← return to the list of all guides

Contents:

PCR primers for off-targets of CCGAGTCCTTAGGCCGCCAG GGG

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__chr9 37.37 Mbp_chr9_37370772_F TCGTCGGCAGCGTCGAAACTGGGAAGGGAGTGGG 59.9 0.68
mm4__chr9 37.37 Mbp_chr9_37370772_R GTCTCGTGGGCTCGGCACGTGCTGGGGTCTTGG 60.6 0.68
mm4__chr1 240.00 Mbp_chr1_239997994_F Primer3: not found at this Tm N.d. 0.46
mm4__chr1 240.00 Mbp_chr1_239997994_R Primer3: not found at this Tm N.d. 0.46
mm4__chr10 73.94 Mbp_chr10_73942030_F Primer3: not found at this Tm N.d. 0.42
mm4__chr10 73.94 Mbp_chr10_73942030_R Primer3: not found at this Tm N.d. 0.42
mm4__chr11 8.93 Mbp_chr11_8933338_F TCGTCGGCAGCGTCCACTAGAGGCAGGAATGGGG 59.5 0.35
mm4__chr11 8.93 Mbp_chr11_8933338_R GTCTCGTGGGCTCGGTAGACAAACAGGCCCACACC 59.8 0.35
mm4__chr18 21.90 Mbp_chr18_21903972_F TCGTCGGCAGCGTCGCTGGCCTCTTGTTCACTCA 60.2 0.33
mm4__chr18 21.90 Mbp_chr18_21903972_R GTCTCGTGGGCTCGGCCGTGATCTCAAAGGCCCC 60.4 0.33
mm3__chr22 18.04 Mbp_chr22_18044207_F TCGTCGGCAGCGTCGCTGCTGATGGAGGCTACAA 60.1 0.31
mm3__chr22 18.04 Mbp_chr22_18044207_R GTCTCGTGGGCTCGGGAGTTTCAGAAGCCAGCCCT 59.9 0.31
mm4__chr16 471.21 Kbp_chr16_471215_F TCGTCGGCAGCGTCTCCCTTGCTTGTCTTGACCC 59.8 0.29
mm4__chr16 471.21 Kbp_chr16_471215_R GTCTCGTGGGCTCGGAAGACCTCGTGCTCAACAGG 59.9 0.29
mm4__chr7 151.14 Mbp_chr7_151137344_F TCGTCGGCAGCGTCCCACTAACCTCCAGCACCTG 60.0 0.25
mm4__chr7 151.14 Mbp_chr7_151137344_R GTCTCGTGGGCTCGGCACCCAACACTGAGACCACA 59.8 0.25
mm4__chr17 81.17 Mbp_chr17_81165776_F TCGTCGGCAGCGTCGAGGCCGGTTTGTGCTGG 61.3 0.22
mm4__chr17 81.17 Mbp_chr17_81165776_R GTCTCGTGGGCTCGGAATTAACCCTTTCCCCGCCC 60.3 0.22
mm3__chr15 40.95 Mbp_chr15_40952429_F TCGTCGGCAGCGTCTTCAGCTGCCTCTGTTTCCC 60.2 0.18
mm3__chr15 40.95 Mbp_chr15_40952429_R GTCTCGTGGGCTCGGGTCTTCTCCCTCGGCTTCTG 59.8 0.18
mm4__chr19 19.63 Mbp_chr19_19627184_F Primer3: not found at this Tm N.d. 0.14
mm4__chr19 19.63 Mbp_chr19_19627184_R Primer3: not found at this Tm N.d. 0.14
mm4__chr15 63.94 Mbp_chr15_63941541_F Primer3: not found at this Tm N.d. 0.13
mm4__chr15 63.94 Mbp_chr15_63941541_R Primer3: not found at this Tm N.d. 0.13
mm3__chr17 63.70 Mbp_chr17_63700684_F Primer3: not found at this Tm N.d. 0.11
