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PCR primers for off-targets of GGCCTAAGGACTCGGCGCGC 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_5529718_F TCGTCGGCAGCGTCTGGTGAGCTGCGAGAATAGC 60.1 1.00
ontarget_mm0__chr7 5.53 Mbp_chr7_5529718_R GTCTCGTGGGCTCGGCGGCTTCCTTTGTCCCCAAT 60.6 1.00
mm4__chr1 31.24 Mbp_chr1_31239718_F Primer3: not found at this Tm N.d. 0.37
mm4__chr1 31.24 Mbp_chr1_31239718_R Primer3: not found at this Tm N.d. 0.37
mm4__chr14 70.42 Mbp_chr14_70417093_F TCGTCGGCAGCGTCCACAGCGGTTTCGGTTTCAG 60.0 0.31
mm4__chr14 70.42 Mbp_chr14_70417093_R GTCTCGTGGGCTCGGAAACTGCAATCCATTGGCGG 59.7 0.31
mm4__chr15 44.43 Mbp_chr15_44427059_F TCGTCGGCAGCGTCACCGAAATCCCAGGAAAGGC 60.3 0.20
mm4__chr15 44.43 Mbp_chr15_44427059_R GTCTCGTGGGCTCGGAGGTGGAGCTGAGGGGATAA 59.6 0.20
mm4__chr19 17.95 Mbp_chr19_17951373_F TCGTCGGCAGCGTCACAGCAAGACATATCCGGCG 60.5 0.16
mm4__chr19 17.95 Mbp_chr19_17951373_R GTCTCGTGGGCTCGGAGCCTCAGTTTCCCTTCAGC 59.9 0.16
mm4__chr3 72.10 Mbp_chr3_72098682_F Primer3: not found at this Tm N.d. 0.15
mm4__chr3 72.10 Mbp_chr3_72098682_R Primer3: not found at this Tm N.d. 0.15
mm4__chr20 62.93 Mbp_chr20_62929568_F TCGTCGGCAGCGTCGGTCGTGAGTCGTGTCTGTG 60.6 0.12
mm4__chr20 62.93 Mbp_chr20_62929568_R GTCTCGTGGGCTCGGTCCTGGGTAAAGGAGAGGGT 59.2 0.12
mm4__chr19 14.55 Mbp_chr19_14551729_F TCGTCGGCAGCGTCACAGCTGTAAACCCTGCCTG 60.2 0.11
mm4__chr19 14.55 Mbp_chr19_14551729_R GTCTCGTGGGCTCGGAGAACTGAGCCTCTCTGCCT 60.2 0.11
mm4__chr10 123.43 Mbp_chr10_123425788_F TCGTCGGCAGCGTCTGCAAATAAAATCCAGCACCACT 59.4 0.11
mm4__chr10 123.43 Mbp_chr10_123425788_R GTCTCGTGGGCTCGGGAGCCTTCCCTCCCATATGC 59.9 0.11
mm4__chr14 104.14 Mbp_chr14_104135984_F Primer3: not found at this Tm N.d. 0.10
mm4__chr14 104.14 Mbp_chr14_104135984_R Primer3: not found at this Tm N.d. 0.10
mm4__chr19 4.34 Mbp_chr19_4343461_F TCGTCGGCAGCGTCCCCGAGGCCTCAGTTTCTC 59.7 0.08
mm4__chr19 4.34 Mbp_chr19_4343461_R GTCTCGTGGGCTCGGGAGCTCTAGACTCCGGCTTC 59.3 0.08
mm4__chr19 5.14 Mbp_chr19_5144255_F Primer3: not found at this Tm N.d. 0.08
mm4__chr19 5.14 Mbp_chr19_5144255_R Primer3: not found at this Tm N.d. 0.08
mm4__chr15 51.74 Mbp_chr15_51737556_F Primer3: not found at this Tm N.d. 0.07
