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Contents:

PCR primers for off-targets of ACCTCGGCTCACAGCGCGCC 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_5529675_F TCGTCGGCAGCGTCCCATGGTGAGCTGCGAGAAT 60.4 1.00
ontarget_mm0__chr7 5.53 Mbp_chr7_5529675_R GTCTCGTGGGCTCGGCGGCTTCCTTTGTCCCCAAT 60.6 1.00
mm3__chr19 46.49 Mbp_chr19_46493427_F Primer3: not found at this Tm N.d. 0.60
mm3__chr19 46.49 Mbp_chr19_46493427_R Primer3: not found at this Tm N.d. 0.60
mm4__chr2 82.30 Mbp_chr2_82297926_F Primer3: not found at this Tm N.d. 0.47
mm4__chr2 82.30 Mbp_chr2_82297926_R Primer3: not found at this Tm N.d. 0.47
mm4__chr17 80.15 Mbp_chr17_80152145_F Primer3: not found at this Tm N.d. 0.40
mm4__chr17 80.15 Mbp_chr17_80152145_R Primer3: not found at this Tm N.d. 0.40
mm4__chr4 189.19 Mbp_chr4_189193700_F Primer3: not found at this Tm N.d. 0.26
mm4__chr4 189.19 Mbp_chr4_189193700_R Primer3: not found at this Tm N.d. 0.26
mm4__chr19 19.26 Mbp_chr19_19261516_F TCGTCGGCAGCGTCCTGTGAGCAGCAGGACGC 61.1 0.25
mm4__chr19 19.26 Mbp_chr19_19261516_R GTCTCGTGGGCTCGGAGGCCTCCGAAAAGCCAAG 60.3 0.25
mm4__chr7 74.29 Mbp_chr7_74289644_F Primer3: not found at this Tm N.d. 0.25
mm4__chr7 74.29 Mbp_chr7_74289644_R Primer3: not found at this Tm N.d. 0.25
mm4__chr3 45.73 Mbp_chr3_45730581_F Primer3: not found at this Tm N.d. 0.22
mm4__chr3 45.73 Mbp_chr3_45730581_R Primer3: not found at this Tm N.d. 0.22
mm4__chrX 3.63 Mbp_chrX_3633695_F TCGTCGGCAGCGTCTAAAGTGGATGGTGCAGGCA 59.5 0.20
mm4__chrX 3.63 Mbp_chrX_3633695_R GTCTCGTGGGCTCGGTCCTCAGAACTGGAGCAGGT 60.1 0.20
mm4__chr19 272.57 Kbp_chr19_272566_F Primer3: not found at this Tm N.d. 0.18
mm4__chr19 272.57 Kbp_chr19_272566_R Primer3: not found at this Tm N.d. 0.18
mm4__chr9 96.46 Mbp_chr9_96463015_F Primer3: not found at this Tm N.d. 0.18
mm4__chr9 96.46 Mbp_chr9_96463015_R Primer3: not found at this Tm N.d. 0.18
mm4__chr2 106.87 Mbp_chr2_106872673_F Primer3: not found at this Tm N.d. 0.18
mm4__chr2 106.87 Mbp_chr2_106872673_R Primer3: not found at this Tm N.d. 0.18
mm3__chr1 20.55 Mbp_chr1_20553950_F Primer3: not found at this Tm N.d. 0.18
mm3__chr1 20.55 Mbp_chr1_20553950_R Primer3: not found at this Tm N.d. 0.18
mm4__chr1 178.62 Mbp_chr1_178615136_F Primer3: not found at this Tm N.d. 0.17
mm4__chr1 178.62 Mbp_chr1_178615136_R Primer3: not found at this Tm N.d. 0.17