mm3__chr17 63.70 Mbp_chr17_63700684_R Primer3: not found at this Tm N.d. 0.11
mm4__chr4 40.70 Mbp_chr4_40698878_F TCGTCGGCAGCGTCCAAGTTCAATGACCACAGGGC 59.7 0.09
mm4__chr4 40.70 Mbp_chr4_40698878_R GTCTCGTGGGCTCGGCCCATGCATTGTTTTGCTCCA 59.9 0.09
mm4__chr8 51.41 Mbp_chr8_51408556_F TCGTCGGCAGCGTCCTCGGTAACCCCTCAGCATC 59.8 0.09
mm4__chr8 51.41 Mbp_chr8_51408556_R GTCTCGTGGGCTCGGACGGTTTACCAGGAAGCCAG 59.9 0.09
mm4__chr4 8.38 Mbp_chr4_8384463_F TCGTCGGCAGCGTCCGGGCAGTGAATTCTCTTGC 59.5 0.07
mm4__chr4 8.38 Mbp_chr4_8384463_R GTCTCGTGGGCTCGGGAGTCCTTCTGGTGTGAGGC 60.0 0.07
mm4__chr20 62.95 Mbp_chr20_62945192_F TCGTCGGCAGCGTCCTCTGGCACTCGCTGAAGAA 60.0 0.07
mm4__chr20 62.95 Mbp_chr20_62945192_R GTCTCGTGGGCTCGGTTTTGAGTGGGATGCAGCCT 59.8 0.07
mm4__chr6 125.96 Mbp_chr6_125956946_F TCGTCGGCAGCGTCGGCGACGTCTCGAGGTAAAA 60.1 0.06
mm4__chr6 125.96 Mbp_chr6_125956946_R GTCTCGTGGGCTCGGCGCTGCGGTTCACCTGTT 60.9 0.06
mm4__chr6 100.46 Mbp_chr6_100455318_F Primer3: not found at this Tm N.d. 0.06
mm4__chr6 100.46 Mbp_chr6_100455318_R Primer3: not found at this Tm N.d. 0.06
mm4__chr9 136.44 Mbp_chr9_136439893_F Primer3: not found at this Tm N.d. 0.05
mm4__chr9 136.44 Mbp_chr9_136439893_R Primer3: not found at this Tm N.d. 0.05
mm4__chr16 18.74 Mbp_chr16_18743876_F Primer3: not found at this Tm N.d. 0.05
mm4__chr16 18.74 Mbp_chr16_18743876_R Primer3: not found at this Tm N.d. 0.05
mm4__chr2 96.89 Mbp_chr2_96891703_F TCGTCGGCAGCGTCCACCAACAGCAGCTCTCTCA 59.9 0.04
mm4__chr2 96.89 Mbp_chr2_96891703_R GTCTCGTGGGCTCGGAAACACTTCTGCCCAGCTCC 60.5 0.04
mm4__chr21 33.10 Mbp_chr21_33101787_F TCGTCGGCAGCGTCCTCAAGTGGGAGCTGAAGGG 60.0 0.04
mm4__chr21 33.10 Mbp_chr21_33101787_R GTCTCGTGGGCTCGGATGAATGGGAGCTGTCAGCC 60.1 0.04
mm4__chr11 1.28 Mbp_chr11_1276307_F TCGTCGGCAGCGTCGCAGCAGGAGAGACGGAC 59.8 0.03
mm4__chr11 1.28 Mbp_chr11_1276307_R GTCTCGTGGGCTCGGGGCAGAATGAACCCACACCT 60.2 0.03
mm4__chr10 87.10 Mbp_chr10_87095463_F TCGTCGGCAGCGTCGGGTCATGTGAGTCACGGG 60.0 0.03
mm4__chr10 87.10 Mbp_chr10_87095463_R GTCTCGTGGGCTCGGTTTCCTGCCCACGTGTCAG 60.2 0.03
mm4__chr19 39.36 Mbp_chr19_39355529_F TCGTCGGCAGCGTCAGACCTGAGCCCAGTAGGTT 59.8 0.03
mm4__chr19 39.36 Mbp_chr19_39355529_R GTCTCGTGGGCTCGGACCACATTCAGCTCCATCCC 59.7 0.03
mm4__chr6 147.51 Mbp_chr6_147508196_F Primer3: not found at this Tm N.d. 0.02
