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Contents:

PCR primers for off-targets of CCCCTGGCGGCCTAAGGACT CGG

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_5529726_F TCGTCGGCAGCGTCTGGTGAGCTGCGAGAATAGC 60.1 1.00
ontarget_mm0__chr7 5.53 Mbp_chr7_5529726_R GTCTCGTGGGCTCGGCGGCTTCCTTTGTCCCCAAT 60.6 1.00
mm4__chr1 43.94 Mbp_chr1_43943502_F Primer3: not found at this Tm N.d. 0.53
mm4__chr1 43.94 Mbp_chr1_43943502_R Primer3: not found at this Tm N.d. 0.53
mm4__chr20 62.96 Mbp_chr20_62963019_F TCGTCGGCAGCGTCCTAGGGCTAAGGCAGACACC 59.5 0.39
mm4__chr20 62.96 Mbp_chr20_62963019_R GTCTCGTGGGCTCGGCACCTTTGAGAACCGCGTTC 59.7 0.39
mm4__chrX 18.88 Mbp_chrX_18879194_F TCGTCGGCAGCGTCTTTCACCAGCTCTCTGTGGC 60.2 0.31
mm4__chrX 18.88 Mbp_chrX_18879194_R GTCTCGTGGGCTCGGGGAATTCACAGGTGGCAGGA 59.9 0.31
mm4__chr17 81.73 Mbp_chr17_81727274_F Primer3: not found at this Tm N.d. 0.31
mm4__chr17 81.73 Mbp_chr17_81727274_R Primer3: not found at this Tm N.d. 0.31
mm4__chr10 48.90 Mbp_chr10_48898354_F TCGTCGGCAGCGTCACCCCAAGCTCAGCAATAGC 60.3 0.30
mm4__chr10 48.90 Mbp_chr10_48898354_R GTCTCGTGGGCTCGGGTGGTCCCTAGGATCCCCTT 60.0 0.30
mm4__chr8 41.70 Mbp_chr8_41701860_F TCGTCGGCAGCGTCCTTCCCATCTCCCCAAACCC 60.0 0.26
mm4__chr8 41.70 Mbp_chr8_41701860_R GTCTCGTGGGCTCGGGGAGCTTGTCCTCCTTCCAG 59.7 0.26
mm4__chr10 126.82 Mbp_chr10_126824022_F Primer3: not found at this Tm N.d. 0.26
mm4__chr10 126.82 Mbp_chr10_126824022_R Primer3: not found at this Tm N.d. 0.26
mm4__chr5 7.82 Mbp_chr5_7816421_F Primer3: not found at this Tm N.d. 0.24
mm4__chr5 7.82 Mbp_chr5_7816421_R Primer3: not found at this Tm N.d. 0.24
mm4__chr17 18.85 Mbp_chr17_18850909_F TCGTCGGCAGCGTCCAGGAAGCAAAGCCACCAAG 59.6 0.24
mm4__chr17 18.85 Mbp_chr17_18850909_R GTCTCGTGGGCTCGGCCTATGCCACTGTCCTGCAA 60.0 0.24
mm4__chr1 156.60 Mbp_chr1_156595898_F TCGTCGGCAGCGTCAGGGTCCAAGTCAAAGCGAG 59.9 0.24
mm4__chr1 156.60 Mbp_chr1_156595898_R GTCTCGTGGGCTCGGGAAGATAGGCAGCTCCCCAC 59.8 0.24
mm4__chr20 62.33 Mbp_chr20_62328812_F TCGTCGGCAGCGTCCTCTGGCACCAACTCCCTG 60.0 0.23
mm4__chr20 62.33 Mbp_chr20_62328812_R GTCTCGTGGGCTCGGCTGCCATGCCCATGTCATTG 59.8 0.23
mm4__chr2 43.33 Mbp_chr2_43330777_F TCGTCGGCAGCGTCGGCAAGAAGGTCTGGAGCAT 60.0 0.22
mm4__chr2 43.33 Mbp_chr2_43330777_R GTCTCGTGGGCTCGGCCTGCTTTCTTCCTCTCCCG 60.1 0.22
mm4__chr1 155.21 Mbp_chr1_155207412_F TCGTCGGCAGCGTCTCCAGCTACCTCTCCCACAT 59.6 0.21
mm4__chr1 155.21 Mbp_chr1_155207412_R GTCTCGTGGGCTCGGGTACTGTAGGTCCCTGGGCT 60.3 0.21
mm4__chr3 51.70 Mbp_chr3_51698892_F TCGTCGGCAGCGTCTGGTGTTTAGCTGGCCTTGA 59.5 0.20
mm4__chr3 51.70 Mbp_chr3_51698892_R GTCTCGTGGGCTCGGCTCCTCTCCACCCTGGACAA 60.5 0.20
mm4__chr9 91.07 Mbp_chr9_91072327_F TCGTCGGCAGCGTCAGGCAGTCAGAGGACAAACG 59.9 0.18
mm4__chr9 91.07 Mbp_chr9_91072327_R GTCTCGTGGGCTCGGTACTCAGCCAAATGCCAGCC 60.6 0.18
mm4__chr9 133.46 Mbp_chr9_133460900_F TCGTCGGCAGCGTCCACGCATCCCAGTCACAGA 59.7 0.18
mm4__chr9 133.46 Mbp_chr9_133460900_R GTCTCGTGGGCTCGGACGGCTTCCATTCACTCCTG 60.0 0.18
mm4__chr14 28.68 Mbp_chr14_28684038_F Primer3: not found at this Tm N.d. 0.17
mm4__chr14 28.68 Mbp_chr14_28684038_R Primer3: not found at this Tm N.d. 0.17
mm3__chr19 5.88 Mbp_chr19_5876669_F TCGTCGGCAGCGTCGCTGGGTGGGTGATAAAGCT 60.0 0.17
mm3__chr19 5.88 Mbp_chr19_5876669_R GTCTCGTGGGCTCGGGCCTTCTCCCTCCTCCTGA 59.9 0.17
mm4__chr1 119.57 Mbp_chr1_119570822_F Primer3: not found at this Tm N.d. 0.16
mm4__chr1 119.57 Mbp_chr1_119570822_R Primer3: not found at this Tm N.d. 0.16
mm4__chr2 33.71 Mbp_chr2_33708531_F Primer3: not found at this Tm N.d. 0.16
mm4__chr2 33.71 Mbp_chr2_33708531_R Primer3: not found at this Tm N.d. 0.16