mm3__chr12 131.56 Mbp_chr12_131560517_F Primer3: not found at this Tm N.d. 0.13
mm3__chr12 131.56 Mbp_chr12_131560517_R Primer3: not found at this Tm N.d. 0.13
mm3__chr12 131.07 Mbp_chr12_131070644_F Primer3: not found at this Tm N.d. 0.13
mm3__chr12 131.07 Mbp_chr12_131070644_R Primer3: not found at this Tm N.d. 0.13
mm4__chr2 69.21 Mbp_chr2_69211892_F TCGTCGGCAGCGTCGCTATTTCAGCCTACTCACCA 57.4 0.13
mm4__chr2 69.21 Mbp_chr2_69211892_R GTCTCGTGGGCTCGGACGAGAGGAGTGGGTTGACT 60.1 0.13
mm4__chr17 1.58 Mbp_chr17_1580820_F Primer3: not found at this Tm N.d. 0.13
mm4__chr17 1.58 Mbp_chr17_1580820_R Primer3: not found at this Tm N.d. 0.13
mm4__chrX 71.43 Mbp_chrX_71430314_F Primer3: not found at this Tm N.d. 0.12
mm4__chrX 71.43 Mbp_chrX_71430314_R Primer3: not found at this Tm N.d. 0.12
mm4__chrX 19.38 Mbp_chrX_19382174_F Primer3: not found at this Tm N.d. 0.12
mm4__chrX 19.38 Mbp_chrX_19382174_R Primer3: not found at this Tm N.d. 0.12
mm4__chr9 133.20 Mbp_chr9_133196810_F Primer3: not found at this Tm N.d. 0.12
mm4__chr9 133.20 Mbp_chr9_133196810_R Primer3: not found at this Tm N.d. 0.12
mm4__chr8 119.78 Mbp_chr8_119784429_F Primer3: not found at this Tm N.d. 0.12
mm4__chr8 119.78 Mbp_chr8_119784429_R Primer3: not found at this Tm N.d. 0.12
mm4__chr3 8.80 Mbp_chr3_8799435_F Primer3: not found at this Tm N.d. 0.12
mm4__chr3 8.80 Mbp_chr3_8799435_R Primer3: not found at this Tm N.d. 0.12
mm4__chr14 32.75 Mbp_chr14_32750806_F Primer3: not found at this Tm N.d. 0.12
mm4__chr14 32.75 Mbp_chr14_32750806_R Primer3: not found at this Tm N.d. 0.12
mm4__chr1 66.86 Mbp_chr1_66858463_F Primer3: not found at this Tm N.d. 0.12
mm4__chr1 66.86 Mbp_chr1_66858463_R Primer3: not found at this Tm N.d. 0.12
mm4__chr16 2.22 Mbp_chr16_2223412_F TCGTCGGCAGCGTCGGCAATCTGCTCCACCGTAA 60.3 0.12
mm4__chr16 2.22 Mbp_chr16_2223412_R GTCTCGTGGGCTCGGTAGCGGTGTGGCCTTAAAGG 60.0 0.12
mm4__chr19 33.62 Mbp_chr19_33622703_F Primer3: not found at this Tm N.d. 0.11
mm4__chr19 33.62 Mbp_chr19_33622703_R Primer3: not found at this Tm N.d. 0.11
mm4__chr16 16.56 Mbp_chr16_16559438_F TCGTCGGCAGCGTCCTTTAGTGGCCACCAGGAGG 60.0 0.09
mm4__chr16 16.56 Mbp_chr16_16559438_R GTCTCGTGGGCTCGGCTTCAGTGACAGCAGAGGGC 60.6 0.09
mm4__chr11 68.21 Mbp_chr11_68213418_F Primer3: not found at this Tm N.d. 0.09