mm4__chr15 51.74 Mbp_chr15_51737556_R Primer3: not found at this Tm N.d. 0.07
mm4__chr14 105.44 Mbp_chr14_105438582_F Primer3: not found at this Tm N.d. 0.07
mm4__chr14 105.44 Mbp_chr14_105438582_R Primer3: not found at this Tm N.d. 0.07
mm4__chr19 4.06 Mbp_chr19_4062326_F TCGTCGGCAGCGTCGAGCGCCGGATTCTCTGAG 60.3 0.06
mm4__chr19 4.06 Mbp_chr19_4062326_R GTCTCGTGGGCTCGGTCTGGGGCGATTATCAAGGC 59.8 0.06
mm4__chr16 71.85 Mbp_chr16_71846285_F TCGTCGGCAGCGTCCTTCTCTCTGGCCTGTCCTG 59.4 0.06
mm4__chr16 71.85 Mbp_chr16_71846285_R GTCTCGTGGGCTCGGCACAGACTCGGACACCTTGG 60.3 0.06
mm4__chrY 11.31 Mbp_chrY_11306675_F Primer3: not found at this Tm N.d. 0.06
mm4__chrY 11.31 Mbp_chrY_11306675_R Primer3: not found at this Tm N.d. 0.06
mm4__chr11 47.44 Mbp_chr11_47438783_F TCGTCGGCAGCGTCGGTGGAAGATGTGGGAGCAA 59.9 0.06
mm4__chr11 47.44 Mbp_chr11_47438783_R GTCTCGTGGGCTCGGTGGAGGAGACGGAGCTCTAC 60.1 0.06
mm4__chr17 47.42 Mbp_chr17_47423482_F Primer3: not found at this Tm N.d. 0.06
mm4__chr17 47.42 Mbp_chr17_47423482_R Primer3: not found at this Tm N.d. 0.06
mm4__chr8 73.88 Mbp_chr8_73878095_F TCGTCGGCAGCGTCGCCTTGCAGTGGGAAACAAA 59.5 0.06
mm4__chr8 73.88 Mbp_chr8_73878095_R GTCTCGTGGGCTCGGCTCCAGCAGTCCACTGTCTC 59.7 0.06
mm4__chr11 909.45 Kbp_chr11_909452_F TCGTCGGCAGCGTCATAAGGTGGAGCGCTACTGC 59.8 0.05
mm4__chr11 909.45 Kbp_chr11_909452_R GTCTCGTGGGCTCGGTTCCATCAACACCACCGAGG 59.9 0.05
mm4__chr14 77.14 Mbp_chr14_77140899_F TCGTCGGCAGCGTCGAAATAGGATTCCGTGCGCC 59.4 0.04
mm4__chr14 77.14 Mbp_chr14_77140899_R GTCTCGTGGGCTCGGACCGCCTTCCCAGAACTTTT 59.8 0.04
mm4__chr21 45.98 Mbp_chr21_45984052_F TCGTCGGCAGCGTCCAGGGCCACACACTCAGG 59.9 0.04
mm4__chr21 45.98 Mbp_chr21_45984052_R GTCTCGTGGGCTCGGTGACACACAGCTGGACTTGC 60.8 0.04
mm4__chr9 133.47 Mbp_chr9_133473154_F TCGTCGGCAGCGTCGGACTTGGTGAGGACGAAGG 60.0 0.04
mm4__chr9 133.47 Mbp_chr9_133473154_R GTCTCGTGGGCTCGGATCACCTGGCTGCTCATGTC 60.1 0.04
mm4__chr2 119.49 Mbp_chr2_119488102_F Primer3: not found at this Tm N.d. 0.04
mm4__chr2 119.49 Mbp_chr2_119488102_R Primer3: not found at this Tm N.d. 0.04
mm4__chr12 57.22 Mbp_chr12_57216891_F Primer3: not found at this Tm N.d. 0.03