mm4__chr18 59.94 Mbp_chr18_59938530_F Primer3: not found at this Tm N.d. 0.16
mm4__chr18 59.94 Mbp_chr18_59938530_R Primer3: not found at this Tm N.d. 0.16
mm3__chr7 2.61 Mbp_chr7_2607987_F TCGTCGGCAGCGTCGGCAGCCTTAAGACCCTGTT 59.9 0.15
mm3__chr7 2.61 Mbp_chr7_2607987_R GTCTCGTGGGCTCGGTCTCCTCCTTCCCTGACTCC 59.6 0.15
mm4__chr1 52.84 Mbp_chr1_52838333_F Primer3: not found at this Tm N.d. 0.15
mm4__chr1 52.84 Mbp_chr1_52838333_R Primer3: not found at this Tm N.d. 0.15
mm4__chr8 142.36 Mbp_chr8_142363478_F Primer3: not found at this Tm N.d. 0.15
mm4__chr8 142.36 Mbp_chr8_142363478_R Primer3: not found at this Tm N.d. 0.15
mm4__chr22 18.04 Mbp_chr22_18044207_F TCGTCGGCAGCGTCGCTGCTGATGGAGGCTACAA 60.1 0.14
mm4__chr22 18.04 Mbp_chr22_18044207_R GTCTCGTGGGCTCGGGAGTTTCAGAAGCCAGCCCT 59.9 0.14
mm4__chr12 48.08 Mbp_chr12_48080987_F TCGTCGGCAGCGTCCTCCACTGACCCAACCTGTG 60.2 0.14
mm4__chr12 48.08 Mbp_chr12_48080987_R GTCTCGTGGGCTCGGGGACCACTCAGCCTTCCTTC 60.0 0.14
mm4__chr9 128.92 Mbp_chr9_128916409_F TCGTCGGCAGCGTCCTGTGGAGGGCTGACAAGG 60.0 0.14
mm4__chr9 128.92 Mbp_chr9_128916409_R GTCTCGTGGGCTCGGTTCTGGGAGAAGCTAGGCCT 59.9 0.14
mm4__chr15 25.01 Mbp_chr15_25013568_F Primer3: not found at this Tm N.d. 0.13
mm4__chr15 25.01 Mbp_chr15_25013568_R Primer3: not found at this Tm N.d. 0.13
mm4__chr11 69.92 Mbp_chr11_69916092_F Primer3: not found at this Tm N.d. 0.12
mm4__chr11 69.92 Mbp_chr11_69916092_R Primer3: not found at this Tm N.d. 0.12
mm4__chr21 25.90 Mbp_chr21_25898811_F Primer3: not found at this Tm N.d. 0.12
mm4__chr21 25.90 Mbp_chr21_25898811_R Primer3: not found at this Tm N.d. 0.12
mm4__chr1 87.61 Mbp_chr1_87613196_F TCGTCGGCAGCGTCTGTCCTCCAAATTGCCACCT 59.5 0.11
mm4__chr1 87.61 Mbp_chr1_87613196_R GTCTCGTGGGCTCGGAGTCATGTGATCTTGCTGCCA 59.9 0.11
mm4__chr17 73.03 Mbp_chr17_73032966_F Primer3: not found at this Tm N.d. 0.11
mm4__chr17 73.03 Mbp_chr17_73032966_R Primer3: not found at this Tm N.d. 0.11
mm4__chr11 120.80 Mbp_chr11_120799117_F Primer3: not found at this Tm N.d. 0.11
mm4__chr11 120.80 Mbp_chr11_120799117_R Primer3: not found at this Tm N.d. 0.11
mm4__chr17 49.49 Mbp_chr17_49487072_F TCGTCGGCAGCGTCCTGCTGCTCTCTCTGGCAG 60.1 0.11
mm4__chr17 49.49 Mbp_chr17_49487072_R GTCTCGTGGGCTCGGTGGGCTGAAAATCGAGGCAA 60.2 0.11
mm3__chr6 168.07 Mbp_chr6_168073381_F TCGTCGGCAGCGTCGAGTCTGACACAGGAAGCCC 60.0 0.10
mm3__chr6 168.07 Mbp_chr6_168073381_R GTCTCGTGGGCTCGGGGCCAGCCTTTCTGATGTGA 60.3 0.10
mm4__chr1 1.04 Mbp_chr1_1037018_F TCGTCGGCAGCGTCGCTTGTCCTGGAAGACCCTC 60.0 0.09
mm4__chr1 1.04 Mbp_chr1_1037018_R GTCTCGTGGGCTCGGGCAAGACTCGGGTCCTTCTC 60.1 0.09
mm4__chr3 127.20 Mbp_chr3_127195686_F TCGTCGGCAGCGTCTCTTCCATTCCATGCTGCCC 60.3 0.09
mm4__chr3 127.20 Mbp_chr3_127195686_R GTCTCGTGGGCTCGGAGAGAGACGGTGGAGAGGTC 60.0 0.09
mm4__chr10 61.98 Mbp_chr10_61979634_F TCGTCGGCAGCGTCTCCAAATGTCCTTCCCCAGC 59.9 0.09
mm4__chr10 61.98 Mbp_chr10_61979634_R GTCTCGTGGGCTCGGCAGACCTGGATAGAGGGTAGA 57.1 0.09
mm3__chr15 40.95 Mbp_chr15_40952429_F TCGTCGGCAGCGTCTTCAGCTGCCTCTGTTTCCC 60.2 0.09
mm3__chr15 40.95 Mbp_chr15_40952429_R GTCTCGTGGGCTCGGGTCTTCTCCCTCGGCTTCTG 59.8 0.09
mm4__chr11 80.24 Mbp_chr11_80244079_F Primer3: not found at this Tm N.d. 0.09
mm4__chr11 80.24 Mbp_chr11_80244079_R Primer3: not found at this Tm N.d. 0.09
mm4__chr20 17.93 Mbp_chr20_17929848_F TCGTCGGCAGCGTCCATCCCCAACTATCAGCCCG 60.2 0.08
mm4__chr20 17.93 Mbp_chr20_17929848_R GTCTCGTGGGCTCGGATACTGGCTCACACACTGGC 60.0 0.08
mm4__chr6 125.96 Mbp_chr6_125956946_F TCGTCGGCAGCGTCGGCGACGTCTCGAGGTAAAA 60.1 0.08
mm4__chr6 125.96 Mbp_chr6_125956946_R GTCTCGTGGGCTCGGCGCTGCGGTTCACCTGTT 60.9 0.08
