← return to the list of all guides

Contents:

PCR primers for off-targets of TCGCGGGCGACGATGCCCCC 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_5529573_F TCGTCGGCAGCGTCCACGATGGAGGGGAAGACG 59.8 1.00
ontarget_mm0__chr7 5.53 Mbp_chr7_5529573_R GTCTCGTGGGCTCGGGCTATTCTCGCAGCTCACCA 60.1 1.00
mm1__chr2 131.26 Mbp_chr2_131263616_F TCGTCGGCAGCGTCGTGCTCGTCATTGACAACGG 59.8 0.90
mm1__chr2 131.26 Mbp_chr2_131263616_R GTCTCGTGGGCTCGGCCCACGATGGAAGGGAAGAC 60.1 0.90
mm1__chr2 130.66 Mbp_chr2_130656810_F TCGTCGGCAGCGTCGTGCTCGTCATTGACAACGG 59.8 0.90
mm1__chr2 130.66 Mbp_chr2_130656810_R GTCTCGTGGGCTCGGCCCACGATGGAAGGGAAGAC 60.1 0.90
mm1__chr2 130.46 Mbp_chr2_130463859_F TCGTCGGCAGCGTCCCCACGATGGAAGGGAAGAC 60.1 0.90
mm1__chr2 130.46 Mbp_chr2_130463859_R GTCTCGTGGGCTCGGGTGCTCGTCATTGACAACGG 59.8 0.90
mm1__chr2 130.08 Mbp_chr2_130075287_F TCGTCGGCAGCGTCCCCACGATGGAAGGGAAGAC 60.1 0.90
mm1__chr2 130.08 Mbp_chr2_130075287_R GTCTCGTGGGCTCGGGTGCTCGTCATTGACAACGG 59.8 0.90
mm3__chr9 6.83 Mbp_chr9_6834516_F TCGTCGGCAGCGTCCCGCTACCAGCTCACCATAG 59.9 0.75
mm3__chr9 6.83 Mbp_chr9_6834516_R GTCTCGTGGGCTCGGACACGATGAAGGGGAAGACG 59.7 0.75
mm2__chr19 9.52 Mbp_chr19_9518210_F TCGTCGGCAGCGTCAGTTAACAATGGCTCCGGCA 59.9 0.74
mm2__chr19 9.52 Mbp_chr19_9518210_R GTCTCGTGGGCTCGGCACGATGGAGGGGAAGATGG 59.8 0.74
mm3__chr22 15.72 Mbp_chr22_15721547_F TCGTCGGCAGCGTCGTGCTCGTCATTGACAACGG 59.8 0.68
mm3__chr22 15.72 Mbp_chr22_15721547_R GTCTCGTGGGCTCGGATCATGTTCTGGTGCCTGGG 60.0 0.68
mm3__chr14 19.40 Mbp_chr14_19402824_F TCGTCGGCAGCGTCATCATGTTCTGGTGCCTGGG 60.0 0.68
mm3__chr14 19.40 Mbp_chr14_19402824_R GTCTCGTGGGCTCGGGTGCTCGTCATTGACAACGG 59.8 0.68
mm3__chr14 19.00 Mbp_chr14_18998928_F TCGTCGGCAGCGTCGTGCTCGTCATTGACAACGG 59.8 0.68
mm3__chr14 19.00 Mbp_chr14_18998928_R GTCTCGTGGGCTCGGATCATGTTCTGGTGCCTGGG 60.0 0.68
mm3__chr11 1.80 Mbp_chr11_1804011_F TCGTCGGCAGCGTCCGCCACCCACATAGAAGTCC 60.4 0.58
mm3__chr11 1.80 Mbp_chr11_1804011_R GTCTCGTGGGCTCGGAACACCTCTGGCATGTGCAA 60.4 0.58
mm2__chr3 175.98 Mbp_chr3_175978495_F TCGTCGGCAGCGTCGAGTCCTTCTGACCCATGCC 60.1 0.55
mm2__chr3 175.98 Mbp_chr3_175978495_R GTCTCGTGGGCTCGGGCAAAGGCTCCTGTATGTGC 59.5 0.55
mm4__chr5 98.34 Mbp_chr5_98338804_F TCGTCGGCAGCGTCGCTCCTCATCAACAAGGGCT 60.0 0.53