mm4__chr6 147.51 Mbp_chr6_147508196_R Primer3: not found at this Tm N.d. 0.02
mm3__chr6 9.05 Mbp_chr6_9050342_F TCGTCGGCAGCGTCTCAGAGAGCTCCCATCTCCC 60.1 0.02
mm3__chr6 9.05 Mbp_chr6_9050342_R GTCTCGTGGGCTCGGGCACCATTGACAACTGCAGG 60.0 0.02
mm4__chr4 71.71 Mbp_chr4_71714482_F TCGTCGGCAGCGTCACCTAGCAACTTTAGGAGCACT 59.0 0.02
mm4__chr4 71.71 Mbp_chr4_71714482_R GTCTCGTGGGCTCGGTGTTGACTCAATAAGGGGATAGCT 59.2 0.02
mm4__chr20 62.96 Mbp_chr20_62963019_F TCGTCGGCAGCGTCCTAGGGCTAAGGCAGACACC 59.5 0.02
mm4__chr20 62.96 Mbp_chr20_62963019_R GTCTCGTGGGCTCGGCACCTTTGAGAACCGCGTTC 59.7 0.02
mm4__chr5 7.82 Mbp_chr5_7816421_F Primer3: not found at this Tm N.d. 0.01
mm4__chr5 7.82 Mbp_chr5_7816421_R Primer3: not found at this Tm N.d. 0.01
mm4__chr9 127.46 Mbp_chr9_127460417_F Primer3: not found at this Tm N.d. 0.01
mm4__chr9 127.46 Mbp_chr9_127460417_R Primer3: not found at this Tm N.d. 0.01
mm4__chr2 96.23 Mbp_chr2_96228909_F Primer3: not found at this Tm N.d. 0.00
mm4__chr2 96.23 Mbp_chr2_96228909_R Primer3: not found at this Tm N.d. 0.00
mm4__chr2 239.11 Mbp_chr2_239111613_F TCGTCGGCAGCGTCCACAGACACGGGGAAGGTG 60.3 0.00
mm4__chr2 239.11 Mbp_chr2_239111613_R GTCTCGTGGGCTCGGCAGCTGAGGAACTACCAGGC 60.1 0.00
mm4__chr12 48.08 Mbp_chr12_48080987_F TCGTCGGCAGCGTCCTCCACTGACCCAACCTGTG 60.2 0.00
mm4__chr12 48.08 Mbp_chr12_48080987_R GTCTCGTGGGCTCGGGGACCACTCAGCCTTCCTTC 60.0 0.00
mm4__chrX 71.16 Mbp_chrX_71163385_F Primer3: not found at this Tm N.d. 0.00
mm4__chrX 71.16 Mbp_chrX_71163385_R Primer3: not found at this Tm N.d. 0.00
mm4__chr9 125.53 Mbp_chr9_125527768_F Primer3: not found at this Tm N.d. 0.00
mm4__chr9 125.53 Mbp_chr9_125527768_R Primer3: not found at this Tm N.d. 0.00
mm4__chr7 94.01 Mbp_chr7_94012128_F Primer3: not found at this Tm N.d. 0.00
mm4__chr7 94.01 Mbp_chr7_94012128_R Primer3: not found at this Tm N.d. 0.00
mm4__chr7 54.70 Mbp_chr7_54697856_F TCGTCGGCAGCGTCCACTTACGCGGGTCAGGAC 60.4 0.00
mm4__chr7 54.70 Mbp_chr7_54697856_R GTCTCGTGGGCTCGGGTTACCGCCAGCTCCTCAG 60.1 0.00
mm4__chr6 168.07 Mbp_chr6_168073381_F TCGTCGGCAGCGTCGAGTCTGACACAGGAAGCCC 60.0 0.00
mm4__chr6 168.07 Mbp_chr6_168073381_R GTCTCGTGGGCTCGGGGCCAGCCTTTCTGATGTGA 60.3 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__chr20 62.33 Mbp_chr20_62328812_F TCGTCGGCAGCGTCCTCTGGCACCAACTCCCTG 60.0 0.00