mm4__chr12 57.22 Mbp_chr12_57216891_R Primer3: not found at this Tm N.d. 0.03
mm4__chr13 95.64 Mbp_chr13_95642137_F TCGTCGGCAGCGTCCCCTCAGGAGCGGGAGAA 60.3 0.03
mm4__chr13 95.64 Mbp_chr13_95642137_R GTCTCGTGGGCTCGGGACCTGGGCGCTGCTATAG 60.0 0.03
mm4__chr14_GL000225v1_random 90.74 Kbp_chr14_GL000225v1_random_90739_F Primer3: not found at this Tm N.d. 0.03
mm4__chr14_GL000225v1_random 90.74 Kbp_chr14_GL000225v1_random_90739_R Primer3: not found at this Tm N.d. 0.03
mm4__chr21 42.54 Mbp_chr21_42540562_F TCGTCGGCAGCGTCGTGTGAGGCAGTCAGTGGAG 60.3 0.03
mm4__chr21 42.54 Mbp_chr21_42540562_R GTCTCGTGGGCTCGGCAGAAGCCAGGAGATTCCGG 60.1 0.03
mm4__chr12 114.44 Mbp_chr12_114444998_F TCGTCGGCAGCGTCGCTCACCAGCTCTAAGTGCA 60.0 0.03
mm4__chr12 114.44 Mbp_chr12_114444998_R GTCTCGTGGGCTCGGTTAATGCGTGGCCTTGGTCA 60.2 0.03
mm4__chr20 13.22 Mbp_chr20_13221738_F TCGTCGGCAGCGTCGCTCCTACTCCTCCTCCCC 60.1 0.03
mm4__chr20 13.22 Mbp_chr20_13221738_R GTCTCGTGGGCTCGGGCACCATCCTTTTGAGACGC 59.8 0.03
mm4__chr14 96.36 Mbp_chr14_96363615_F Primer3: not found at this Tm N.d. 0.03
mm4__chr14 96.36 Mbp_chr14_96363615_R Primer3: not found at this Tm N.d. 0.03
mm4__chr4 184.65 Mbp_chr4_184649622_F TCGTCGGCAGCGTCCGAGAACCCAGCCCCAGG 62.1 0.02
mm4__chr4 184.65 Mbp_chr4_184649622_R GTCTCGTGGGCTCGGGACCAAAGCGGGAGGACTG 60.3 0.02
mm4__chr1 19.32 Mbp_chr1_19324180_F TCGTCGGCAGCGTCCTGTCTTGGCTACAGCTGCT 60.0 0.02
mm4__chr1 19.32 Mbp_chr1_19324180_R GTCTCGTGGGCTCGGGCAACAAGAACAGTGCTGGG 59.9 0.02
mm4__chr17 9.23 Mbp_chr17_9226042_F TCGTCGGCAGCGTCAGAGGGTGGAAGGCTGGG 60.6 0.02
mm4__chr17 9.23 Mbp_chr17_9226042_R GTCTCGTGGGCTCGGTGGCTCTCTGTAAGCGTGTG 60.0 0.02
mm4__chr8 23.26 Mbp_chr8_23262850_F Primer3: not found at this Tm N.d. 0.02
mm4__chr8 23.26 Mbp_chr8_23262850_R Primer3: not found at this Tm N.d. 0.02
mm4__chr1 167.36 Mbp_chr1_167357663_F Primer3: not found at this Tm N.d. 0.02
mm4__chr1 167.36 Mbp_chr1_167357663_R Primer3: not found at this Tm N.d. 0.02
mm4__chr7 151.41 Mbp_chr7_151410398_F TCGTCGGCAGCGTCCAAGCCAGGTCCTCCCATG 60.0 0.02
mm4__chr7 151.41 Mbp_chr7_151410398_R GTCTCGTGGGCTCGGCTTTCCCTGTCGCACCCTC 60.3 0.02
mm4__chr3 51.39 Mbp_chr3_51391279_F Primer3: not found at this Tm N.d. 0.02
