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PCR primers for off-targets of TCCCCAATCTGGGCGCGCGC 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_5529752_F Primer3: not found at this Tm N.d. 1.00
ontarget_mm0__chr7 5.53 Mbp_chr7_5529752_R Primer3: not found at this Tm N.d. 1.00
mm4__chr19 16.39 Mbp_chr19_16385973_F TCGTCGGCAGCGTCACTGCCAAAATTCCTTTCTGGA 58.4 0.29
mm4__chr19 16.39 Mbp_chr19_16385973_R GTCTCGTGGGCTCGGTGGCCTCTGTGTTTGTGTCA 59.7 0.29
mm4__chr17 60.39 Mbp_chr17_60392325_F TCGTCGGCAGCGTCCCAGACACTGTTCCCGGTAA 59.3 0.28
mm4__chr17 60.39 Mbp_chr17_60392325_R GTCTCGTGGGCTCGGGGAAGATGGGACGATGCGTT 60.4 0.28
mm4__chr22 50.46 Mbp_chr22_50457152_F TCGTCGGCAGCGTCCAGCAGAGAGAAGGCTCAGG 59.8 0.26
mm4__chr22 50.46 Mbp_chr22_50457152_R GTCTCGTGGGCTCGGCTTGGTGGAACCCTCTGACC 59.9 0.26
mm4__chr4 8.51 Mbp_chr4_8507274_F Primer3: not found at this Tm N.d. 0.24
mm4__chr4 8.51 Mbp_chr4_8507274_R Primer3: not found at this Tm N.d. 0.24
mm4__chr11 777.73 Kbp_chr11_777725_F TCGTCGGCAGCGTCCAATAGGTAGGGTCGCGAGG 59.6 0.22
mm4__chr11 777.73 Kbp_chr11_777725_R GTCTCGTGGGCTCGGCTGGCTCTGCTGATGCCC 60.5 0.22
mm4__chr22 30.29 Mbp_chr22_30289364_F TCGTCGGCAGCGTCGCGATCCTAATCCTCCGACC 59.7 0.22
mm4__chr22 30.29 Mbp_chr22_30289364_R GTCTCGTGGGCTCGGATCAAGCTGCTCTTCCTGCC 60.3 0.22
mm4__chr6 170.17 Mbp_chr6_170166980_F Primer3: not found at this Tm N.d. 0.19
mm4__chr6 170.17 Mbp_chr6_170166980_R Primer3: not found at this Tm N.d. 0.19
mm4__chr19 1.59 Mbp_chr19_1592773_F Primer3: not found at this Tm N.d. 0.17
mm4__chr19 1.59 Mbp_chr19_1592773_R Primer3: not found at this Tm N.d. 0.17
mm4__chr7 131.31 Mbp_chr7_131305085_F Primer3: not found at this Tm N.d. 0.17
mm4__chr7 131.31 Mbp_chr7_131305085_R Primer3: not found at this Tm N.d. 0.17
mm4__chr10 132.31 Mbp_chr10_132305867_F TCGTCGGCAGCGTCTGCCCTCCTGATTTCACCAC 59.9 0.16
mm4__chr10 132.31 Mbp_chr10_132305867_R GTCTCGTGGGCTCGGGGCTCCGTATGGCTTGGTAT 59.6 0.16
mm4__chr12 98.21 Mbp_chr12_98212281_F Primer3: not found at this Tm N.d. 0.15
mm4__chr12 98.21 Mbp_chr12_98212281_R Primer3: not found at this Tm N.d. 0.15
mm4__chr6 30.16 Mbp_chr6_30163804_F Primer3: not found at this Tm N.d. 0.15