mm4__chr20 62.33 Mbp_chr20_62328812_R GTCTCGTGGGCTCGGCTGCCATGCCCATGTCATTG 59.8 0.00
mm4__chr2 34.37 Mbp_chr2_34368486_F TCGTCGGCAGCGTCAGAACCCTCCTGTGTGCATG 59.9 0.00
mm4__chr2 34.37 Mbp_chr2_34368486_R GTCTCGTGGGCTCGGCTAGCTGAGGGGCAGGAAAC 60.1 0.00
mm4__chr2 20.53 Mbp_chr2_20525357_F TCGTCGGCAGCGTCCTGCAGGGTCAGATGTGGAG 60.1 0.00
mm4__chr2 20.53 Mbp_chr2_20525357_R GTCTCGTGGGCTCGGACAAACCAACATCCCAGGGG 60.1 0.00
mm4__chr19 5.88 Mbp_chr19_5876669_F TCGTCGGCAGCGTCGCTGGGTGGGTGATAAAGCT 60.0 0.00
mm4__chr19 5.88 Mbp_chr19_5876669_R GTCTCGTGGGCTCGGGCCTTCTCCCTCCTCCTGA 59.9 0.00
mm4__chr17 18.85 Mbp_chr17_18850909_F TCGTCGGCAGCGTCCAGGAAGCAAAGCCACCAAG 59.6 0.00
mm4__chr17 18.85 Mbp_chr17_18850909_R GTCTCGTGGGCTCGGCCTATGCCACTGTCCTGCAA 60.0 0.00
mm4__chr16 271.75 Kbp_chr16_271750_F TCGTCGGCAGCGTCGCCCCTTCTTCCAATCAGGG 60.3 0.00
mm4__chr16 271.75 Kbp_chr16_271750_R GTCTCGTGGGCTCGGAACCTGAGGTTCCGTGGAAT 58.9 0.00
mm4__chr15 83.65 Mbp_chr15_83654414_F TCGTCGGCAGCGTCGTCTCCAAGCAGAGTCGGG 59.7 0.00
mm4__chr15 83.65 Mbp_chr15_83654414_R GTCTCGTGGGCTCGGGACTCTCCCTGAACCTTCCG 59.4 0.00
mm4__chr15 25.01 Mbp_chr15_25013568_F Primer3: not found at this Tm N.d. 0.00
mm4__chr15 25.01 Mbp_chr15_25013568_R Primer3: not found at this Tm N.d. 0.00
mm4__chr13 47.55 Mbp_chr13_47553695_F Primer3: not found at this Tm N.d. 0.00
mm4__chr13 47.55 Mbp_chr13_47553695_R Primer3: not found at this Tm N.d. 0.00
mm4__chr11 65.00 Mbp_chr11_64996966_F TCGTCGGCAGCGTCACAGAGGTGCATGGCTTAGG 59.7 0.00
mm4__chr11 65.00 Mbp_chr11_64996966_R GTCTCGTGGGCTCGGACTGAAACTTGGCCCTCTGG 59.8 0.00
mm4__chr10 113.09 Mbp_chr10_113087620_F TCGTCGGCAGCGTCAAATGCAGAGTGGGAGGCTC 60.0 0.00
mm4__chr10 113.09 Mbp_chr10_113087620_R GTCTCGTGGGCTCGGGAAGCTGAGAGATCTGCCCC 59.8 0.00
mm4__chr1 94.54 Mbp_chr1_94541354_F TCGTCGGCAGCGTCAAAACTCTCCAGCGGAAGGG 59.9 0.00
mm4__chr1 94.54 Mbp_chr1_94541354_R GTCTCGTGGGCTCGGCCAGCCCGGCTTGAATGAA 60.6 0.00
mm3__chr20 50.25 Mbp_chr20_50246450_F TCGTCGGCAGCGTCCCCACTGACCGGTTTTGGAT 60.2 0.00
mm3__chr20 50.25 Mbp_chr20_50246450_R GTCTCGTGGGCTCGGCTCACAACCAGGAAGCCAGA 59.6 0.00

Off-target amplicon sequences

Primers underlined, off-targets in bold.