mm4__chr11 68.21 Mbp_chr11_68213418_R Primer3: not found at this Tm N.d. 0.09
mm4__chr16 67.88 Mbp_chr16_67881511_F TCGTCGGCAGCGTCAGAGGGTGGTCTCTAGGCTG 60.0 0.09
mm4__chr16 67.88 Mbp_chr16_67881511_R GTCTCGTGGGCTCGGCCCAGGGTGAAGTTCCACAA 59.8 0.09
mm4__chr18 5.30 Mbp_chr18_5295092_F Primer3: not found at this Tm N.d. 0.09
mm4__chr18 5.30 Mbp_chr18_5295092_R Primer3: not found at this Tm N.d. 0.09
mm4__chr16 78.52 Mbp_chr16_78516172_F TCGTCGGCAGCGTCCAGAAGTACCTGCTGCCCAA 59.9 0.08
mm4__chr16 78.52 Mbp_chr16_78516172_R GTCTCGTGGGCTCGGAGCAAACCCTCCCTGCATTT 60.1 0.08
mm4__chr6 41.33 Mbp_chr6_41334857_F TCGTCGGCAGCGTCATGGAGTGGAGAGCAGGAGT 59.9 0.08
mm4__chr6 41.33 Mbp_chr6_41334857_R GTCTCGTGGGCTCGGCTGGACTGGCGATCTGCTG 60.5 0.08
mm4__chr22 50.68 Mbp_chr22_50679182_F TCGTCGGCAGCGTCGGGATCACCGACGAGAATGG 60.2 0.08
mm4__chr22 50.68 Mbp_chr22_50679182_R GTCTCGTGGGCTCGGCCCTACAGACAGAGCCAGGA 60.3 0.08
mm4__chr1 51.33 Mbp_chr1_51330451_F Primer3: not found at this Tm N.d. 0.07
mm4__chr1 51.33 Mbp_chr1_51330451_R Primer3: not found at this Tm N.d. 0.07
mm4__chr21 36.70 Mbp_chr21_36700863_F Primer3: not found at this Tm N.d. 0.07
mm4__chr21 36.70 Mbp_chr21_36700863_R Primer3: not found at this Tm N.d. 0.07
mm4__chr18 73.64 Mbp_chr18_73639944_F Primer3: not found at this Tm N.d. 0.07
mm4__chr18 73.64 Mbp_chr18_73639944_R Primer3: not found at this Tm N.d. 0.07
mm4__chr9 23.82 Mbp_chr9_23820992_F TCGTCGGCAGCGTCTCATCATTGCTCCTGCCCTG 60.1 0.05
mm4__chr9 23.82 Mbp_chr9_23820992_R GTCTCGTGGGCTCGGCGGGGCGTTTGGAGACTTAA 60.3 0.05
mm3__chr14_GL000225v1_random 135.99 Kbp_chr14_GL000225v1_random_135990_F TCGTCGGCAGCGTCAGGAATGGTTGTGCCTGCTG 60.8 0.05
mm3__chr14_GL000225v1_random 135.99 Kbp_chr14_GL000225v1_random_135990_R GTCTCGTGGGCTCGGAGCAGGGGCAGATGCAAG 60.0 0.05
mm4__chr3 98.90 Mbp_chr3_98901438_F TCGTCGGCAGCGTCGCGGGAGAACAAGAGGCAG 60.7 0.05
mm4__chr3 98.90 Mbp_chr3_98901438_R GTCTCGTGGGCTCGGGGGACGAAGGAGGAGTAGGT 60.0 0.05
mm4__chr17 8.12 Mbp_chr17_8121693_F Primer3: not found at this Tm N.d. 0.04
mm4__chr17 8.12 Mbp_chr17_8121693_R Primer3: not found at this Tm N.d. 0.04
mm4__chr20 41.33 Mbp_chr20_41325975_F Primer3: not found at this Tm N.d. 0.04
mm4__chr20 41.33 Mbp_chr20_41325975_R Primer3: not found at this Tm N.d. 0.04
mm4__chr2 34.12 Mbp_chr2_34116602_F Primer3: not found at this Tm N.d. 0.04