mm4__chr6 30.16 Mbp_chr6_30163804_R Primer3: not found at this Tm N.d. 0.15
mm4__chr7 111.90 Mbp_chr7_111900125_F TCGTCGGCAGCGTCAAAGGCTTTCCCAGTGGCTT 60.1 0.15
mm4__chr7 111.90 Mbp_chr7_111900125_R GTCTCGTGGGCTCGGCTGGTGGTCTTAGGCAACCC 60.3 0.15
mm4__chr5 93.62 Mbp_chr5_93621577_F Primer3: not found at this Tm N.d. 0.14
mm4__chr5 93.62 Mbp_chr5_93621577_R Primer3: not found at this Tm N.d. 0.14
mm4__chr1 44.81 Mbp_chr1_44813242_F TCGTCGGCAGCGTCGACGAGGCTGAACTGGTCC 60.0 0.12
mm4__chr1 44.81 Mbp_chr1_44813242_R GTCTCGTGGGCTCGGCCTCCTTCCGTGCCCTTG 60.0 0.12
mm4__chr1 201.40 Mbp_chr1_201399008_F Primer3: not found at this Tm N.d. 0.12
mm4__chr1 201.40 Mbp_chr1_201399008_R Primer3: not found at this Tm N.d. 0.12
mm4__chr4 4.73 Mbp_chr4_4729392_F Primer3: not found at this Tm N.d. 0.10
mm4__chr4 4.73 Mbp_chr4_4729392_R Primer3: not found at this Tm N.d. 0.10
mm4__chr5 173.44 Mbp_chr5_173435432_F TCGTCGGCAGCGTCGGCTTGCTGAAATGCTTCTCA 59.4 0.09
mm4__chr5 173.44 Mbp_chr5_173435432_R GTCTCGTGGGCTCGGGCCAAAGCAACTGCATCTCC 60.1 0.09
mm4__chr9 136.20 Mbp_chr9_136198392_F TCGTCGGCAGCGTCCTAGGAGCCAGAGAGACGGC 61.4 0.07
mm4__chr9 136.20 Mbp_chr9_136198392_R GTCTCGTGGGCTCGGACTCCGGACCACTGCTTTTC 60.2 0.07
mm4__chr22 41.29 Mbp_chr22_41286311_F TCGTCGGCAGCGTCTCTCGGGTAGAGTAGTCCGG 59.5 0.07
mm4__chr22 41.29 Mbp_chr22_41286311_R GTCTCGTGGGCTCGGAAAGAGCCAGAAGCCACCAG 60.2 0.07
mm4__chr3 52.77 Mbp_chr3_52770750_F TCGTCGGCAGCGTCCACCTCTCCATAGCTCCCCT 60.1 0.07
mm4__chr3 52.77 Mbp_chr3_52770750_R GTCTCGTGGGCTCGGGAACCGAGCTTCTTGTTGCC 59.7 0.07
mm4__chr10 109.36 Mbp_chr10_109362967_F Primer3: not found at this Tm N.d. 0.06
mm4__chr10 109.36 Mbp_chr10_109362967_R Primer3: not found at this Tm N.d. 0.06
mm4__chr19 13.99 Mbp_chr19_13986620_F TCGTCGGCAGCGTCAGCGTCTGCATCTATCTGCC 59.9 0.06
mm4__chr19 13.99 Mbp_chr19_13986620_R GTCTCGTGGGCTCGGCGTTTCCTGAGACAGTGGGG 60.3 0.06
mm4__chr14 69.48 Mbp_chr14_69484563_F TCGTCGGCAGCGTCCCTTCTGGACGCACGGAG 60.1 0.06
mm4__chr14 69.48 Mbp_chr14_69484563_R GTCTCGTGGGCTCGGAATTCTGGTGGCCCCGATTG 60.6 0.06
mm4__chr22 45.98 Mbp_chr22_45977713_F TCGTCGGCAGCGTCGAGATTCCCACAACCCCAGG 60.0 0.06
mm4__chr22 45.98 Mbp_chr22_45977713_R GTCTCGTGGGCTCGGCAATGGGTTCTGCAGGAGGT 59.9 0.06