mm4__chr7 151.14 Mbp_chr7_151137344_F TCGTCGGCAGCGTCCCACTAACCTCCAGCACCTG 60.0 0.08
mm4__chr7 151.14 Mbp_chr7_151137344_R GTCTCGTGGGCTCGGCACCCAACACTGAGACCACA 59.8 0.08
mm4__chr6 43.17 Mbp_chr6_43170524_F Primer3: not found at this Tm N.d. 0.07
mm4__chr6 43.17 Mbp_chr6_43170524_R Primer3: not found at this Tm N.d. 0.07
mm4__chr17 81.17 Mbp_chr17_81165776_F TCGTCGGCAGCGTCGAGGCCGGTTTGTGCTGG 61.3 0.07
mm4__chr17 81.17 Mbp_chr17_81165776_R GTCTCGTGGGCTCGGAATTAACCCTTTCCCCGCCC 60.3 0.07
mm4__chr7 129.16 Mbp_chr7_129160488_F Primer3: not found at this Tm N.d. 0.07
mm4__chr7 129.16 Mbp_chr7_129160488_R Primer3: not found at this Tm N.d. 0.07
mm4__chr9 30.56 Mbp_chr9_30558436_F Primer3: not found at this Tm N.d. 0.07
mm4__chr9 30.56 Mbp_chr9_30558436_R Primer3: not found at this Tm N.d. 0.07
mm4__chr10 78.78 Mbp_chr10_78779999_F TCGTCGGCAGCGTCAGATGAGGGTGTCAGGGTCA 59.8 0.07
mm4__chr10 78.78 Mbp_chr10_78779999_R GTCTCGTGGGCTCGGTATGTTCCCGTGTGCTGTCC 60.0 0.07
mm4__chr4 186.34 Mbp_chr4_186339450_F Primer3: not found at this Tm N.d. 0.07
mm4__chr4 186.34 Mbp_chr4_186339450_R Primer3: not found at this Tm N.d. 0.07
mm3__chr4 71.71 Mbp_chr4_71714482_F TCGTCGGCAGCGTCACCTAGCAACTTTAGGAGCACT 59.0 0.06
mm3__chr4 71.71 Mbp_chr4_71714482_R GTCTCGTGGGCTCGGTGTTGACTCAATAAGGGGATAGCT 59.2 0.06
mm3__chr15 83.65 Mbp_chr15_83654414_F TCGTCGGCAGCGTCGTCTCCAAGCAGAGTCGGG 59.7 0.06
mm3__chr15 83.65 Mbp_chr15_83654414_R GTCTCGTGGGCTCGGGACTCTCCCTGAACCTTCCG 59.4 0.06
mm4__chr1 24.10 Mbp_chr1_24101897_F Primer3: not found at this Tm N.d. 0.06
mm4__chr1 24.10 Mbp_chr1_24101897_R Primer3: not found at this Tm N.d. 0.06
mm4__chr16 35.03 Mbp_chr16_35027206_F TCGTCGGCAGCGTCAAGGAGAGTGAGGGGACTGC 60.9 0.06
mm4__chr16 35.03 Mbp_chr16_35027206_R GTCTCGTGGGCTCGGGGCATGGTAAGCCCCTAGTG 60.1 0.06
mm4__chr16 34.38 Mbp_chr16_34384599_F TCGTCGGCAGCGTCGGCATGGTAAGCCCCTAGTG 60.1 0.06
mm4__chr16 34.38 Mbp_chr16_34384599_R GTCTCGTGGGCTCGGAAGGAGAGTGAGGGGACTGC 60.9 0.06
mm4__chr19 4.05 Mbp_chr19_4052799_F TCGTCGGCAGCGTCGACCGAATTGCAAACTGCCC 60.3 0.06
mm4__chr19 4.05 Mbp_chr19_4052799_R GTCTCGTGGGCTCGGAGCTTGAGAGATCACTGTGCC 60.0 0.06
mm4__chr1 81.44 Mbp_chr1_81440280_F Primer3: not found at this Tm N.d. 0.05
mm4__chr1 81.44 Mbp_chr1_81440280_R Primer3: not found at this Tm N.d. 0.05
mm4__chr19 19.63 Mbp_chr19_19627184_F Primer3: not found at this Tm N.d. 0.05
mm4__chr19 19.63 Mbp_chr19_19627184_R Primer3: not found at this Tm N.d. 0.05
mm3__chr17 63.70 Mbp_chr17_63700684_F Primer3: not found at this Tm N.d. 0.05
mm3__chr17 63.70 Mbp_chr17_63700684_R Primer3: not found at this Tm N.d. 0.05
mm4__chr8 131.04 Mbp_chr8_131043391_F TCGTCGGCAGCGTCTGGCAATGGAAGGCATCACT 59.9 0.05
mm4__chr8 131.04 Mbp_chr8_131043391_R GTCTCGTGGGCTCGGCTGCATCCAGCCCCTCATTT 60.3 0.05
mm4__chr9 127.46 Mbp_chr9_127460417_F Primer3: not found at this Tm N.d. 0.05
mm4__chr9 127.46 Mbp_chr9_127460417_R Primer3: not found at this Tm N.d. 0.05
mm4__chr1 34.91 Mbp_chr1_34913068_F TCGTCGGCAGCGTCGTTGGGCTGGTGTCCTAGTC 60.0 0.05
mm4__chr1 34.91 Mbp_chr1_34913068_R GTCTCGTGGGCTCGGGCAGTGAGGGGAAAAGGAGG 60.3 0.05
mm4__chr5 131.34 Mbp_chr5_131341489_F Primer3: not found at this Tm N.d. 0.05
mm4__chr5 131.34 Mbp_chr5_131341489_R Primer3: not found at this Tm N.d. 0.05
mm4__chr6 7.72 Mbp_chr6_7723333_F TCGTCGGCAGCGTCATCTGCTCCTGTCCCTCCAA 60.2 0.05
mm4__chr6 7.72 Mbp_chr6_7723333_R GTCTCGTGGGCTCGGCATTAGACAGCCCGAGTGCT 59.8 0.05
mm4__chr12 19.69 Mbp_chr12_19688055_F Primer3: not found at this Tm N.d. 0.04
mm4__chr12 19.69 Mbp_chr12_19688055_R Primer3: not found at this Tm N.d. 0.04
mm4__chr4 186.57 Mbp_chr4_186574210_F Primer3: not found at this Tm N.d. 0.04