mm4__chr2 34.12 Mbp_chr2_34116602_R Primer3: not found at this Tm N.d. 0.04
mm4__chr11 79.33 Mbp_chr11_79325700_F TCGTCGGCAGCGTCAGGAAAGTACCCAGTACCCAGT 60.1 0.03
mm4__chr11 79.33 Mbp_chr11_79325700_R GTCTCGTGGGCTCGGTTGGGTGTGTTCTCGTGGAG 59.8 0.03
mm4__chr7 66.24 Mbp_chr7_66244012_F Primer3: not found at this Tm N.d. 0.03
mm4__chr7 66.24 Mbp_chr7_66244012_R Primer3: not found at this Tm N.d. 0.03
mm4__chr12 85.67 Mbp_chr12_85668080_F Primer3: not found at this Tm N.d. 0.03
mm4__chr12 85.67 Mbp_chr12_85668080_R Primer3: not found at this Tm N.d. 0.03
mm4__chrX 11.70 Mbp_chrX_11702545_F TCGTCGGCAGCGTCTGCAAGCTCACAGTTAGGAGG 59.9 0.03
mm4__chrX 11.70 Mbp_chrX_11702545_R GTCTCGTGGGCTCGGGGAAAGCTCTGAGGTGACCC 60.0 0.03
mm4__chr19 3.20 Mbp_chr19_3201221_F TCGTCGGCAGCGTCCCTGGGCTCCAAATTCTGCA 60.6 0.02
mm4__chr19 3.20 Mbp_chr19_3201221_R GTCTCGTGGGCTCGGTCGCTCCCCTCCTGTATTCA 60.0 0.02
mm4__chr1 115.64 Mbp_chr1_115642029_F TCGTCGGCAGCGTCTCTGCCTCTCCAGGAGCC 60.3 0.02
mm4__chr1 115.64 Mbp_chr1_115642029_R GTCTCGTGGGCTCGGCCTCTCGCGGGACTCACC 61.8 0.02
mm4__chrY 5.90 Mbp_chrY_5901812_F Primer3: not found at this Tm N.d. 0.02
mm4__chrY 5.90 Mbp_chrY_5901812_R Primer3: not found at this Tm N.d. 0.02
mm4__chrX 92.79 Mbp_chrX_92785178_F Primer3: not found at this Tm N.d. 0.02
mm4__chrX 92.79 Mbp_chrX_92785178_R Primer3: not found at this Tm N.d. 0.02
mm4__chr6 1.61 Mbp_chr6_1608153_F TCGTCGGCAGCGTCCCGCAAACCACCTGGAAAAG 59.9 0.02
mm4__chr6 1.61 Mbp_chr6_1608153_R GTCTCGTGGGCTCGGGAGGTTGCTCTGAATCCCGG 60.4 0.02
mm4__chr12 6.28 Mbp_chr12_6275772_F Primer3: not found at this Tm N.d. 0.02
mm4__chr12 6.28 Mbp_chr12_6275772_R Primer3: not found at this Tm N.d. 0.02
mm4__chr20 34.98 Mbp_chr20_34978655_F Primer3: not found at this Tm N.d. 0.01
mm4__chr20 34.98 Mbp_chr20_34978655_R Primer3: not found at this Tm N.d. 0.01
mm4__chr2 56.89 Mbp_chr2_56886058_F Primer3: not found at this Tm N.d. 0.01
mm4__chr2 56.89 Mbp_chr2_56886058_R Primer3: not found at this Tm N.d. 0.01
mm3__chr3 54.66 Mbp_chr3_54663358_F TCGTCGGCAGCGTCGGCACCTCCTGTTGTCTTCA 59.8 0.01
mm3__chr3 54.66 Mbp_chr3_54663358_R GTCTCGTGGGCTCGGAAGTCTTGGTGCCTGGAAGG 59.8 0.01
mm4__chr15 63.34 Mbp_chr15_63338664_F TCGTCGGCAGCGTCTGCAAAGACTCACTGAAGGGG 60.2 0.01
mm4__chr15 63.34 Mbp_chr15_63338664_R GTCTCGTGGGCTCGGAATGCAGCTCTGGCACTGAT 60.0 0.01