mm4__chr11 60.92 Mbp_chr11_60924365_F Primer3: not found at this Tm N.d. 0.05
mm4__chr11 60.92 Mbp_chr11_60924365_R Primer3: not found at this Tm N.d. 0.05
mm4__chr16 56.56 Mbp_chr16_56563811_F Primer3: not found at this Tm N.d. 0.05
mm4__chr16 56.56 Mbp_chr16_56563811_R Primer3: not found at this Tm N.d. 0.05
mm4__chr2 212.54 Mbp_chr2_212538607_F Primer3: not found at this Tm N.d. 0.05
mm4__chr2 212.54 Mbp_chr2_212538607_R Primer3: not found at this Tm N.d. 0.05
mm4__chr8 1.84 Mbp_chr8_1838433_F TCGTCGGCAGCGTCGTCTTCTCCTTCCCACAGCC 60.0 0.05
mm4__chr8 1.84 Mbp_chr8_1838433_R GTCTCGTGGGCTCGGAGTGCAGAGAAAGGGATGGC 60.0 0.05
mm4__chr16 51.88 Mbp_chr16_51878323_F TCGTCGGCAGCGTCGTCTCCTAAGAAATGGCCTGGA 59.4 0.04
mm4__chr16 51.88 Mbp_chr16_51878323_R GTCTCGTGGGCTCGGTGTCATAGCAGGCAAGGTGC 60.6 0.04
mm4__chr16 57.01 Mbp_chr16_57014788_F Primer3: not found at this Tm N.d. 0.03
mm4__chr16 57.01 Mbp_chr16_57014788_R Primer3: not found at this Tm N.d. 0.03
mm4__chr10 97.71 Mbp_chr10_97714135_F TCGTCGGCAGCGTCCCTCTACTTCCTCACGCTGC 60.1 0.03
mm4__chr10 97.71 Mbp_chr10_97714135_R GTCTCGTGGGCTCGGATCTGGTCGCTCATGATGCC 60.2 0.03
mm4__chr16 87.93 Mbp_chr16_87933050_F TCGTCGGCAGCGTCTGCGAAGGGAGGATGAGAGA 60.0 0.03
mm4__chr16 87.93 Mbp_chr16_87933050_R GTCTCGTGGGCTCGGGCTCAGGTGTGTGTGAGTCT 59.6 0.03
mm4__chr3 14.37 Mbp_chr3_14374801_F TCGTCGGCAGCGTCTGCCCAACTATGTCCACAGC 60.3 0.03
mm4__chr3 14.37 Mbp_chr3_14374801_R GTCTCGTGGGCTCGGACAAAGCCACTGGTGAGCAT 60.1 0.03
mm4__chr22 27.18 Mbp_chr22_27179498_F TCGTCGGCAGCGTCCCATCACACCTTGCTTTGCA 59.3 0.02
mm4__chr22 27.18 Mbp_chr22_27179498_R GTCTCGTGGGCTCGGCACTTGTTAGCAAAGCAGCCA 59.6 0.02
mm4__chr6 15.50 Mbp_chr6_15497065_F TCGTCGGCAGCGTCCGAGTGCAAGCTCAACGATG 59.9 0.02
mm4__chr6 15.50 Mbp_chr6_15497065_R GTCTCGTGGGCTCGGGCCCTGAGATTTGAGGTGCT 60.0 0.02
mm4__chr17 11.33 Mbp_chr17_11331070_F TCGTCGGCAGCGTCCTGGCTGCATTCCTTGAGGT 60.3 0.02
mm4__chr17 11.33 Mbp_chr17_11331070_R GTCTCGTGGGCTCGGCACCCTGGGAGAGTTACTGC 59.7 0.02
mm4__chr21 46.43 Mbp_chr21_46427628_F TCGTCGGCAGCGTCACGCCACGTTTCTTCCTTCT 59.8 0.01
mm4__chr21 46.43 Mbp_chr21_46427628_R GTCTCGTGGGCTCGGCAAAGGCCTCTTGCACAACC 59.9 0.01
mm4__chr4 110.63 Mbp_chr4_110630892_F TCGTCGGCAGCGTCGGGGAAGGAGACATTTTGCG 59.1 0.01