mm4__chr4 186.57 Mbp_chr4_186574210_R Primer3: not found at this Tm N.d. 0.04
mm4__chr1 7.12 Mbp_chr1_7123874_F TCGTCGGCAGCGTCCCATTCACTGCCAAGTCCCT 59.9 0.04
mm4__chr1 7.12 Mbp_chr1_7123874_R GTCTCGTGGGCTCGGCCCCATGAGACACTTTCCCC 60.0 0.04
mm4__chr2 129.67 Mbp_chr2_129669480_F TCGTCGGCAGCGTCCAAGGAACCCGCATGAGCTA 60.1 0.04
mm4__chr2 129.67 Mbp_chr2_129669480_R GTCTCGTGGGCTCGGGATGATGGGGCAGCCACTG 60.8 0.04
mm4__chr5 127.23 Mbp_chr5_127229754_F TCGTCGGCAGCGTCTCAAGTGGCTTCCTCCCTCA 60.4 0.04
mm4__chr5 127.23 Mbp_chr5_127229754_R GTCTCGTGGGCTCGGCTCCCCTCGCTCCACCTC 61.1 0.04
mm4__chrX 89.58 Mbp_chrX_89584304_F Primer3: not found at this Tm N.d. 0.04
mm4__chrX 89.58 Mbp_chrX_89584304_R Primer3: not found at this Tm N.d. 0.04
mm4__chr7 138.56 Mbp_chr7_138563159_F Primer3: not found at this Tm N.d. 0.04
mm4__chr7 138.56 Mbp_chr7_138563159_R Primer3: not found at this Tm N.d. 0.04
mm4__chr7 120.06 Mbp_chr7_120059051_F Primer3: not found at this Tm N.d. 0.04
mm4__chr7 120.06 Mbp_chr7_120059051_R Primer3: not found at this Tm N.d. 0.04
mm4__chr6 109.89 Mbp_chr6_109891846_F Primer3: not found at this Tm N.d. 0.04
mm4__chr6 109.89 Mbp_chr6_109891846_R Primer3: not found at this Tm N.d. 0.04
mm4__chr1 4.90 Mbp_chr1_4896883_F Primer3: not found at this Tm N.d. 0.04
mm4__chr1 4.90 Mbp_chr1_4896883_R Primer3: not found at this Tm N.d. 0.04
mm4__chr10 133.22 Mbp_chr10_133218508_F TCGTCGGCAGCGTCCATCTGCCTGTGGACACGAC 61.0 0.03
mm4__chr10 133.22 Mbp_chr10_133218508_R GTCTCGTGGGCTCGGGCAAGATTGTGCCTGGATGC 60.1 0.03
mm4__chr5 24.49 Mbp_chr5_24491615_F TCGTCGGCAGCGTCGAGGAGGATGGCGATCAAGG 59.9 0.03
mm4__chr5 24.49 Mbp_chr5_24491615_R GTCTCGTGGGCTCGGGTGTGCTTGTGACAGCCAAG 59.9 0.03
mm4__chr11 65.00 Mbp_chr11_64996966_F TCGTCGGCAGCGTCACAGAGGTGCATGGCTTAGG 59.7 0.03
mm4__chr11 65.00 Mbp_chr11_64996966_R GTCTCGTGGGCTCGGACTGAAACTTGGCCCTCTGG 59.8 0.03
mm4__chr9 18.36 Mbp_chr9_18356349_F Primer3: not found at this Tm N.d. 0.03
mm4__chr9 18.36 Mbp_chr9_18356349_R Primer3: not found at this Tm N.d. 0.03
mm4__chr14 96.48 Mbp_chr14_96479831_F TCGTCGGCAGCGTCTCCTCCTATGGGCTTGGTGA 59.9 0.03
mm4__chr14 96.48 Mbp_chr14_96479831_R GTCTCGTGGGCTCGGCAAATGCTGTCCCATTGGGC 60.1 0.03
mm4__chr14 99.59 Mbp_chr14_99586877_F TCGTCGGCAGCGTCGCCCTACCTATAGCACACCC 59.3 0.03
mm4__chr14 99.59 Mbp_chr14_99586877_R GTCTCGTGGGCTCGGCAGGTCCCCGGTAGGAGG 60.4 0.03
mm4__chr12 52.91 Mbp_chr12_52907621_F TCGTCGGCAGCGTCCAGTATGCAGGCTGGAGGG 59.8 0.03
mm4__chr12 52.91 Mbp_chr12_52907621_R GTCTCGTGGGCTCGGTGGGGTCTCTGGGCAATAGA 59.9 0.03
mm4__chr4 76.42 Mbp_chr4_76421360_F TCGTCGGCAGCGTCCATCCGAGCGTCGAAGTCC 60.5 0.02
mm4__chr4 76.42 Mbp_chr4_76421360_R GTCTCGTGGGCTCGGCAGGGTAGTTTCTGGGGCAG 60.0 0.02
mm4__chr19 344.33 Kbp_chr19_344333_F Primer3: not found at this Tm N.d. 0.02
mm4__chr19 344.33 Kbp_chr19_344333_R Primer3: not found at this Tm N.d. 0.02
mm4__chr3 14.54 Mbp_chr3_14544540_F Primer3: not found at this Tm N.d. 0.02
mm4__chr3 14.54 Mbp_chr3_14544540_R Primer3: not found at this Tm N.d. 0.02
mm4__chr17 47.70 Mbp_chr17_47700811_F TCGTCGGCAGCGTCCAAGAAAGGGGCAGCAGAGA 59.9 0.02
mm4__chr17 47.70 Mbp_chr17_47700811_R GTCTCGTGGGCTCGGGAAAGGCACCAGGTTCCACT 60.1 0.02
mm4__chr5 137.03 Mbp_chr5_137033153_F TCGTCGGCAGCGTCTCAGCTCGGCTATGATGCAG 59.9 0.02
mm4__chr5 137.03 Mbp_chr5_137033153_R GTCTCGTGGGCTCGGAGTCTCCTCTTGCAGATCGC 59.5 0.02
mm4__chr14 90.61 Mbp_chr14_90613709_F TCGTCGGCAGCGTCATAGCCCAGTCACCTCACCT 59.9 0.02
mm4__chr14 90.61 Mbp_chr14_90613709_R GTCTCGTGGGCTCGGCTGGGGTCCTTCCAGTTTCC 59.9 0.02
mm4__chr8 51.41 Mbp_chr8_51408556_F TCGTCGGCAGCGTCCTCGGTAACCCCTCAGCATC 59.8 0.02