mm4__chr5 98.34 Mbp_chr5_98338804_R GTCTCGTGGGCTCGGTTTTGACCCATGCCCACCAT 60.1 0.53
mm2__chr5 131.66 Mbp_chr5_131660031_F TCGTCGGCAGCGTCATGCCCATCATCACACCCTG 60.1 0.48
mm2__chr5 131.66 Mbp_chr5_131660031_R GTCTCGTGGGCTCGGTCTGGCATGTGGAAGGTCTG 59.6 0.48
mm3__chr1 1.78 Mbp_chr1_1778219_F TCGTCGGCAGCGTCCTCCTCAGCAGGCCAGATG 59.8 0.35
mm3__chr1 1.78 Mbp_chr1_1778219_R GTCTCGTGGGCTCGGGAACGGTGAGTGAGCAGACC 60.6 0.35
mm4__chrX 71.76 Mbp_chrX_71763048_F Primer3: not found at this Tm N.d. 0.29
mm4__chrX 71.76 Mbp_chrX_71763048_R Primer3: not found at this Tm N.d. 0.29
mm4__chrX 71.72 Mbp_chrX_71718503_F TCGTCGGCAGCGTCTAACCAATCGGGACACAGGC 60.0 0.29
mm4__chrX 71.72 Mbp_chrX_71718503_R GTCTCGTGGGCTCGGCCAGAGGCAGAAGGACAGGA 60.9 0.29
mm4__chr4 1.37 Mbp_chr4_1365979_F Primer3: not found at this Tm N.d. 0.29
mm4__chr4 1.37 Mbp_chr4_1365979_R Primer3: not found at this Tm N.d. 0.29
mm4__chr6 131.63 Mbp_chr6_131628375_F TCGTCGGCAGCGTCGTTCCGTCTGTGGAGAAGGG 60.0 0.28
mm4__chr6 131.63 Mbp_chr6_131628375_R GTCTCGTGGGCTCGGAAGCAACTCCTTCTCCAGCC 59.9 0.28
mm2__chr22 41.08 Mbp_chr22_41075155_F TCGTCGGCAGCGTCGGAGTCCTTCTGACCCATGC 60.1 0.26
mm2__chr22 41.08 Mbp_chr22_41075155_R GTCTCGTGGGCTCGGTGTTGACAACAGCTCTGGCA 60.1 0.26
mm1__chr2 131.63 Mbp_chr2_131626199_F TCGTCGGCAGCGTCGTGCTCGTCATTGACAACGG 59.8 0.23
mm1__chr2 131.63 Mbp_chr2_131626199_R GTCTCGTGGGCTCGGACTCCTTCTGATGCATGCCC 60.1 0.23
mm3__chr2 73.90 Mbp_chr2_73901375_F TCGTCGGCAGCGTCGTGTGAAGAGGAGACCACCG 60.0 0.17
mm3__chr2 73.90 Mbp_chr2_73901375_R GTCTCGTGGGCTCGGCCCACAATGGAGGGGAAGAC 60.0 0.17
mm4__chr12 132.33 Mbp_chr12_132325942_F TCGTCGGCAGCGTCTCCTCTCCCAGCAGAGTGAG 60.3 0.16
mm4__chr12 132.33 Mbp_chr12_132325942_R GTCTCGTGGGCTCGGCCAGGCTGTTTGTTGCTGTG 60.2 0.16
mm4__chr11 67.27 Mbp_chr11_67266337_F Primer3: not found at this Tm N.d. 0.12
mm4__chr11 67.27 Mbp_chr11_67266337_R Primer3: not found at this Tm N.d. 0.12
mm4__chr17 6.54 Mbp_chr17_6538050_F Primer3: not found at this Tm N.d. 0.11
mm4__chr17 6.54 Mbp_chr17_6538050_R Primer3: not found at this Tm N.d. 0.11
mm4__chr5 57.48 Mbp_chr5_57482620_F TCGTCGGCAGCGTCATCTCCCACGTAGCAGTCCT 60.0 0.11
mm4__chr5 57.48 Mbp_chr5_57482620_R GTCTCGTGGGCTCGGATGGGTCAGGGATGTGCAAG 60.0 0.11
