTCCGGGGAGGCAGCGGCACCCGCGGGGAGCGGGACACCTAGAGCTA
GCCA
mm4__chr12 130.42 Mbp_chr12_130424629 CTGTGCTTCACCGGGAACCAGGAGCCCCGAGGGGCCTCGTCGCCCCTGTAGGGCCTGCCGGGCCTGGGCTCTCTGGCCAG
CCCCGTCCTGGCCCTGGGGGACGGCCCTGCACCCTGCTTGTGTAGCAGCCCACAGC
mm4__chr4 74.67 Mbp_chr4_74671272 GCCTATTTACAGACACGGATGGGTAAGAAAGGGCAACGATGCCCCCCAGAGGCTAAAGGCAGGAGCTTGGA
mm3__chr5 77.78 Mbp_chr5_77784948 ATATCACCGCGCTCGTCATTGACAACGGCTCCGGCATGTGCAAGGCCAGCTTCACGGGCGACAATGCCGCCCGGGCAGTC
TTCCCCTCCATCGTT
mm4__chr6 22.57 Mbp_chr6_22570261 CTCAGCCAGAGGAGGAGGAGCTCCGGGAGGAAGAAGTCGCGGACGAGGAGGCCTCCCAGGAGTGGCATGCCGAGGCACCG
GGCGGCGGAGATCGCGACAGCCTGTAGTTAC
mm3__chr1 237.93 Mbp_chr1_237926892 TGACAATGGCTCCAGCATGTGCAAAGCTGGCTTTGCTGGGGACGATGCCCCCCAAGCTGTGTTTCCCTCCATCATTGGGC
ACCCCCGGCACAAGAGCATGATGGTGGGCATGGGCCAGAAGGACTCCTACGTG
mm4__chr22 37.05 Mbp_chr22_37051773 GAGGAGGATGCAGACGCCGCGGCCGGCGATGAGGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNAAGTGGGTGCGGCTCAACGTGGGGGGCACGGTGTTCCTGACCA
mm4__chr9 134.81 Mbp_chr9_134810346 AGGTAAGTATTGGCACGGGGGCGCGCGGCAGCCCCCAGGTCCCGGGGGGCCTCGTCGCAGGCTGTAGGCCGTGTGCCATG
CACGTTCTCTTCCAACGTTGCTGATGACTAGCGGGACATGCTG
mm4__chrX 48.83 Mbp_chrX_48826477 CTGCGCATGTCCACTCCCCCAACCGCCGCCGGGGTGCCCCGGGGAGCAGCGTCGCCCCCCGCCAGGCCTGTCAGAGCGTC
mm4__chr7 6.85 Mbp_chr7_6854999 TAGGTCAGGGCCTCTCACCACCGCGCCCAGAGGCCGGGCCAGCCGGGCGTGCATCCCAGGGGCGCTCCGTCCCCCGCGGC
CTGGGACTCTCCAGTCAGGACAGTACAAAATCT
mm4__chr11 71.61 Mbp_chr11_71608060 TGTACTGTCCTGACTGGGGAGTCCCAGGCCGCGGGGGACGGAGCGCCCCTGGGATGCACGCCCGGCTGGCCCGGCCTCTG
GGCGCGGTGGTGACAGGCCCTGACCTA
mm4__chr11 67.71 Mbp_chr11_67711211 CCTAGGTCAGGGCCTGTCACCACCGCGCCCAGAGGCCGGGCCAGCCGGGCGTGCATCCCAGGGGCGCTCCGTCCCCCGCG
GCCTGGGACTCCCCAGTAAGGACAG
mm4__chr17 75.63 Mbp_chr17_75634103 CTCCAGGACGACCAACAACAAAAAAGCCAGGCAGAGACAGCAGCTGGCTGTCAGCAGAGGAGCTGGGCTGAGGCGCCCAG
GGGAGCAGCGGCGCCCACG
AAGGAAGTACGAGGACAGCACGTG
mm3__chr3 175.98 Mbp_chr3_175978494 GAGTCCTTCTGACCCATGCCCACCATCACACCTTGGTGCCTGGGGCGCCCCACGATGGATGGGAAGACGGCCCCGGAGGC
ATCGTCGCCTGCG
AAGCTGGTCTTGCACATACAGGAGCCTTTGC
mm4__chr22 19.45 Mbp_chr22_19447974 GGGGTCGCAGGGTAAATCCGGGGCGAGACCTGGCGCGAAGCCTACGCGACCACCGCGACGACAGCGCCATTCACCCCGGG
CCAGGCGGGCATCCTGGGCCGCGCAGCTACCTTACGTCAGCCGCCTCTCAAATCA
mm4__chr22 20.36 Mbp_chr22_20359162 CTAACGAGGTCGCTGCCCATGGCATCGCGAACGAGGATGCCGCCCAGGGCATCGCGAACGAGGACGCCGCCCAGGGCATC
GCACACGAGGACGCCGTCCAGGGCATCGCTAACGAGGAC
mm4__chr6 131.63 Mbp_chr6_131628374 GTTCCGTCTGTGGAGAAGGGCGGCCCGCAAGCCGGACGAGAGCGCCCCCAAACGGAACCTTGAGCCCAAGGACCCCGGAG
GCATCGTCGACCGCA
GGCCGCCACCTCCCGGCTGGAGAAGGAGTTGCTT