mm4__chr8 51.41 Mbp_chr8_51408556_R GTCTCGTGGGCTCGGACGGTTTACCAGGAAGCCAG 59.9 0.02
mm4__chr19 14.56 Mbp_chr19_14558954_F TCGTCGGCAGCGTCCTGTTCAGCAGCTGCCTGTA 60.3 0.02
mm4__chr19 14.56 Mbp_chr19_14558954_R GTCTCGTGGGCTCGGCCACCCCAATCTCTGCTCTG 60.1 0.02
mm4__chr4 143.34 Mbp_chr4_143337396_F TCGTCGGCAGCGTCCGGGGCTGGTTCTTAAACGA 60.3 0.02
mm4__chr4 143.34 Mbp_chr4_143337396_R GTCTCGTGGGCTCGGAGAAAGTTGTCCGGCCAAGT 59.8 0.02
mm4__chr8 142.15 Mbp_chr8_142146752_F Primer3: not found at this Tm N.d. 0.01
mm4__chr8 142.15 Mbp_chr8_142146752_R Primer3: not found at this Tm N.d. 0.01
mm4__chr10 1.51 Mbp_chr10_1514593_F Primer3: not found at this Tm N.d. 0.01
mm4__chr10 1.51 Mbp_chr10_1514593_R Primer3: not found at this Tm N.d. 0.01
mm4__chr2 96.89 Mbp_chr2_96891703_F TCGTCGGCAGCGTCCACCAACAGCAGCTCTCTCA 59.9 0.01
mm4__chr2 96.89 Mbp_chr2_96891703_R GTCTCGTGGGCTCGGAAACACTTCTGCCCAGCTCC 60.5 0.01
mm4__chr1 205.27 Mbp_chr1_205268871_F TCGTCGGCAGCGTCACTGCTCTTGTGGTGGTTGT 59.7 0.01
mm4__chr1 205.27 Mbp_chr1_205268871_R GTCTCGTGGGCTCGGGGCAGAGGAAGCATGGGTAA 59.7 0.01
mm4__chr14 24.16 Mbp_chr14_24161667_F TCGTCGGCAGCGTCCCAGCCTCAGTGGACCATTT 59.9 0.01
mm4__chr14 24.16 Mbp_chr14_24161667_R GTCTCGTGGGCTCGGACAGCCTACACAACCTAGCC 59.3 0.01
mm4__chr2 3.29 Mbp_chr2_3291936_F TCGTCGGCAGCGTCGGATGCTGTCAGCCCCAAG 60.7 0.01
mm4__chr2 3.29 Mbp_chr2_3291936_R GTCTCGTGGGCTCGGGTGGACATAGGCTGCCATGT 60.1 0.01
mm4__chr4 8.47 Mbp_chr4_8473258_F TCGTCGGCAGCGTCCCTGAGCATGACCCATGAGG 60.1 0.01
mm4__chr4 8.47 Mbp_chr4_8473258_R GTCTCGTGGGCTCGGCCATACCAGCCAGCATGGAT 59.8 0.01
mm4__chr3 193.81 Mbp_chr3_193813153_F TCGTCGGCAGCGTCACTGCAGTGCTCTGATGAGG 59.7 0.01
mm4__chr3 193.81 Mbp_chr3_193813153_R GTCTCGTGGGCTCGGTCATTGGAAGTAGTGCCCCA 58.6 0.01
mm4__chr20 32.88 Mbp_chr20_32880205_F TCGTCGGCAGCGTCTGTGGGTGGGTCTGTCCTAA 60.1 0.01
mm4__chr20 32.88 Mbp_chr20_32880205_R GTCTCGTGGGCTCGGTCATTCAAGCCGCCTTCTCT 59.3 0.01
mm4__chr7 907.21 Kbp_chr7_907208_F TCGTCGGCAGCGTCACCACACACAGCCACAGAAA 60.0 0.00
mm4__chr7 907.21 Kbp_chr7_907208_R GTCTCGTGGGCTCGGGCACGGTGTGTTTTGCCATA 59.6 0.00
mm4__chr4 21.22 Mbp_chr4_21221089_F Primer3: not found at this Tm N.d. 0.00
mm4__chr4 21.22 Mbp_chr4_21221089_R Primer3: not found at this Tm N.d. 0.00
mm4__chr18 77.08 Mbp_chr18_77078876_F TCGTCGGCAGCGTCCAATCCTGTGCTCTGGTCCC 60.3 0.00
mm4__chr18 77.08 Mbp_chr18_77078876_R GTCTCGTGGGCTCGGTCATGGAGCCACAGTCTTGG 59.6 0.00
mm4__chr20 46.81 Mbp_chr20_46811122_F TCGTCGGCAGCGTCGCCACCGTCTTCTCCAATGA 60.0 0.00
mm4__chr20 46.81 Mbp_chr20_46811122_R GTCTCGTGGGCTCGGCTAACCCCTTTGTCGCACCC 60.9 0.00
mm4__chr10 87.10 Mbp_chr10_87095463_F TCGTCGGCAGCGTCGGGTCATGTGAGTCACGGG 60.0 0.00
mm4__chr10 87.10 Mbp_chr10_87095463_R GTCTCGTGGGCTCGGTTTCCTGCCCACGTGTCAG 60.2 0.00
mm4__chr2 104.69 Mbp_chr2_104687203_F Primer3: not found at this Tm N.d. 0.00
mm4__chr2 104.69 Mbp_chr2_104687203_R Primer3: not found at this Tm N.d. 0.00
mm4__chr2 231.71 Mbp_chr2_231710430_F Primer3: not found at this Tm N.d. 0.00
mm4__chr2 231.71 Mbp_chr2_231710430_R Primer3: not found at this Tm N.d. 0.00
mm4__chr9 136.66 Mbp_chr9_136661864_F TCGTCGGCAGCGTCTCAAGTTGCCCAGCTGAGTG 60.5 0.00
mm4__chr9 136.66 Mbp_chr9_136661864_R GTCTCGTGGGCTCGGGGGTGTGAGCCCTGCTTT 59.8 0.00
mm4__chr19 16.00 Mbp_chr19_16000802_F Primer3: not found at this Tm N.d. 0.00
mm4__chr19 16.00 Mbp_chr19_16000802_R Primer3: not found at this Tm N.d. 0.00
mm3__chr6 9.05 Mbp_chr6_9050342_F TCGTCGGCAGCGTCTCAGAGAGCTCCCATCTCCC 60.1 0.00
mm3__chr6 9.05 Mbp_chr6_9050342_R GTCTCGTGGGCTCGGGCACCATTGACAACTGCAGG 60.0 0.00

Off-target amplicon sequences

Primers underlined, off-targets in bold.