mm4__chr3 51.39 Mbp_chr3_51391279_R Primer3: not found at this Tm N.d. 0.02
mm4__chr22 50.61 Mbp_chr22_50605362_F TCGTCGGCAGCGTCACTCTGTCTCCCTGTCTCCC 59.9 0.02
mm4__chr22 50.61 Mbp_chr22_50605362_R GTCTCGTGGGCTCGGCCGTTGACCAGACAGGAGAA 59.3 0.02
mm4__chr11 15.65 Mbp_chr11_15650470_F TCGTCGGCAGCGTCGCTGTGCTGTCATGGGGAG 60.7 0.01
mm4__chr11 15.65 Mbp_chr11_15650470_R GTCTCGTGGGCTCGGGAAGAAAATTCCCACGCTGG 57.3 0.01
mm3__chr3 51.70 Mbp_chr3_51698900_F TCGTCGGCAGCGTCTGGTGTTTAGCTGGCCTTGA 59.5 0.01
mm3__chr3 51.70 Mbp_chr3_51698900_R GTCTCGTGGGCTCGGCTCCTCTCCACCCTGGACAA 60.5 0.01
mm4__chr11 72.24 Mbp_chr11_72242951_F Primer3: not found at this Tm N.d. 0.01
mm4__chr11 72.24 Mbp_chr11_72242951_R Primer3: not found at this Tm N.d. 0.01
mm4__chr4 37.57 Mbp_chr4_37566866_F Primer3: not found at this Tm N.d. 0.01
mm4__chr4 37.57 Mbp_chr4_37566866_R Primer3: not found at this Tm N.d. 0.01
mm4__chr22 20.44 Mbp_chr22_20438128_F TCGTCGGCAGCGTCAGACATCTACCGAAGCAGCC 59.5 0.00
mm4__chr22 20.44 Mbp_chr22_20438128_R GTCTCGTGGGCTCGGCACTCCCTTGGCCGGTTC 60.3 0.00
mm4__chr8 142.22 Mbp_chr8_142216953_F Primer3: not found at this Tm N.d. 0.00
mm4__chr8 142.22 Mbp_chr8_142216953_R Primer3: not found at this Tm N.d. 0.00
mm4__chrX 48.19 Mbp_chrX_48191187_F Primer3: not found at this Tm N.d. 0.00
mm4__chrX 48.19 Mbp_chrX_48191187_R Primer3: not found at this Tm N.d. 0.00
mm4__chr14 73.13 Mbp_chr14_73132063_F Primer3: not found at this Tm N.d. 0.00
mm4__chr14 73.13 Mbp_chr14_73132063_R Primer3: not found at this Tm N.d. 0.00
mm4__chrX 104.21 Mbp_chrX_104206172_F Primer3: not found at this Tm N.d. 0.00
mm4__chrX 104.21 Mbp_chrX_104206172_R Primer3: not found at this Tm N.d. 0.00
mm4__chr7 77.47 Mbp_chr7_77468132_F Primer3: not found at this Tm N.d. 0.00
mm4__chr7 77.47 Mbp_chr7_77468132_R Primer3: not found at this Tm N.d. 0.00
mm4__chr17 67.17 Mbp_chr17_67172890_F Primer3: not found at this Tm N.d. 0.00
mm4__chr17 67.17 Mbp_chr17_67172890_R Primer3: not found at this Tm N.d. 0.00
mm4__chr2 31.83 Mbp_chr2_31829271_F Primer3: not found at this Tm N.d. 0.00