mm3__chr5 77.78 Mbp_chr5_77784947_F TCGTCGGCAGCGTCATATCACCGCGCTCGTCATT 59.9 0.09
mm3__chr5 77.78 Mbp_chr5_77784947_R GTCTCGTGGGCTCGGAACGATGGAGGGGAAGACTG 59.0 0.09
mm4__chr9 112.49 Mbp_chr9_112486447_F TCGTCGGCAGCGTCAGGTTCTGTCTGCTCCTTGC 59.9 0.08
mm4__chr9 112.49 Mbp_chr9_112486447_R GTCTCGTGGGCTCGGTCCCTACTACACGTCCTGGG 60.0 0.08
mm4__chr19 19.37 Mbp_chr19_19367028_F TCGTCGGCAGCGTCCCCACTCTGTCTTCATCTGCA 59.7 0.08
mm4__chr19 19.37 Mbp_chr19_19367028_R GTCTCGTGGGCTCGGTCCTACCTGGTGGGGACATT 59.8 0.08
mm4__chr10 88.95 Mbp_chr10_88948840_F Primer3: not found at this Tm N.d. 0.08
mm4__chr10 88.95 Mbp_chr10_88948840_R Primer3: not found at this Tm N.d. 0.08
mm3__chr10 43.27 Mbp_chr10_43268022_F TCGTCGGCAGCGTCCAGAGTGACTCTTGCAGGCA 59.9 0.07
mm3__chr10 43.27 Mbp_chr10_43268022_R GTCTCGTGGGCTCGGCTCAGCCTCTTCAAGGGGTG 60.0 0.07
mm4__chr14 93.12 Mbp_chr14_93115938_F Primer3: not found at this Tm N.d. 0.07
mm4__chr14 93.12 Mbp_chr14_93115938_R Primer3: not found at this Tm N.d. 0.07
mm3__chr9 87.65 Mbp_chr9_87650718_F Primer3: not found at this Tm N.d. 0.05
mm3__chr9 87.65 Mbp_chr9_87650718_R Primer3: not found at this Tm N.d. 0.05
mm4__chr12 130.16 Mbp_chr12_130162289_F Primer3: not found at this Tm N.d. 0.05
mm4__chr12 130.16 Mbp_chr12_130162289_R Primer3: not found at this Tm N.d. 0.05
mm3__chrX 46.29 Mbp_chrX_46289044_F Primer3: not found at this Tm N.d. 0.04
mm3__chrX 46.29 Mbp_chrX_46289044_R Primer3: not found at this Tm N.d. 0.04
mm4__chr11 44.86 Mbp_chr11_44861661_F Primer3: not found at this Tm N.d. 0.04
mm4__chr11 44.86 Mbp_chr11_44861661_R Primer3: not found at this Tm N.d. 0.04
mm4__chr11 2.42 Mbp_chr11_2419811_F TCGTCGGCAGCGTCAGCTTTTGAACGTGCGACTG 59.6 0.04
mm4__chr11 2.42 Mbp_chr11_2419811_R GTCTCGTGGGCTCGGTCCGGGACTCTAAGAGGCAA 59.9 0.04
mm4__chr2 112.18 Mbp_chr2_112181743_F TCGTCGGCAGCGTCCACTGAGCGTGTCTTCTCCC 60.3 0.04
mm4__chr2 112.18 Mbp_chr2_112181743_R GTCTCGTGGGCTCGGCAGGTGGAATCCGGCCTC 59.8 0.04
mm4__chr11 9.07 Mbp_chr11_9069416_F TCGTCGGCAGCGTCTCTTGGCCAGCTCAAAACCA 60.1 0.04
mm4__chr11 9.07 Mbp_chr11_9069416_R GTCTCGTGGGCTCGGAGTCACATCTGCAAGGAGGC 60.0 0.04
mm4__chrY 6.84 Mbp_chrY_6836919_F TCGTCGGCAGCGTCTCCACTGGGGAGGTCTTGTA 59.5 0.03