ontarget_mm0__chr7 5.53 Mbp_chr7_5529726 TGGTGAGCTGCGAGAATAGCCGGGCGCGCTGTGAGCCGAGGTCGCCCCCGCCCTGGCCACTTCCGGCGCGCCGAGTCCTT
AGGCCGCCAGGGG
GCGCCGGCGCGCGCCCAGATTGGGGACAAAGGAAGCCG
mm4__chr20 62.96 Mbp_chr20_62963019 CTAGGGCTAAGGCAGACACCCAGGAAGACCTGCTGGGCACAGGTCAAGGCAGGGTGCAGGAGCAGCCGAGTCTTTGGGTG
GCCAGGGG
GCTCTGGAGGAGGCCGTGTGGAGGGTCGTTCAGAACGCGGTTCTCAAAGGTG
mm4__chrX 18.88 Mbp_chrX_18879194 TTTCACCAGCTCTCTGTGGCTGTGCCCCCAGTCCTTTGGCCTTCAGGCGAATCCTGCCACCTGTGAATTCC
mm4__chr10 48.90 Mbp_chr10_48898354 ACCCCAAGCTCAGCAATAGCAAAGCTGCATCCCCAGTCCCTGGGCCTCCAGGGCAGCTGGCAGAAAAGGGGATCCTAGGG
ACCAC
mm4__chr8 41.70 Mbp_chr8_41701860 CTTCCCATCTCCCCAAACCCCATCCACTCCACTGCTGCCCGGAAAGCTGGTCCCGCCCCTAGTCCTCGGGCCGCTAGGTG
GCAGCACAGCCCCGCTGGAAGGAGGACAAGCTCC
mm4__chr17 18.85 Mbp_chr17_18850909 CAGGAAGCAAAGCCACCAAGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCTAGGAGGTGCTTCCAGTGA
AGGGGGAAGGAAAAACTGCTTGCAGGACAGTGGCATAGG
mm4__chr1 156.60 Mbp_chr1_156595898 AGGGTCCAAGTCAAAGCGAGGGTATCGGGGGAAATGGGCCTAGTCCTTAAGCCTGCAGGGAAAGTTGGTGGAGGGTAGGA
GTGGGGAGCTGCCTATCTTC
mm4__chr20 62.33 Mbp_chr20_62328812 CTCTGGCACCAACTCCCTGCCACTGGGCGCCCAAGGACTGGGGTACTCACGCCTGCAGTTGGGGAAGCCCCAGTATCCGG
TGGCACAGCGGGAGCAGTCACGGCCAATGACATGGGCATGGCAG
mm4__chr2 43.33 Mbp_chr2_43330777 GGCAAGAAGGTCTGGAGCATGAAGCCCTATCCATGGAAGGCAGCTCCTAAGAGAGGGCCCTTGGCAGCCCAAGGACATGG
AGTTGTAGAATTTTCCACAAGGATGATCAGGCCTCGGGAGAGGAAGAAAGCAGG
mm4__chr1 155.21 Mbp_chr1_155207412 TCCAGCTACCTCTCCCACATCCATCGGCCCATCCCACCACCAGACCTCCGGGAGAGCCCAGGCTTCTTGGTCCCCACCCC
CGCCCTGTCCTTGGGCAGCCAGGAGCCCAGGGGGACGAAGCCCAGGGACCTACAGTAC
mm4__chr3 51.70 Mbp_chr3_51698892 TGGTGTTTAGCTGGCCTTGATCCTTGTTCAGGGTCTATAGTAGCATGTCTGCAAGAGCAGGGGCTGGAGGCCTAAGGACT
GGG
GGTGCTGGTCTTCTGATATCTGTGGGTCAGTCAGCGTTGTCCAGGGTGGAGAGGAG
mm4__chr9 91.07 Mbp_chr9_91072327 AGGCAGTCAGAGGACAAACGGCCTTTGACCCCCCCACTCTCCTGGTGCTGGAAAGGAGGCAGCGCCCAGCAAATGGGACT
CTCCCTGGAGCCATAAGGACTAGGAGGGCTGGCATTTGGCTGAGTA
mm4__chr9 133.46 Mbp_chr9_133460900 CACGCATCCCAGTCACAGACCCTGACCTTAGGCTGCCAGGGAAGCTAGGCTCTTAAGCACAGCCAGAAAAGGACAAAGAG
GGAGGCAGGTCAGCTCCAGGAGTGAATGGAAGCCGT
mm3__chr19 5.88 Mbp_chr19_5876669 GCTGGGTGGGTGATAAAGCTGTCAGCCTGCTGGAAATTTCTCTCCCCTTGGGGCCTAAGGGCTGGGAGCCAAGGGCAGCT
GCCGCTCAGGAGGAGGGAGAAGGC
mm3__chr7 2.61 Mbp_chr7_2607987 GGCAGCCTTAAGACCCTGTTGAGGAGGGGAGTGTGGCGTGCGGGGCTGTTTCACGTGGGAAGTGTCAGGCGAAGGGCTTT
GCTGTGCTGAGTCCTTAGGTCTCCAGGGTGGAGTCAGGGAAGGAGGAGA
mm4__chr22 18.04 Mbp_chr22_18044207 GCTGCTGATGGAGGCTACAAACAGTGATAGAAGCATGCAGAAGCTACACAGCACAGGCCAAGGTGCTGTGGGAGAGGCGG
AGGAGGAACACTGACCACTGGCGGCCTGGGGACACGGGAGGGCTGGCTTCTGAAACTC
mm4__chr12 48.08 Mbp_chr12_48080987 CTCCACTGACCCAACCTGTGGCCTGGAGGGCTGTTTGGAAGGGTAAAATTGCCCAAGCAACCCCCAGTCCTCAGGCTGGC
AGAGG
AGGCAAAAGAAGGAAGGCTGAGTGGTCC
mm4__chr9 128.92 Mbp_chr9_128916409 CTGTGGAGGGCTGACAAGGAGCAGGCCTGAGCGAGGCCGGCCCAGCACAGCAAGCAGCAGGACCGCTGCCCAGTCCTCAG
GCCCGGAGGGG
CAGGCCTAGCTTCTCCCAGAA
mm4__chr1 87.61 Mbp_chr1_87613196 TGTCCTCCAAATTGCCACCTTTTCCCCCTAACCTACACCTGGCGGACTAAGGTATGGGAATAGTTCTGACCTCTGGCCTT
AGAGCCAAGGTTAATTGGCAGCAAGATCACATGACT
mm4__chr17 49.49 Mbp_chr17_49487072 CTGCTGCTCTCTCTGGCAGGGCCTGCGGCACTGGCAGCTCCAGGCCAGGCCCCTGACCTCAGGCCGCCATGGGCCAGCCC
CCAGACACCTCTCAGTGTTTTTGCCTCGATTTTCAGCCCA
mm3__chr6 168.07 Mbp_chr6_168073381 GAGTCTGACACAGGAAGCCCCAGATCCACACCTGCCCTCAGGGGCTCATGGTGTCCACTCAGGGTCCCCTGGGGGACTCA
GGACTGGG
TCTAAATGCATGAGGTCACATCAGAAAGGCTGGCC
mm4__chr1 1.04 Mbp_chr1_1037018 GCTTGTCCTGGAAGACCCTCTCCCTCCTGGCAGCCCCAGGACTGGGGGCAGGAGGGTATGGACTCAGAGAAGGACCCGAG
TCTTGC
mm4__chr3 127.20 Mbp_chr3_127195686 TCTTCCATTCCATGCTGCCCCTGACCCCAGCCCTCAGGACCCCAGGGGTCCTGACCGCACCAGCCTCCGCTCCTTGATGC