mm4__chr9 95.07 Mbp_chr9_95067561_F TCGTCGGCAGCGTCGAACCAGCCAGCGCAAAG 59.7 0.01
mm4__chr9 95.07 Mbp_chr9_95067561_R GTCTCGTGGGCTCGGACCCCTCACCCTAAGAACCA 59.8 0.01
mm4__chr16 4.39 Mbp_chr16_4392710_F TCGTCGGCAGCGTCCCACTAGGCAGGAAGGAGGA 60.3 0.01
mm4__chr16 4.39 Mbp_chr16_4392710_R GTCTCGTGGGCTCGGGCCCACACCTGGCTTCTATT 60.0 0.01
mm4__chr2 214.72 Mbp_chr2_214717606_F Primer3: not found at this Tm N.d. 0.01
mm4__chr2 214.72 Mbp_chr2_214717606_R Primer3: not found at this Tm N.d. 0.01
mm4__chr2 241.54 Mbp_chr2_241541849_F Primer3: not found at this Tm N.d. 0.00
mm4__chr2 241.54 Mbp_chr2_241541849_R Primer3: not found at this Tm N.d. 0.00
mm4__chr8 10.52 Mbp_chr8_10517863_F TCGTCGGCAGCGTCAGGTAAGAGGTGGCATCCCT 59.9 0.00
mm4__chr8 10.52 Mbp_chr8_10517863_R GTCTCGTGGGCTCGGACATGCCCAGGACAATCCAG 60.0 0.00
mm4__chr19 8.15 Mbp_chr19_8146124_F TCGTCGGCAGCGTCCTTCTTCTCCCTCCCGCAAG 60.1 0.00
mm4__chr19 8.15 Mbp_chr19_8146124_R GTCTCGTGGGCTCGGGTGAAGGCTTCTGCTCCCAG 60.6 0.00
mm4__chr1 25.03 Mbp_chr1_25034735_F Primer3: not found at this Tm N.d. 0.00
mm4__chr1 25.03 Mbp_chr1_25034735_R Primer3: not found at this Tm N.d. 0.00
mm4__chr17 13.79 Mbp_chr17_13785229_F Primer3: not found at this Tm N.d. 0.00
mm4__chr17 13.79 Mbp_chr17_13785229_R Primer3: not found at this Tm N.d. 0.00
mm4__chr1 2.24 Mbp_chr1_2238786_F TCGTCGGCAGCGTCTGCTGAAGGTGTACACGTCC 59.9 0.00
mm4__chr1 2.24 Mbp_chr1_2238786_R GTCTCGTGGGCTCGGGGAATACCTCCCTCCCCAGT 60.0 0.00
mm4__chr7 157.84 Mbp_chr7_157835613_F TCGTCGGCAGCGTCAGGAAACAGGGATCTGCAGC 60.0 0.00
mm4__chr7 157.84 Mbp_chr7_157835613_R GTCTCGTGGGCTCGGTTTCCCACGCATTTGCAGTG 59.9 0.00
mm4__chrX 107.74 Mbp_chrX_107737157_F TCGTCGGCAGCGTCACACAGGAATCCAGCAAGGG 59.9 0.00
mm4__chrX 107.74 Mbp_chrX_107737157_R GTCTCGTGGGCTCGGGGGACTTGGCCAGGATCTTC 60.1 0.00
mm4__chr9 124.00 Mbp_chr9_123999896_F Primer3: not found at this Tm N.d. 0.00
mm4__chr9 124.00 Mbp_chr9_123999896_R Primer3: not found at this Tm N.d. 0.00
mm4__chr10 132.96 Mbp_chr10_132964793_F TCGTCGGCAGCGTCTTTAACAGGCTCATCGGCGT 60.0 0.00
mm4__chr10 132.96 Mbp_chr10_132964793_R GTCTCGTGGGCTCGGCAGTGGGAGGAGGGAGGTG 60.9 0.00
mm4__chr15 37.05 Mbp_chr15_37049734_F Primer3: not found at this Tm N.d. 0.00
mm4__chr15 37.05 Mbp_chr15_37049734_R Primer3: not found at this Tm N.d. 0.00
mm4__chr16 1.17 Mbp_chr16_1165722_F TCGTCGGCAGCGTCCCTGAGGATGTAGAGGGGCT 60.1 0.00