mm4__chrY 6.84 Mbp_chrY_6836919_R GTCTCGTGGGCTCGGTCATGAGTCAGGCAGCACAG 60.0 0.03
mm4__chr16 2.47 Mbp_chr16_2473991_F TCGTCGGCAGCGTCCGCCGCTACCTCCTGCTG 62.8 0.02
mm4__chr16 2.47 Mbp_chr16_2473991_R GTCTCGTGGGCTCGGTCCAGGGTAGCACGAGGC 61.0 0.02
mm4__chr13 113.93 Mbp_chr13_113927306_F TCGTCGGCAGCGTCTAGGGGCTAAGGGTATGGGG 59.8 0.02
mm4__chr13 113.93 Mbp_chr13_113927306_R GTCTCGTGGGCTCGGAGCTGCAGCAAGTGGAACTT 60.4 0.02
mm4__chr5 6.57 Mbp_chr5_6573348_F Primer3: not found at this Tm N.d. 0.01
mm4__chr5 6.57 Mbp_chr5_6573348_R Primer3: not found at this Tm N.d. 0.01
mm4__chr7 100.16 Mbp_chr7_100158203_F TCGTCGGCAGCGTCCCCCAGGATCCCCTCCCC 62.9 0.01
mm4__chr7 100.16 Mbp_chr7_100158203_R GTCTCGTGGGCTCGGGGAGCCTGGGCAGAACTG 60.0 0.01
mm4__chr2 8.69 Mbp_chr2_8685808_F TCGTCGGCAGCGTCGGCCCTTTCGAGCCCCTG 62.8 0.01
mm4__chr2 8.69 Mbp_chr2_8685808_R GTCTCGTGGGCTCGGGGGAAGTCGCCTCCGAGA 60.7 0.01
mm3__chr10 69.02 Mbp_chr10_69022814_F Primer3: not found at this Tm N.d. 0.01
mm3__chr10 69.02 Mbp_chr10_69022814_R Primer3: not found at this Tm N.d. 0.01
mm4__chr7 152.76 Mbp_chr7_152759783_F Primer3: not found at this Tm N.d. 0.00
mm4__chr7 152.76 Mbp_chr7_152759783_R Primer3: not found at this Tm N.d. 0.00
mm4__chr13 99.90 Mbp_chr13_99896056_F Primer3: not found at this Tm N.d. 0.00
mm4__chr13 99.90 Mbp_chr13_99896056_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_5529573 CACGATGGAGGGGAAGACGGCCCGGGGGGCATCGTCGCCCGCGAAGCCGGCCTTGCACATGCCGGAGCCGTTGTCGACGA
CGAGCGCGGCGATATCATCATCCATGGTGAGCTGCGAGAATAGC
mm1__chr2 131.26 Mbp_chr2_131263616 GTGCTCGTCATTGACAACGGCTCTGGCATGTGCAAGGCCGGCTTTGCGGGCGACGATGCCCCCCGGGCTGTCTTCCCTTC
CATCGTGGG
mm1__chr2 130.66 Mbp_chr2_130656810 GTGCTCGTCATTGACAACGGCTCTGGCATGTGCAAGGCCGGCTTTGCGGGCGACGATGCCCCCCGGGCTGTCTTCCCTTC
CATCGTGGG
mm1__chr2 130.46 Mbp_chr2_130463859 CCCACGATGGAAGGGAAGACAGCCCGGGGGGCATCGTCGCCCGCAAAGCCGGCCTTGCACATGCCAGAGCCGTTGTCAAT
GACGAGCAC
mm1__chr2 130.08 Mbp_chr2_130075287 CCCACGATGGAAGGGAAGACAGCCCGGGGGGCATCGTCGCCCGCAAAGCCGGCCTTGCACATGCCAGAGCCGTTGTCAAT
GACGAGCAC
mm3__chr9 6.83 Mbp_chr9_6834516 CCGCTACCAGCTCACCATAGATGATGATATTGCTACGCCCGTCGTCGACAACGGCTCCGGCATGTGGAAGGCTGGCTTCG
CAGGTGACGATGACCCCCGGCCGTCTTCCCCTTCATCGTGT