TGGGGCTGGGGGTGTCCTCTCCTGGCCACAGGACCTCTCCACCGTCTCTCT
mm4__chr10 61.98 Mbp_chr10_61979634 TCCAAATGTCCTTCCCCAGCTCCAAGTCCTTAGCAAACCAGGGGTCTACCCTCTATCCAGGTCTG
mm3__chr15 40.95 Mbp_chr15_40952429 TTCAGCTGCCTCTGTTTCCCTTTTACAGTCAGTGACATCCCCTGAGGGCAGTCCCTTGCTGCGTATTGGGTCAACCCCCG
GCGGCCTGTGGACTCGG
CTGGGAGGCCAGAAGCCGAGGGAGAAGAC
mm4__chr20 17.93 Mbp_chr20_17929848 CATCCCCAACTATCAGCCCGGCCACAGTCCCGGGGCTCCCTGTCCTTGGACTGCCAGGGGTCAGGTGCCAGTGTGTGAGC
CAGTAT
mm4__chr6 125.96 Mbp_chr6_125956946 GGCGACGTCTCGAGGTAAAACGGAGGAGGTGCGGGACGCGGAGACTGCGCGGGCCCGGTAGCCCTGGANNNNNNNNNNNN
NNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNAACAGGTGAACCGCAGCG
mm4__chr7 151.14 Mbp_chr7_151137344 CCACTAACCTCCAGCACCTGGCGGGCTCCTCCGCTTCAAGGTTGAAGCACCTCAGGTTCGGCCCCCGTGTTCTTAGACCG
CCTGGGG
CCATTTCTTTGTGGTCTCAGTGTTGGGTG
mm4__chr17 81.17 Mbp_chr17_81165776 GAGGCCGGTTTGTGCTGGGGCCCAGGGCCTGCCCCTCCGAGATCTGGGGCCGCCAGGGGGTCCGGCTGCTTCTGCTGCTG
GGCTCGGGGCGGGGAAAGGGTTAATT
mm4__chr10 78.78 Mbp_chr10_78779999 AGATGAGGGTGTCAGGGTCAGGAAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNCCCTTGAGGACAGCACACGGGAACATA
mm3__chr4 71.71 Mbp_chr4_71714482 ACCTAGCAACTTTAGGAGCACTCCAAGACCTGAGGCTGCCAGGGGTGTTGAGGAAACCAGAAAAGAGTATAGCTATCCCC
TTATTGAGTCAACA
mm3__chr15 83.65 Mbp_chr15_83654414 GTCTCCAAGCAGAGTCGGGGCGTGCCACGCGGGCCCCAGGGGGCCTCAGGACTGGGGTGCTCCTCACTGCTGGGCACCTC
GGGTCGGGCGCGCTTCGTGCCGTCCCGGAAGGTTCAGGGAGAGTC
mm4__chr16 35.03 Mbp_chr16_35027206 AAGGAGAGTGAGGGGACTGCTCCTGCCAGGGCCCAGTTCAGCCGCAGGACCCCATGGCGGCCCATGGTCTTGGTCCATGC
TGTGGGAGCAGTACAGGATTTATTCACTCAATAAACATTCACTAGGGGCTTACCATGCC
mm4__chr16 34.38 Mbp_chr16_34384599 GGCATGGTAAGCCCCTAGTGAATGTTTATTGAGTGAATAAATCCTGTACTGCTCCCACAGCATGGACCAAGACCATGGGC
CGCCATGGG
GTCCTGCGGCTGAACTGGGCCCTGGCAGGAGCAGTCCCCTCACTCTCCTT
mm4__chr19 4.05 Mbp_chr19_4052799 GACCGAATTGCAAACTGCCCGGGCCTGGCCTTGAACTCCTGCTGTTTAGGGACCAAGTCCTGTGGCTCCCAGGGGGGCAC
AGTGATCTCTCAAGCT
mm4__chr8 131.04 Mbp_chr8_131043391 TGGCAATGGAAGGCATCACTTTATTTTCTCACTTCTTTCTCCTTGGGGCCCTAAGGACTCAGCCTGAATAAATGAGGGGC
TGGATGCAG
mm4__chr1 34.91 Mbp_chr1_34913068 GTTGGGCTGGTGTCCTAGTCCCTGGCCTCCCTCAACCCCACTAGCCAGCCCTGTTGCTGAAGACTTGGCATGCCTTGTAT
CCAACCCCACTCCTTAGGACCCCAAGGGAAATCACCTCCTTTTCCCCTCACTGC
mm4__chr6 7.72 Mbp_chr6_7723333 ATCTGCTCCTGTCCCTCCAACTCCACCCACCCCATGCCTCCTCCTCTTGAATCACATGTGGACGTTGTCTAGCTCCCTGT
CCTGAGGCTTCCAGGGG
AGCACTCGGGCTGTCTAATG
mm4__chr1 7.12 Mbp_chr1_7123874 CCATTCACTGCCAAGTCCCTTTGAGGGCACAGTGAGAACCAAGGCCTTGCAGAGGGAGAGGTCTGTGGGGTTGCATCCAA
GTCCAAGGGCAGCCAGGGG
AGGTGGCTGTGGGCTTCACGGGGAAAGTGTCTCATGGGG
mm4__chr2 129.67 Mbp_chr2_129669480 CAAGGAACCCGCATGAGCTAGCCGAGTCCTGAGACTGCCAGGGTCCACACACCCTTCCCGGGTGAGGTGTTGGCTCGGTG
GGCCTGTGCACCAGGTGGGCAGGACCCCAGTGGCTGCCCCATCATC
mm4__chr5 127.23 Mbp_chr5_127229754 TCAAGTGGCTTCCTCCCTCACCTCCTCCGGGCGTGTGTATCAGCCGGCATGGCGTCTCTGCCCCATGCCCTGGGCCGCCA
GGGG
CCCGCAGGCTACGCGGGAGGTGGAGCGAGGGGAG
mm4__chr10 133.22 Mbp_chr10_133218508 CATCTGCCTGTGGACACGACAGCGGCCTCTCCCTGGGTGGGGTCGCCTTTCCCAGTCCTGAAGCTGCCTGGGGAGGTGCA
TCCAGGCACAATCTTGC
mm4__chr5 24.49 Mbp_chr5_24491615 GAGGAGGATGGCGATCAAGGCCCCAGTGCTGAGGCCGGCAGGGAGGAGCAGGGCTTCAGCACTGCAGGATTGCATGTTGC
CTTGGCTGTCACAAGCACAC
mm4__chr11 65.00 Mbp_chr11_64996966 ACAGAGGTGCATGGCTTAGGCGGGGGAGCAGAGTGGTCCCTCAGCAGCTGTGACTTCCCAGTGCCCTCTGGAGGCCTAAG
GAAGTGG
CAGCTCTTTAAATCCCCAGTGGCCACTCCGCCCCCAGAGGGCCAAGTTTCAGT
mm4__chr14 96.48 Mbp_chr14_96479831 TCCTCCTATGGGCTTGGTGAGAAAGAACCAGCTTCTGCCTGGTGGAAGCTTCCTGGCCAGGCCCACACCTTGGGCCTCCA
GGGG
CTGCTCTCTACCCCCAACTGCCCAATGGGACAGCATTTG
mm4__chr14 99.59 Mbp_chr14_99586877 GCCCTACCTATAGCACACCCCAAATCCCACCAGGCGGCCTCAGGGCTGGGCACCACAGCCAAGCCCGCAGCCACGGGCGG