mm4__chr16 1.17 Mbp_chr16_1165722_R GTCTCGTGGGCTCGGGTTCATCTGGTGGGGAACGT 59.9 0.00
mm4__chr9 93.59 Mbp_chr9_93592819_F Primer3: not found at this Tm N.d. 0.00
mm4__chr9 93.59 Mbp_chr9_93592819_R Primer3: not found at this Tm N.d. 0.00
mm4__chr8 134.14 Mbp_chr8_134144310_F Primer3: not found at this Tm N.d. 0.00
mm4__chr8 134.14 Mbp_chr8_134144310_R Primer3: not found at this Tm N.d. 0.00
mm4__chr5 169.93 Mbp_chr5_169929056_F TCGTCGGCAGCGTCTTGTGCCCTGAGAAGAGCAG 59.9 0.00
mm4__chr5 169.93 Mbp_chr5_169929056_R GTCTCGTGGGCTCGGGGCACTCTGGTTCCCTTTCA 59.8 0.00
mm4__chr22 28.97 Mbp_chr22_28965484_F Primer3: not found at this Tm N.d. 0.00
mm4__chr22 28.97 Mbp_chr22_28965484_R Primer3: not found at this Tm N.d. 0.00
mm4__chr2 38.10 Mbp_chr2_38098428_F TCGTCGGCAGCGTCTTGAGGGAGAAGCGTTCCTG 59.6 0.00
mm4__chr2 38.10 Mbp_chr2_38098428_R GTCTCGTGGGCTCGGCCCTCCCCACACTTCCTTTT 59.5 0.00
mm4__chr18 75.87 Mbp_chr18_75870883_F Primer3: not found at this Tm N.d. 0.00
mm4__chr18 75.87 Mbp_chr18_75870883_R Primer3: not found at this Tm N.d. 0.00
mm4__chr11 119.47 Mbp_chr11_119470751_F TCGTCGGCAGCGTCCGGCCCATTTGTAGAGCTCA 60.1 0.00
mm4__chr11 119.47 Mbp_chr11_119470751_R GTCTCGTGGGCTCGGGCAGGCATCAGAGAGTCTGG 60.1 0.00
mm4__chr10 118.50 Mbp_chr10_118501213_F TCGTCGGCAGCGTCCCTTCCTGCCTCATCTGCTC 60.1 0.00
mm4__chr10 118.50 Mbp_chr10_118501213_R GTCTCGTGGGCTCGGACTACACTTCCAGGAGGGCT 59.8 0.00
mm3__chr15 67.82 Mbp_chr15_67823618_F Primer3: not found at this Tm N.d. 0.00
mm3__chr15 67.82 Mbp_chr15_67823618_R Primer3: not found at this Tm N.d. 0.00
mm3__chr1 13.50 Mbp_chr1_13497184_F Primer3: not found at this Tm N.d. 0.00
mm3__chr1 13.50 Mbp_chr1_13497184_R Primer3: not found at this Tm N.d. 0.00

Off-target amplicon sequences

Primers underlined, off-targets in bold.

ontarget_mm0__chr7 5.53 Mbp_chr7_5529675 CCATGGTGAGCTGCGAGAATAGCCGGGCGCGCTGTGAGCCGAGGTCGCCCCCGCCCTGGCCACTTCCGGCGCGCCGAGTC
CTTAGGCCGCCAGGGGGCGCCGGCGCGCGCCCAGATTGGGGACAAAGGAAGCCG
mm4__chr19 19.26 Mbp_chr19_19261516 CTGTGAGCAGCAGGACGCCCCAGGCCGCGGCCCAGAGCGCGCCGGGACCGAGGGCCGCCCGAGCGCACACCTGGGGGGCG
GGCACGGGGCGCTCAGTCCAGCCTCCCAGCCTTGGCTTTTCGGAGGCCT
mm4__chrX 3.63 Mbp_chrX_3633695 TAAAGTGGATGGTGCAGGCAGAGATACCCTGGGCGCTGTGAGCTGATGTTCTCCCTCCTACTCAGCTGGAAAAACACCCT
CCTAAACTATCAGCTGACACACTACCTGCTCCAGTTCTGAGGA