mm2__chr19 9.52 Mbp_chr19_9518210 AGTTAACAATGGCTCCGGCATGTGCAAGGTCAACTTCGTGGGCGACAATGCCCCCCGGGCCATCTTCCCCTCCATCGTG
mm3__chr22 15.72 Mbp_chr22_15721547 GTGCTCGTCATTGACAACGGCTCTGGCATGTGCAAGGCCGGCTTTGCAGGTGACGATGCCCCCCGGGCTGTCTTCCCTTC
CATCGTGGGGTGCCCCAGGCACCAGAACATGAT
mm3__chr14 19.40 Mbp_chr14_19402824 ATCATGTTCTGGTGCCTGGGGCACCCCACGATGGAAGGGAAGACAGCCCGGGGGGCATCGTCACCTGCAAAGCCGGCCTT
GCACATGCCAGAGCCGTTGTCAATGACGAGCAC
mm3__chr14 19.00 Mbp_chr14_18998928 GTGCTCGTCATTGACAACGGCTCTGGCATGTGCAAGGCCGGCTTTGCAGGTGACGATGCCCCCCGGGCTGTCTTCCCTTC
CATCGTGGGGTGCCCCAGGCACCAGAACATGAT
mm3__chr11 1.80 Mbp_chr11_1804011 CGCCACCCACATAGAAGTCCTTCTGACCCATGCCCACCGTCATGCCCTGGTGTCTGGGGCACCCCACGATGGAGGGGAAG
ACGGCCCAGGGGGCATCGTCGTCGGTGAAGCTGGCCTTGCACATGCCAGAGGTGTT
mm2__chr3 175.98 Mbp_chr3_175978495 GAGTCCTTCTGACCCATGCCCACCATCACACCTTGGTGCCTGGGGCGCCCCACGATGGATGGGAAGACGGCCCCGGAGGC
ATCGTCGCCTGCGAAGCTGGTCTTGCACATACAGGAGCCTTTGC
mm4__chr5 98.34 Mbp_chr5_98338804 GCTCCTCATCAACAAGGGCTCTGGCATGTGCAAGGCCGGCTTCACAGGTGACAATGCCCCCGGGCCATCTTCCCCTCTGT
CATGGGTGCCAGGGAGTGATGGTGGGCATGGGTCAAAA
mm2__chr5 131.66 Mbp_chr5_131660031 ATGCCCATCATCACACCCTGGTGCCTCGGGTGCCCCATTATGGAGGGGAAGACGGCCCGGGGGCATCGTTGCCCGTGAAG
CAGACCTTCCACATGCCAGA
mm3__chr1 1.78 Mbp_chr1_1778219 CTCCTCAGCAGGCCAGATGGGCAGGGCCGGCCTGGTGTCTCCCCGCCTGGCCGCGCGCTCGCGGGCAGCGATGACCCCAG
GCAGCGGGCGACCCCAGGCGGACGGCAGGCCGGGTCTGCTCACTCACCGTTC
mm4__chrX 71.72 Mbp_chrX_71718503 TAACCAATCGGGACACAGGCTCTTGGTTTGCCTCCATGCCCGTCATTTGACTGGGTGGCTGCGCTCTGGTCGGGTCTTGG
GGCCAGGGGGCACCGTAGCTCTCGATCACCTCTTTCTTCCTGTCCTTCTGCCTCTGG
mm4__chr6 131.63 Mbp_chr6_131628375 GTTCCGTCTGTGGAGAAGGGCGGCCCGCAAGCCGGACGAGAGCGCCCCCAAACGGAACCTTGAGCCCAAGGACCCCGGAG
GCATCGTCGACCGCAGGCCGCCACCTCCCGGCTGGAGAAGGAGTTGCTT
mm2__chr22 41.08 Mbp_chr22_41075155 GGAGTCCTTCTGACCCATGCCCACCATCATGACCTGGTGCCTGGTGCACCCCACGATGGAAGGGAAGATGGCCCAGGGGA
CATCGTCACCCGCGAAGCCGGCCTTGCACATGCCAGAGCTGTTGTCAACA
mm1__chr2 131.63 Mbp_chr2_131626199 GTGCTCGTCATTGACAACGGCTCTGGCATGTGCAAGGCCGGCTTTGCGGGCGACGATGCCCCCCAGGCTGTCTTCCCTTC
TATCGTGGGGCGCCCCAGGCACCAGGGCATGATGGAGGGCATGCATCAGAAGGAGT
mm3__chr2 73.90 Mbp_chr2_73901375 GTGTGAAGAGGAGACCACCGCGCTCGTGTGTGACAATGGCTCTGGCCTGTGCAAGGCAGGCTTCGCAGGAGATGATGCCC