CACTCCCGCGCTCACAGAGGGCCTCTGCCCTCCTACCGGGGACCTG
mm4__chr12 52.91 Mbp_chr12_52907621 CAGTATGCAGGCTGGAGGGCTGACCCAGACCTTACCCAGCCAGGGGAAGCCCTTTTTTTCTGGGGCAGCCCAGAACCGTC
TAGGGCCAGAAGTGTTTGTGTCTCATTTGTCATCTCTCTATTGCCCAGAGACCCCA
mm4__chr4 76.42 Mbp_chr4_76421360 CATCCGAGCGTCGAAGTCCCCACCACCGCCCGGGCGCCCTAAGGAGTGGGGGTGTACCCAGCCCGGAGTCAAATCCTGGA
GCCCTGCCCCAGAAACTACCCTG
mm4__chr17 47.70 Mbp_chr17_47700811 CAAGAAAGGGGCAGCAGAGAGCGGCAAGGGAGCTGTGTTGGTGGGGGGCCCAGTGCTGGGGCCTCCAGGGGGGCACTGGA
CAGCAAGGGAGGGGTGAGCAGCCACCCGGCAACAGTGGAACCTGGTGCCTTTC
mm4__chr5 137.03 Mbp_chr5_137033153 TCAGCTCGGCTATGATGCAGCTGAATGAGAGCCCAGTGGGGGTCAGGGGAGATGAACTCCCTCGTGGCGGCCGAAGGCCT
GGG
TGAGGGTGGAGCAGCTGGCGATCTGCAAGAGGAGACT
mm4__chr14 90.61 Mbp_chr14_90613709 ATAGCCCAGTCACCTCACCTCTTCTCTGCCGGGCCCTTAGGCTGCCAGGAGCACTTCCCAAGGAGGGAGGCAGGAAGGGA
GAGAAAACCATTCCTGGTGAGTGTTGTAGTAGAGCGAAAGGAAACTGGAAGGACCCCAG
mm4__chr8 51.41 Mbp_chr8_51408556 CTCGGTAACCCCTCAGCATCCTAGTGCCAGGGTCCCCCAGGACCTTAGGCAGCCAGTGGCTGTAGGTGATGTGCTGCAGC
TCCGCGCCCACGATCTTCCTGGCTTCCTGGTAAACCGT
mm4__chr19 14.56 Mbp_chr19_14558954 CTGTTCAGCAGCTGCCTGTACCCTCTGCAGCCCTGGGCTTCCCCTGGGAGCCCCTGCCCCCTGTTGGCCTCAGGCCTGGG
CAGGCGTGTGTGTGTGTGGCAGGCACAGAGCAGAGATTGGGGTGG
mm4__chr4 143.34 Mbp_chr4_143337396 CGGGGCTGGTTCTTAAACGAATGCCGGTCTCTTTCCCCTTGGCCCCTACCCCTGGCGGGCTCGGGACAGGGTGCCTTGCA
CTCCCTCACGCCCAGGCATCCACTTGGCCGGACAACTTTCT
mm4__chr2 96.89 Mbp_chr2_96891703 CACCAACAGCAGCTCTCTCAGCCTCTTCCCAGAGGGAGAGGCTGGGCCAAGGCCTGAGGCAGCCAGAGGAGGTGGGGAAG
GAGCTGGGCAGAAGTGTTT
mm4__chr1 205.27 Mbp_chr1_205268871 ACTGCTCTTGTGGTGGTTGTCTTCTTTTGGACTCCTGCATCCATTTTCTAGATAGAAAAACCAAGTCCAGAGGCATCCAG
GGG
CACTCCTATGGTCCCAGGGTTTACCCATGCTTCCTCTGCC
mm4__chr14 24.16 Mbp_chr14_24161667 CCAGCCTCAGTGGACCATTTGTTTCCTTGCCATCTGGCCCTGCCCACTTCTGCTGCAGCTCCAACCCCACCCCTACTTCC
TGCCCCACCTACTCCTGGGGCCGGCAGGGGGTGGGGGTCAGGCTAGGTTGTGTAGGCTGT
mm4__chr2 3.29 Mbp_chr2_3291936 GGATGCTGTCAGCCCCAAGCCTGTCTGTGTCCTGGTCCTGTGGCCGTCAGGGGCCCCGCTGGGCCATCCACTCCAGGGGC
ACCATGCACACGTGCTCGCCACGGGGCCACATGGCAGCCTATGTCCAC
mm4__chr4 8.47 Mbp_chr4_8473258 CCTGAGCATGACCCATGAGGGCCACAAGGGCCAGCCCTGCCTCTGTCCCTGCCCCTTCCTGAGGCCGCCAAGGGGCGGCG
CGCTGCATCCATGCTGGCTGGTATGG
mm4__chr3 193.81 Mbp_chr3_193813153 ACTGCAGTGCTCTGATGAGGACAGGTCTCAAGTGTGGATCAGCCTTTTGGATAAGCATGAATCCTGTTTGCCTACTCCTT
AGCCTCCCAGGGG
TGGGGCACTACTTCCAATGA
mm4__chr20 32.88 Mbp_chr20_32880205 TGTGGGTGGGTCTGTCCTAAGAGGACCAGACCCAGACCAGGCCACGGGGAAGTCAAAGAGCTGGAAGGCAGCCCCGGTCC
TCAGGCAGCCTGGGG
TTTAATAGAGAAGGCGGCTTGAATGA
mm4__chr7 907.21 Kbp_chr7_907208 ACCACACACAGCCACAGAAAAGTAGCCCGGGCATCCCCCTGGGAGCCTAAGCACCTGGACACGCCACCTTCTATGGCAAA
ACACACCGTGC
mm4__chr18 77.08 Mbp_chr18_77078876 CAATCCTGTGCTCTGGTCCCTGCCTGTGACCCAGTGGAGCTGGGAGCCCCAGGCGGGCTCAGCACTGGGACTCCAGGAGC
CTGGCTGTGCCCTGGGCACTCCTGCCCAGCACCCTCCCAAGACTGTGGCTCCATGA
mm4__chr20 46.81 Mbp_chr20_46811122 GCCACCGTCTTCTCCAATGAGAGCGATGACAGGATCTAAGGGGCCCCCTGGCGCTCTAAGGTCCTGGCCAGTGGAGACCC
TGGGGTGCGACAAAGGGGTTAG
mm4__chr10 87.10 Mbp_chr10_87095463 GGGTCATGTGAGTCACGGGCGCCCCTCCTTTCCGCCCGCGCGCCCTCGGAACGGGCGGCCCACCCTGGCCTGTCCTCTGG
CGGCCTCAGGCCGGGG
CCGGGCGTGCAGGGGCTGACACGTGGGCAGGAAA
mm4__chr9 136.66 Mbp_chr9_136661864 TCAAGTTGCCCAGCTGAGTGGGGCTGGAGAGGTGGGGGCACACTGACCGCCCAGGGCCAGGGAAATGGGGGTGTCCCAGG
CATCAGGCCGACAGGGG
CTGACCCCAAAGCAGGGCTCACACCC
mm3__chr6 9.05 Mbp_chr6_9050342 TCAGAGAGCTCCCATCTCCCACTGTGTGCAGCTGAGTTCCAAGCACTCCTGGCGGCATAATGACTGGGACAAAGATATTT
CCTGCAGTTGTCAATGGTGC

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

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