mm4__chr2 69.21 Mbp_chr2_69211892 GCTATTTCAGCCTACTCACCATATGTATTCCCACCTGTGGACCTCTGCTCACACCACCCCCGGCCCAAATTATGCTGTTC
CTTCTCTTCTCATTGTAAGTCAACCCACTCCTCTCGT
mm4__chr16 2.22 Mbp_chr16_2223412 GGCAATCTGCTCCACCGTAACCACGCCCTCCCCACAGTCCCGCCCCATCTTCGCTCTCAGCGCGCCCGGCCCCGCCTCTG
CCCTTTAAGGCCACACCGCTA
mm4__chr16 16.56 Mbp_chr16_16559438 CTTTAGTGGCCACCAGGAGGTGAATGACTCATGCTACCTTTTCTCAGCAAAGGCTCTTCAGGATGGGACACTCCAAGTTT
TTAACTCCCAGCAACAGTTCGGCTCACAGCGAGACCGGGCCCTCTGCTGTCACTGAAG
mm4__chr16 67.88 Mbp_chr16_67881511 AGAGGGTGGTCTCTAGGCTGCCTCACATAGCCTGAGGTGCTTCTCGCCTATGGCAGGGATGCAGCCATGGGATCCCGGCT
CACAGAGCACCAGG
TAAGTGAATGAGCCCACTTTGTACTTGTGGAACTTCACCCTGGG
mm4__chr16 78.52 Mbp_chr16_78516172 CAGAAGTACCTGCTGCCCAAGACCACAGCTGACAGCGCCCCGGGAGTCCTTCACACTCTTCTCTGAGCTCTTCCATCCTT
AAACAGACATCTATGCCAAATGCAGGGAGGGTTTGCT
mm4__chr6 41.33 Mbp_chr6_41334857 ATGGAGTGGAGAGCAGGAGTCCAGGGGCAGGCAAAGCAGTGGACTTGGAATCGAGTCCACTTGACAAGTTCCAATTCCCG
TCTCAGTTATTACCTCTGTTCACAGAGCTCCCGGCAGCAGATCGCCAGTCCAG
mm4__chr22 50.68 Mbp_chr22_50679182 GGGATCACCGACGAGAATGGCTGGCAGGAGATCCACCAGGTGTGCAGGGAGCCGAGGTGGGGTCCCGGCCTCTGTGTGCT
GGGTTGGGGGTCCTGGCTCTGTCTGTAGGG
mm4__chr9 23.82 Mbp_chr9_23820992 TCATCATTGCTCCTGCCCTGGGCGCCCGCGGCCCTACACCACCTCCGCACACAACGCGGCCGGTGTTAAGTCTCCAAACG
CCCCG
mm3__chr14_GL000225v1_random 135.99 Kbp_chr14_GL000225v1_random_135990 AGGAATGGTTGTGCCTGCTGCAGAAACTCCGGGCTCGCCAGGAGCTCATCCAGCAGCTGGCCGGAGGGGAGTGCAGAAGA
GCACCCCGGCTCCCAGAGCGCCTGGGAGAGCGCCGGGATGCCTTGCATCTGCCCCTGCT
mm4__chr3 98.90 Mbp_chr3_98901438 GCGGGAGAACAAGAGGCAGCCCTCGCCTCACCCCGCGCCGGGACCCTTCCGCCCCTCACCCCGCTTTCACCTACTCCTCC
TTCGTCCC
mm4__chr11 79.33 Mbp_chr11_79325700 AGGAAAGTACCCAGTACCCAGTACTCTACCCAGGCGCTCAGTGAACAGAGGTTATTGTGATCATTTTATAATTCACTGGG
TCAAAGATACAGATGATTCACCAGATCTCTATCATGTCTCCACGAGAACACACCCAA
mm4__chrX 11.70 Mbp_chrX_11702545 TGCAAGCTCACAGTTAGGAGGATGCAAATCTAGTTGAGCCAAAGAGTCCCTGGAGCTCTGGGAGCCTAGGTGGAGGGTCA
CCTCAGAGCTTTCC
mm4__chr19 3.20 Mbp_chr19_3201221 CCTGGGCTCCAAATTCTGCATGTAGCTTCTCCCGGGCGCGGGCCGAGCCGAGGTGGATGAGGAGAGTCCTGGGCTTGGCG
GGGCCCCGCAGACCCCAGGCCATCAGTCGGGGATTGAATACAGGAGGGGAGCGA
mm4__chr1 115.64 Mbp_chr1_115642029 TCTGCCTCTCCAGGAGCCCAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNGGTGAGTCCCGCGAGAGG
mm4__chr6 1.61 Mbp_chr6_1608153 CCGCAAACCACCTGGAAAAGGAGTCTCCAGAGACCCCGGCGCACAGCAGGCCAGGAGGCAGCTGCCCCGGGATTCAGAGC
AACCTC