mm4__chr4 110.63 Mbp_chr4_110630892_R GTCTCGTGGGCTCGGCTCCGGCCAGACTAGAGGAG 60.8 0.01
mm4__chr21 33.08 Mbp_chr21_33081228_F TCGTCGGCAGCGTCAATGTCTGAAGCCTGGGGTG 59.9 0.01
mm4__chr21 33.08 Mbp_chr21_33081228_R GTCTCGTGGGCTCGGGAAGACCTAGGCCTGGTCGA 60.6 0.01
mm4__chr19 33.11 Mbp_chr19_33110036_F TCGTCGGCAGCGTCCAGGGTCAGAAAGGTGGGTG 60.2 0.00
mm4__chr19 33.11 Mbp_chr19_33110036_R GTCTCGTGGGCTCGGTGGGTCTAGGATGAGAACAGTG 58.9 0.00
mm4__chr16 871.16 Kbp_chr16_871157_F TCGTCGGCAGCGTCCACCACCCGACTTTCTCCTG 60.3 0.00
mm4__chr16 871.16 Kbp_chr16_871157_R GTCTCGTGGGCTCGGGATGCAGAGGGACATCCGAG 59.9 0.00
mm4__chr1 157.14 Mbp_chr1_157138909_F TCGTCGGCAGCGTCCGGGAAACAGTCTCTCCCAC 60.0 0.00
mm4__chr1 157.14 Mbp_chr1_157138909_R GTCTCGTGGGCTCGGGTCCCGTCTTCCCATTGTGA 59.6 0.00
mm4__chr1 64.32 Mbp_chr1_64320655_F Primer3: not found at this Tm N.d. 0.00
mm4__chr1 64.32 Mbp_chr1_64320655_R Primer3: not found at this Tm N.d. 0.00
mm4__chr10 98.13 Mbp_chr10_98132072_F TCGTCGGCAGCGTCAGCTCCTGACAGGCTTTGTT 59.5 0.00
mm4__chr10 98.13 Mbp_chr10_98132072_R GTCTCGTGGGCTCGGTGGTCCCTTTCCCCTTCTCT 59.8 0.00
mm4__chr20 62.48 Mbp_chr20_62480321_F TCGTCGGCAGCGTCTAGCAGTGCCCACATAACCC 59.7 0.00
mm4__chr20 62.48 Mbp_chr20_62480321_R GTCTCGTGGGCTCGGCTCCTGGGAGCTGGTCCTTA 60.3 0.00
mm4__chr20 62.36 Mbp_chr20_62361772_F TCGTCGGCAGCGTCGCCCATTTTACAGGCCAGGA 60.3 0.00
mm4__chr20 62.36 Mbp_chr20_62361772_R GTCTCGTGGGCTCGGGCCTCCAAGCGAAGAGTGAA 60.3 0.00
mm4__chr10 13.66 Mbp_chr10_13657164_F Primer3: not found at this Tm N.d. 0.00
mm4__chr10 13.66 Mbp_chr10_13657164_R Primer3: not found at this Tm N.d. 0.00

Off-target amplicon sequences

Primers underlined, off-targets in bold.

mm4__chr19 16.39 Mbp_chr19_16385973 ACTGCCAAAATTCCTTTCTGGAAAGATGCCAGCGCGTGCCCAGGAAGGGGAGCAGCAGCGGGTGCTTGTTTTGGCCTAAT
GGGCTCAGGCCAGGATCTGGGTGCCACTGACTGATGACACAAACACAGAGGCCA
mm4__chr17 60.39 Mbp_chr17_60392325 CCAGACACTGTTCCCGGTAACGGCCGCCCAGGGCCGCACGCTCCGCCCCTCCCCAAGCTAACCGCGCGCAGGAGCGCCGG
GGAGGGGGACGCATCTCCGCACGTAACGCATCGTCCCATCTTCC
mm4__chr22 50.46 Mbp_chr22_50457152 CAGCAGAGAGAAGGCTCAGGCCTAGCCCCAGGCCTGGGCGTGCCCAGCTTGGGGGTGCCTACAGGTCAGAGGGTTCCACC
AAG