mm4__chrY 345.05 Kbp_chrY_345052 GATGACTCTTAGAGGGGCCGGGAGGCAGTGGCTGCTGTGAGGACACCTGGGCGGCACCGGCTCCCGCGGAGGTATATGAA
CGACCGCTAAGCCTGGGGCTCCACCTAGCCCGGGATTGGATGGAAACT
mm3__chr22 41.08 Mbp_chr22_41075154 GGAGTCCTTCTGACCCATGCCCACCATCATGACCTGGTGCCTGGTGCACCCCACGATGGAAGGGAAGATGGCCCAGGGGA
CATCGTCACCCGCG
AAGCCGGCCTTGCACATGCCAGAGCTGTTGTCAACA
mm4__chr6 100.88 Mbp_chr6_100881496 CTGGGTTCGGAGGAGCAGAGGCGGAAGGTCCCGGCGGCGGCGAGGATGCGCCCCAGGGCGGGAGCGGGACGCTCCACTTT
ACCCTGGCTGCCCGCAACGGGCCAGGCCTGCCGTCTCTACCTCTCT
mm4__chr11 66.70 Mbp_chr11_66701055 TTGCCTCTCGAGTCAGTTCGCCCACCCGGGCGGCGATGGCCTCCAGGTCCCGCTCCGTGCCGGCCAGCTTGCGCTGCAGG
GCCAGCACCCCAGCCAGATCGTTGCCTAGGCCCTGGGTGGACTCGATGACTT
mm4__chr1 227.45 Mbp_chr1_227447817 CAGTTCCAAAAGGCTGGGGAAAGAGCTGTTTTCTGGGAATTTGGAATGTGGGAAAAATTTCCCCAGGGAGTCAAAGTCGC
CCGCG
GCAGGAAGCGGGGTTCCGGCCACTGGACGGCTGGTTTTCCTGCTCTGCCACCTC
mm4__chr16 75.15 Mbp_chr16_75148974 TCTTTGTCAGGAGATGCGCCTCAGACGGGCGGCGAAGGGCTCGGGCCGCGCGGGAGCGAGTTCTGGAGCCCCGGCGGGCG
CGCGCGCGCGGGACGAGGCCCCGCCGGGGCGTGGTGGGGGCGTGGCCTGACACACCTG
mm4__chr3 14.51 Mbp_chr3_14514349 ACTGTCAGGCTCGATGAAGCACACGAGGGGTGGGGAGGACAGGGTCTCGGTGGCGAAGATGCCGCCCTGGAGCTGGAGGC
CAAAGCCGCTGAGGGGGTCTCCACAGAGCACGACCTCCGTGGTCTCCGTGTGCACAATCT
mm4__chr1 185.32 Mbp_chr1_185316570 TTCCTGACAGCAAGAACGGGGAGTCCCGCGCCCTCCTTCCGGCGGGTCATCCCCGCCCGCGGCGCCCTAACCCAGGCCCC
CCAAAACCCTTCGAACAAAAAACTCTTGTTCCTCCCAGCC
mm4__chr15 30.22 Mbp_chr15_30223283 CCAAGGTGTAGTTCTTGTGCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCAGCTTCATGCAGCGCC
mm4__chr6 26.12 Mbp_chr6_26123660 GTCTGGATCTCCCTGGAGGTGATGGTCGAGCGCTTGTTGTAATGCGCCAGGCGGGAAGCCTCGCCCGCGATGCGCTCAAA
TATGTCGTTAACGAAAGAATTCATGATGCCCATGGCCTTGGAAGAGATGCCAGT
mm4__chr3 114.10 Mbp_chr3_114103385 GTCTGGATCTCCCTGGAGGTGATGGTCGAGCGCTTGTTGTAATGCGCCAGGCGGGAAGCCTCGCCCGCGACGTGCTCAAA
GATGTCGTTGACGAAGGAGTTCATGATCCCCATGGCCTTAGAGGAGATGCCGGTGTCA
mm4__chr14 100.21 Mbp_chr14_100214630 GCTCTCAGGGCCCTCGTGCCCCGCCCCGCCCTCCTCCCCGGGGCCCCTCGTCCCCCGCGCCCGCCTAGCCCCGCCCCGGC
TGTGCTGGATCCTCGACG
mm4__chr5 175.80 Mbp_chr5_175796739 CGGAGGAGTCAAGGAAGAGGGGGAGGGAGAAACGCGCCAGAACCTCGGCCCGGGCGCCCTCGTCGGCCGCGGAGGAGCTG
CAGCCTCCAACAGGTTCGTAGAACGCG

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_gYvicTzp9e5VPFC9YwLR.txt --name MY_EXPERIMENT

Version 4.7 - Documentation  - Contact us - Downloads/local installation - Paper - License
CRISPR/Cas9 Guide Designer for chordate vertebrate ecdysozoans lophotrochozoans protostomes spongi corals plants butterflies metazoans genomes fruitflies insects nematodes mammals.