mm4__chr2 31.83 Mbp_chr2_31829271_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_5529718 TGGTGAGCTGCGAGAATAGCCGGGCGCGCTGTGAGCCGAGGTCGCCCCCGCCCTGGCCACTTCCGGCGCGCCGAGTCCTT
AGGCCGCCAGGGGGCGCCGGCGCGCGCCCAGATTGGGGACAAAGGAAGCCG
mm4__chr14 70.42 Mbp_chr14_70417093 CACAGCGGTTTCGGTTTCAGCAGCCTCGAGACCCGGAAAAGGAAGCCCGAAGGACTCGGAGCACTGGGAATGCTGGGAAT
CGTGGTTCCTACCGCCAATGGATTGCAGTTT
mm4__chr15 44.43 Mbp_chr15_44427059 ACCGAAATCCCAGGAAAGGCGCCAGATTCGCTTTCTCCCGGCCTCAGGCAGCTCTCCCTACGAACTACCTCCTCCAGCGC
GCCAAGCCGTTAGTCCCGCCTTATCCCCTCAGCTCCACCT
mm4__chr19 17.95 Mbp_chr19_17951373 ACAGCAAGACATATCCGGCGGCCCTACGGACTCGGAGAGCTGGAGGGACCCCGGAGGTGGGCACTTGTCCGTTCGCTGAA
GGGAAACTGAGGCT
mm4__chr20 62.93 Mbp_chr20_62929568 GGTCGTGAGTCGTGTCTGTGCCAGGCCCCCCACGCTGTGCTCCAGGGCCTCAGTGCCCGGCGCGCCGGGGGCTGTATCGC
CAGCCACTTGGGGCAGGAAAAAGGAATCACAAAATACAACCCTCTCCTTTACCCAGGA
mm4__chr19 14.55 Mbp_chr19_14551729 ACAGCTGTAAACCCTGCCTGGGCCCCGCTGTGGTATGAGTTGCTGATAGACCTTTTGCTCTGGTACAGCCTGGCTGTGTG
AGGCTGTGGGGCAGAGGCCAGCGGGCTGGGTCCTCAGGCCAGGCAGAGAGGCTCAGTTCT
mm4__chr10 123.43 Mbp_chr10_123425788 TGCAAATAAAATCCAGCACCACTGGCCCCAGGAGTCGGAGCGCTGGTCTTTTCTGTGCTACCTGAGGTTTGAGTGTGCAG
TTGCGGGCATATGGGAGGGAAGGCTC
mm4__chr19 4.34 Mbp_chr19_4343461 CCCGAGGCCTCAGTTTCTCCGCCCACCCCAGCGCGCCGAGCCCTTCCCCCGACCCCGGCGACGGCCAATGGTTGGGGCGC
CCCTCCCCTCCCCGGGGCGGGGCCGCGTGACGTGCCGGGAAGCCGGAGTCTAGAGCTC
mm4__chr19 4.06 Mbp_chr19_4062326 GAGCGCCGGATTCTCTGAGGGGCGCCTTCTGCGCTTTGGGGCTCTGGACTCGGCGCTCGGGGCCCAAGGGCCAGAGCCGC
TCCTCGGAGCAGCTGGGGGAGGCTGGGCCTTGATAATCGCCCCAGA
mm4__chr16 71.85 Mbp_chr16_71846285 CTTCTCTCTGGCCTGTCCTGGAAGGTGGCCTCAGGCCCCGGCGCCCCGGAGGCTGTGTGCCTGCGAGCCAAGGTGTCCGA
GTCTGTG
mm4__chr11 47.44 Mbp_chr11_47438783 GGTGGAAGATGTGGGAGCAAGGTAGGGCCTGCAGCCGGCTGTTCTTCTCGCCTATGGACTCGCCGCACAGGCCGCAGTAG
AGCTCCGTCTCCTCCA
mm4__chr8 73.88 Mbp_chr8_73878095 GCCTTGCAGTGGGAAACAAAATAGAAGGCAAGCTATCCCGAGAGGTTTAAGGGGGCTGAGGACTCGGCTCTCGGGAGATC
GCCCATCAGGCGGTGGACACGGGGCAGCTTCGAGAGGAAGGAGACAGTGGACTGCTGGAG
mm4__chr11 909.45 Kbp_chr11_909452 ATAAGGTGGAGCGCTACTGCTCCCACTTTCCTGCGCTCCCAGTCCGTAGGTCCAGGACCTCCTCGGTGGTGTTGATGGAA
mm4__chr14 77.14 Mbp_chr14_77140899 GAAATAGGATTCCGTGCGCCCGAGAGAACTTTTCCAGGGGCTAAGGAATCGGCCAGCCGGAGGCGCGAGAAAAGTTCTGG
GAAGGCGGT