mm4__chr11 777.73 Kbp_chr11_777725 CAATAGGTAGGGTCGCGAGGGTCCTCCCCGGCCGCATGCGCAGTCTGAGCGCGCGCGGGGTAGGGCTCTTGGCCTGGGGT
GGGGGCGCGGGCATCAGCAGAGCCAG
mm4__chr22 30.29 Mbp_chr22_30289364 GCGATCCTAATCCTCCGACCCTGGCCCGGAGCGAGAGCAGAGCCCCCAGCCCCTATCTGCGCTCCCGAACCCGGGCGCGC
ACCGGCTGCGGCGGGGCAGGAAGAGCAGCTTGAT
mm4__chr10 132.31 Mbp_chr10_132305867 TGCCCTCCTGATTTCACCACACAAAGCCCAGCTGAGTCCCGGCGGGTGCTCAGTTTGGGGATGTGGCTGCATACCAAGCC
ATACGGAGCC
mm4__chr7 111.90 Mbp_chr7_111900125 AAAGGCTTTCCCAGTGGCTTCACATGCCATGAAAAGTCCTAGTGGGTTTCCCCAATCTGTGTGAGAGCTGGATCAGCTCC
TGGAGATACCAGAATGGTTAGGGTTGCCTAAGACCACCAG
mm4__chr1 44.81 Mbp_chr1_44813242 GACGAGGCTGAACTGGTCCGCGCGGCCCGAAGCTGGGCGCGCGTGGGCGCGGTGAGTGGGGCTGGGGGAGCGCAAGGGCA
CGGAAGGAGG
mm4__chr5 173.44 Mbp_chr5_173435432 GGCTTGCTGAAATGCTTCTCATTTTCCTGCTCGGGCCCAGACTGGGAAGTCCAGCCAAGCCCAGCGCTGTATCTCCCCCA
CTGCTTCATTTCTTTCCAATCAGACTCTTTTGTTTCCTGGAGATGCAGTTGCTTTGGC
mm4__chr9 136.20 Mbp_chr9_136198392 CTAGGAGCCAGAGAGACGGCCTGGACACGCCCACCCCCCCATGAGAAAGCCCGTAGGCGCCCAGCTTGGGGACAGGTCGG
GCCACAGGGATTGTGTCCCCACCAGGGGAAAAGCAGTGGTCCGGAGT
mm4__chr22 41.29 Mbp_chr22_41286311 TCTCGGGTAGAGTAGTCCGGTTCCCCATCTGGGAGCGCGATGGGGCGCGCACCGCGAACTACCCGTCCCATGGCGCACCG
CGCGCAGAGCGTCCTCCACCGCCCTCCTCTTCGCCCTCCCCTGGTGGCTTCTGGCTCTTT
mm4__chr3 52.77 Mbp_chr3_52770750 CACCTCTCCATAGCTCCCCTTGCCCACGACCCGCAGGTAGCAGTAGGCGGCCAGGGGCATGTTCCCAGCGCTGGCCCAGA
GTCGGGATGCGGCGGCAGCGGCGGGTAGGGCAGCGGGCGGCAACAAGAAGCTCGGTTC
mm4__chr19 13.99 Mbp_chr19_13986620 AGCGTCTGCATCTATCTGCCGGAGATCGCCACTCTGGGCATGCGCAGGAGGCCAGGGAGGCCCCCACTGTCTCAGGAAAC
G
mm4__chr14 69.48 Mbp_chr14_69484563 CCTTCTGGACGCACGGAGCCCGGCCCTCCAGCCGGCGCCCGCCCTGATTGGCGCCCGAGGCCGGCCTCCCGCCGGCTCAC
CTGCCACTCCCAGCCAATCGGGGCCACCAGAATT
mm4__chr22 45.98 Mbp_chr22_45977713 GAGATTCCCACAACCCCAGGTCCCAGCACTGCTGCCACCTGCGCTAGCCCAGCTTTGGGACCTGAAAGATGACAGACGGG
CTAACCTGGCCACATGCAGGGAGATGGCATGCGTGACCTCCTGCAGAACCCATTG
mm4__chr8 1.84 Mbp_chr8_1838433 GTCTTCTCCTTCCCACAGCCACCCGGCACCCGCCCAGCCTGGGGAGAAGCCATCCCTTTCTCTGCACT
mm4__chr16 51.88 Mbp_chr16_51878323 GTCTCCTAAGAAATGGCCTGGACCCAGAGCCTGCCCAGAGTGGGGACATTCCTCCTGTTTGTTGAGTTGAGTTGGACACC
ATCATGCTACTCTGGCAAGACCATGCACCTTGCCTGCTATGACA
mm4__chr10 97.71 Mbp_chr10_97714135 CCTCTACTTCCTCACGCTGCTGGGCAAGCACGAGCTGGTCCCCGTGCTGGGCTCGCGCTGGCTCATGGTCAACGTGGCGC