mm3__chr3 54.66 Mbp_chr3_54663358 GGCACCTCCTGTTGTCTTCAGCCCTTCTGGACTCCAGGGGCAGTGTGAGCCGAGGTGTCCACCCCTCATGCCTTCATGGC
CCTGGGCCTCTCAGTTATGTATGTGATGACTTGGCCTTCCAGGCACCAAGACTT
mm4__chr15 63.34 Mbp_chr15_63338664 TGCAAAGACTCACTGAAGGGGGGACCCCAGTGAGCCCCACACCTAGTCTCACAAGGCGCCTGGTTCCCGTGGCAGCCAGG
GAGCTCTCAGCCAACTTCTTGAGGGCATCAGTGCCAGAGCTGCATT
mm4__chr9 95.07 Mbp_chr9_95067561 GAACCAGCCAGCGCAAAGCTGACTTCATGGCCTCGGCTCTCAGGGCACCAGGTAGTTTTTCTCGAGAGTAGACTGTGTAG
AATAGTACCCTTCGCTGAAACAGCCTTTCTCAACTTGGTTCTTAGGGTGAGGGGT
mm4__chr16 4.39 Mbp_chr16_4392710 CCACTAGGCAGGAAGGAGGATTGCCAGAGAAGGAGCTCCCAGAAGGCCTCTCCCTCGAGCCGGCCCCTCGGCTCACACCG
GCCCTGG
CTGCCAGCAGCGGTTTTCCTAATAGAAGCCAGGTGTGGGC
mm4__chr8 10.52 Mbp_chr8_10517863 AGGTAAGAGGTGGCATCCCTTCCCCCAACCTCTGCTCCTAGCGGGCCTGGCACAGACCTGGATTGTCCTGGGCATGT
mm4__chr19 8.15 Mbp_chr19_8146124 CTTCTTCTCCCTCCCGCAAGAGGCCGCTTCCCGCTCACCTCGGCTCACCCCGCAGCTGGGAGCCAGCGTCCCATCCGCAC
AGGTGCACAGGTTGGGCTGGGAGCAGAAGCCTTCAC
mm4__chr1 2.24 Mbp_chr1_2238786 TGCTGAAGGTGTACACGTCCACTGAGGCCACCTGCGCCGCTGCCTGTGTCCTGTGGGCTGGCACTCACCGAGTGAGAGCT
GTGTGCAGAACCTCCGCTGTCAGCGGGCCAGGCCACACTGGGGAGGGAGGTATTCC
mm4__chr7 157.84 Mbp_chr7_157835613 AGGAAACAGGGATCTGCAGCAATGCCTCGGCTCTCAGGGCGCTCGGGAGGGTGCAGGGGCGAAATTAACAACATAGCCGA
AGGGTGCACTGCAAATGCGTGGGAAA
mm4__chrX 107.74 Mbp_chrX_107737157 ACACAGGAATCCAGCAAGGGAAGTTGCAAAGGCCAGACCACGGCTCCCAGGGCCCCTGGACCAATGGGGGACAAGGGGCA
TGCTGAGGTATAAATGACTTGTGAAGATCCTGGCCAAGTCCC
mm4__chr10 132.96 Mbp_chr10_132964793 TTTAACAGGCTCATCGGCGTGGCCCTAGGCCCTGCCCTCTGTGAGCCCAGGTCACCCCCAGGACGCCCAGCGGCTGCTGC
GCCACCTCCCTCCTCCCACTG
mm4__chr16 1.17 Mbp_chr16_1165722 CCTGAGGATGTAGAGGGGCTGCCTCCCTGCCCCCACCCCGGCTCACAGTGCGGGTGGCTCCCGGCTCTCCTGAGTTGTGC
TGGCCACCTCACGTTCCCCACCAGATGAAC
mm4__chr5 169.93 Mbp_chr5_169929056 TTGTGCCCTGAGAAGAGCAGATGGAAAGCTTGAGGTCAACCTGGGCCCACAGCTGGCCAGGTAGACTGAAGTTCTGTCAT
GCCCTGCCTTGAAAGGGAACCAGAGTGCC
mm4__chr2 38.10 Mbp_chr2_38098428 TTGAGGGAGAAGCGTTCCTGTAATGGAGGGGAAATGAATAAAACCTCGACTCCCAGCTCGACAGGGACCTTTCTTCTCCT
AGCCAGCTGGAATGCAAGCTTTAAAAAAAAAGGAAGTGTGGGGAGGG
mm4__chr11 119.47 Mbp_chr11_119470751 CGGCCCATTTGTAGAGCTCAGAGACCCCGGCTCCCACCCCGCCTGGCCCCTCTCCCTCCAGACTCTCTGATGCCTGC
mm4__chr10 118.50 Mbp_chr10_118501213 CCTTCCTGCCTCATCTGCTCTGCACATCCAGACCTTGGGTCACAGCCCTCCTGGAAGTGTGGTCACAGCCCTCCTGGAAG
TGTAGT

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.