mm4__chr21 45.98 Mbp_chr21_45984052 CAGGGCCACACACTCAGGGCTCCTGGTCTGAGGGCCTGAGGGATCGGGGCGCAGGTCGCTTGCTGGCCACACCCGCCTGC
ACAGCCTTCCAGGAGGGCCGGCCTCAGGGCCACAGGGCAAGTCCAGCTGTGTGTCA
mm4__chr9 133.47 Mbp_chr9_133473154 GGACTTGGTGAGGACGAAGGCGGTGAGCCAGCTGGCCAGCACGCAGAGCCCTGAGGCCACGCCACGGGCACGCAGGGGCA
GGACCTCAGACATGAGCAGCCAGGTGAT
mm4__chr13 95.64 Mbp_chr13_95642137 CCCTCAGGAGCGGGAGAAGGCCGGGTTCCTCGCTTCCGCGGCGGCGGCGGCCTAAGGTCTGGGCGTCCAGGACGTTGCTA
TAGCAGCGCCCAGGTC
mm4__chr21 42.54 Mbp_chr21_42540562 GTGTGAGGCAGTCAGTGGAGAGAACAGGAGAGATCATGAAGGTGCTAGAAGGGGAGAAGGCCTGAGGACAGCGCGCGCTG
GCTTTGCCCTTGGAGCTGGAGCCCTTCCGGAATCTCCTGGCTTCTG
mm4__chr12 114.44 Mbp_chr12_114444998 GCTCACCAGCTCTAAGTGCACACATATCAGGGCTGGGAGCCGGAACCGCCTGGGCATGCGTTCCTGCGCGCTTACTCCTG
AGGCCAGGGAAAAAGGTTTGCCTGCGATCCTGACCAAGGCCACGCATTAA
mm4__chr20 13.22 Mbp_chr20_13221738 GCTCCTACTCCTCCTCCCCCGGCGTCACCGCCGCCGCCGCCGGCCGCCGCGCCGGGTCCTAAAGCCGCGCGTCTCAAAAG
GATGGTGC
mm4__chr4 184.65 Mbp_chr4_184649622 CGAGAACCCAGCCCCAGGCTGGGCCCCAGGAGGCGCCCGCCCACCGCAGCGCGCCCCGCCCCCGCGCCCCGCGTCCTCAC
GCCCTGGTCCCGCCCTCGCGTCCCGCGCCAGTCCTCCCGCTTTGGTC
mm4__chr1 19.32 Mbp_chr1_19324180 CTGTCTTGGCTACAGCTGCTCCTGGAGACCCGGCGTGCCCAGGCCTTCGGCCCGCACGTCCCTTTCCCAGCACTGTTCTT
GTTGC
mm4__chr17 9.23 Mbp_chr17_9226042 AGAGGGTGGAAGGCTGGGGCGGTGGGGGCCCATGAGAAGGGGCCTGTGGGCTCGGGGCGCCGGCCCTGTCCCGTGTTCTC
TCGGGCACACGCTTACAGAGAGCCA
mm4__chr7 151.41 Mbp_chr7_151410398 CAAGCCAGGTCCTCCCATGCTCTGAGCCCTAAGGACTCTGCCCGAGGGGCTCTCGGGGACTTGGGGGCGGTCCCCCAATG
GAGGGTGCGACAGGGAAAG
mm4__chr22 50.61 Mbp_chr22_50605362 ACTCTGTCTCCCTGTCTCCCCCGCCTCTGTCCTGCCGGGTCTCCCAGGCACCGAGTCCTTTGGCCTTTTCTCCTGTCTGG
TCAACGG
mm4__chr11 15.65 Mbp_chr11_15650470 GCTGTGCTGTCATGGGGAGCCCTGGGGACCCTGGCACCCTCGTGAGGGCCCAGCCCGCCGACTCCTTAGCCAGAACTTGT
GCCCAGCGTGGGAATTTTCTTC
mm3__chr3 51.70 Mbp_chr3_51698900 TGGTGTTTAGCTGGCCTTGATCCTTGTTCAGGGTCTATAGTAGCATGTCTGCAAGAGCAGGGGCTGGAGGCCTAAGGACT
GGGGGTGCTGGTCTTCTGATATCTGTGGGTCAGTCAGCGTTGTCCAGGGTGGAGAGGAG
mm4__chr22 20.44 Mbp_chr22_20438128 AGACATCTACCGAAGCAGCCGCCCCTGCGCGCCCACTGCGTAGGCCAGGCCCGGGACGGGAAGGCGGATCGGGGACACGG
ACGCGACTCCGCAAGCCCACCCCCGCTCCCAGCGCCTCGGAACCGGCCAAGGGAGTG

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.