ACGATGTGCTGGCGGCCGCGCTCTACGGCGCCGCCACCGGCATCATGAGCGACCAGAT
mm4__chr16 87.93 Mbp_chr16_87933050 TGCGAAGGGAGGATGAGAGATGCAGTGAGCAGGCCTGCACCCACCCAGAGTGGGGAGCCCAGCCCAACCACGGTCAGCCC
GGGGGGAGCCAAATGCAAGAAGACTCACACACACCTGAGC
mm4__chr3 14.37 Mbp_chr3_14374801 TGCCCAACTATGTCCACAGCCACCTACCAGGGCCCGCCCACCTTGGGGACAGGGCCGGCAGCCGGCAGCTTCAGGCTCCA
AGATGCTCACCAGTGGCTTTGT
mm4__chr22 27.18 Mbp_chr22_27179498 CCATCACACCTTGCTTTGCAATGGAGTTTGTTAGGGCCATCCTTCCTGTGCAGGCCCAGAGTGGGGATATAAGCATGGCT
GCTTTGCTAACAAGTG
mm4__chr6 15.50 Mbp_chr6_15497065 CGAGTGCAAGCTCAACGATGAGATGCGGTTTGTCACGCAGATTCAGCACATCCACAAGCTGGGCCGGCGCTGGGGCCCCA
ACGTGCAGCGGCTGGCCTGCATCAAGAAGCACCTCAAATCTCAGGGC
mm4__chr17 11.33 Mbp_chr17_11331070 CTGGCTGCATTCCTTGAGGTGAGAGTCAGATTCCCCCATCTGGGAGCCTGCAGGAGAAACATCTGCGCAGTAACTCTCCC
AGGGTG
mm4__chr21 46.43 Mbp_chr21_46427628 ACGCCACGTTTCTTCCTTCTTCCTTTAGGAAGTGCCCACCGCGTGCCCCGATTGGAGAGGGGACCTTCTGCAGGTTGTGC
AAGAGGCCTTTG
mm4__chr4 110.63 Mbp_chr4_110630892 GGGGAAGGAGACATTTTGCGTCTCTCTGGCTCCCAGCACAATAAGAAATGTCAGCCTCGGCTTGGCGACTGCGAGCCCGC
CCCGCGCGAAGCGAGATTGGGGAGCTCCTCTAGTCTGGCCGGAG
mm4__chr21 33.08 Mbp_chr21_33081228 AATGTCTGAAGCCTGGGGTGTGAGCTAACATCAGCTTTTCCCCCATCTGGGCGAGGGTGGGCAGGTGTGTGTGGGGTGGG
GGCAAGCACCCCCCTCGACCAGGCCTAGGTCTTC
mm4__chr19 33.11 Mbp_chr19_33110036 CAGGGTCAGAAAGGTGGGTGCTGGGCCTGGGTGTCCCAAATCTCGGCCCGGGCGGGGTCATATTCTCACTGTTCTCATCC
TAGACCCA
mm4__chr16 871.16 Kbp_chr16_871157 CACCACCCGACTTTCTCCTGCCCTTGGGCAGGGGCCCCCAGCTGAGCCACCTACCGAATCTGGGCTCGGGCCGGGCCCCT
CGGATGTCCCTCTGCATC
mm4__chr1 157.14 Mbp_chr1_157138909 CGGGAAACAGTCTCTCCCACACAACAGAGAGGCGGCCCGTCTTTCTCCAGAAATGGGCCCTGCGACCTCCCAGAGTGGGG
ATCCCTCACAATGGGAAGACGGGAC
mm4__chr10 98.13 Mbp_chr10_98132072 AGCTCCTGACAGGCTTTGTTTGATAGGGTAAGGAACATAAACTGATTCCCAATCTGGGCTGGGGCAGGTGGGAGAGAAGG
GGAAAGGGACCA
mm4__chr20 62.48 Mbp_chr20_62480321 TAGCAGTGCCCACATAACCCCCATCCTGCCCGCCCCCAGCTTGGGAACCCTTAACTCAGACATACTTATCAAGGGAAAGA
AAACAGTCTCATTGTTCAGGAGGATAAGGACCAGCTCCCAGGAG
mm4__chr20 62.36 Mbp_chr20_62361772 GCCCATTTTACAGGCCAGGACCTCAAGGCTGGGTACCCGGGCCAAGTCGCCCCCAATCTGGGGGTGCTCAGGGCTGGCAG
CCAGGCAGGCCCACCTTGGGGGTTTCACTCTTCGCTTGGAGGC

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.