CCCGGGCTGTCTTCCCCTCCATTGTGGG
mm4__chr12 132.33 Mbp_chr12_132325942 TCCTCTCCCAGCAGAGTGAGTCCAGCCGCTGCGACGCGGGCGACCGTGCTCCCTGGCGGTGACCTTCACTCGCTCCACGC
CCACAGCAACAAACAGCCTGG
mm4__chr5 57.48 Mbp_chr5_57482620 ATCTCCCACGTAGCAGTCCTTCTGGCCCATGCCTACCATAACGCCCTGGTGTCGAGGACGCCCTATCATGGAGGGGAACA
CAGCCCGGGGGGCATCGTCACCACCAAAGCCTGCCTTGCACATCCCTGACCCAT
mm3__chr5 77.78 Mbp_chr5_77784947 ATATCACCGCGCTCGTCATTGACAACGGCTCCGGCATGTGCAAGGCCAGCTTCACGGGCGACAATGCCGCCCGGGCAGTC
TTCCCCTCCATCGTT
mm4__chr9 112.49 Mbp_chr9_112486447 AGGTTCTGTCTGCTCCTTGCGTTTCAGTGGAGGTGCACAGAGCTCCGGGGGGCATCGGGGACCGCGGGCCCAGGACGTGT
AGTAGGGA
mm4__chr19 19.37 Mbp_chr19_19367028 CCCACTCTGTCTTCATCTGCAAGTGTCCTCAGTTGCTACTGGCGGCCCCTGGCCTGCTCTGGCCTTGGCCACCAGGGGGC
ATGGTGGCCCAGGAGCAGCAAGGGCTGCCCAGGCAATGTCCCCACCAGGTAGGA
mm3__chr10 43.27 Mbp_chr10_43268022 CAGAGTGACTCTTGCAGGCAGTCAGACGAGGGCCAGTGAGAAACAGGTCTGGGGCGACGATGTCCCCAGGTGGAGGGGTC
TGTGTGAAAAAATGGGGAGGAGCCCCACAGCACCCCTTGAAGAGGCTGAG
mm4__chr11 2.42 Mbp_chr11_2419811 AGCTTTTGAACGTGCGACTGGCCAGAGGTGCCCATTTCTCGGGTGACGCTGCCCTCTGGCGGCAGCATACCTCACGCCTG
GCGGCGGGAAGTAGCCCTCTTTCAACTCACGATCTCATTTTGCCTCTTAGAGTCCCGGA
mm4__chr2 112.18 Mbp_chr2_112181743 CACTGAGCGTGTCTTCTCCCCGCAGCCGCCCCCGAGGGCAGCGTGGCCGGCGACTCCGCCTTCAGCCGCGCGCCGCGCTG
TGCGCAGGTGGAGCGGGCTCAGCACTGCAGCTGCGAGGCCGGATTCCACCTG
mm4__chr11 9.07 Mbp_chr11_9069416 TCTTGGCCAGCTCAAAACCAGGCCTGCACTCACAGGCGACGCTGCCCCTTGGGGCCTCCTTGCAGATGTGACT
mm4__chrY 6.84 Mbp_chrY_6836919 TCCACTGGGGAGGTCTTGTAATACAAAGCAAGAAGAAGACCTTCGCTGGAGCCCATGCCCCCTGGGATCCCATCAGAGCC
CTCTTTCCTGGTATTGGCCTGTGCTGCCTGACTCATGA
mm4__chr16 2.47 Mbp_chr16_2473991 CGCCGCTACCTCCTGCTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCATCGCCGC
CCGCGGAAGCCTCGTGCTACCCTGGA
mm4__chr13 113.93 Mbp_chr13_113927306 TAGGGGCTAAGGGTATGGGGACCTTCATATGTGGGACAGGCTCCTCGCTGGGGACGCTGCCACCAGGCCTGTGAGGCAGC
CAGCCAAGTTCCACTTGCTGCAGCT
mm4__chr7 100.16 Mbp_chr7_100158203 CCCCAGGATCCCCTCCCCCTGGGGGCTCCGAATCCTGGTCGCCGGCGCCGCCGCCCCCCGGCATCCCGCCTCCGGCGCTG
ACCGAGGCCAGGGCGGCCAGGGCGGTTGCCAGTTCTGCCCAGGCTCC
mm4__chr2 8.69 Mbp_chr2_8685808 GGCCCTTTCGAGCCCCTGCCGGGCACCGCTGGCGACGTTGGCCCCGGGACCCCTGGAGCCGCAGCCGAGGCGCAGCAGCC
CCTCTCGGAGGCGACTTCCC

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.