ontarget_mm0__chr7 5.53 Mbp_chr7_5529726 TGGTGAGCTGCGAGAATAGCCGGGCGCGCTGTGAGCCGAGGTCGCCCCCGCCCTGGCCACTTCCGGCGCGCCGAGTCCTT
AGGCCGCCAGGGG
GCGCCGGCGCGCGCCCAGATTGGGGACAAAGGAAGCCG
mm4__chr9 37.37 Mbp_chr9_37370772 GAAACTGGGAAGGGAGTGGGGAGCAGCAGCAGAGCAAACAGAAAAGATGCCCGAAGGAAGCGAGTTCCTAGGCCACCAGG
GG
CCAAGACCCCAGCACGTG
mm4__chr11 8.93 Mbp_chr11_8933338 CACTAGAGGCAGGAATGGGGGAGCCACTGGCGGCCTGGGGACTCTAGGATAGAATTTGTCCCTAGTCTAAACCAAAATAA
CCAAAGGTGTGGGCCTGTTTGTCTA
mm4__chr18 21.90 Mbp_chr18_21903972 GCTGGCCTCTTGTTCACTCATCTCCCTCTCCTCCTAATCTTCTAATAACTTTATTACTGGGAAAAAGGCCAACTAGGGAA
AACCCCACTGGCGGCCTGAGGATTCTTGATCTGAAGGGGGCCTTTGAGATCACGG
mm3__chr22 18.04 Mbp_chr22_18044207 GCTGCTGATGGAGGCTACAAACAGTGATAGAAGCATGCAGAAGCTACACAGCACAGGCCAAGGTGCTGTGGGAGAGGCGG
AGGAGGAACACTGACCACTGGCGGCCTGGGGACACGGGAGGGCTGGCTTCTGAAACTC
mm4__chr16 471.21 Kbp_chr16_471215 TCCCTTGCTTGTCTTGACCCCCCCCAGGGCCCCCAACTCCCACACATCTGTCCCTGGGGGCCTCCTTCCCAGGGAGTCCC
GAGGCCGCCAGGGG
TCCCGTCACTGGGTGGCTATGGGTGGCCTGTTGAGCACGAGGTCTT
mm4__chr7 151.14 Mbp_chr7_151137344 CCACTAACCTCCAGCACCTGGCGGGCTCCTCCGCTTCAAGGTTGAAGCACCTCAGGTTCGGCCCCCGTGTTCTTAGACCG
CCTGGGG
CCATTTCTTTGTGGTCTCAGTGTTGGGTG
mm4__chr17 81.17 Mbp_chr17_81165776 GAGGCCGGTTTGTGCTGGGGCCCAGGGCCTGCCCCTCCGAGATCTGGGGCCGCCAGGGGGTCCGGCTGCTTCTGCTGCTG
GGCTCGGGGCGGGGAAAGGGTTAATT
mm3__chr15 40.95 Mbp_chr15_40952429 TTCAGCTGCCTCTGTTTCCCTTTTACAGTCAGTGACATCCCCTGAGGGCAGTCCCTTGCTGCGTATTGGGTCAACCCCCG
GCGGCCTGTGGACTCGG
CTGGGAGGCCAGAAGCCGAGGGAGAAGAC
mm4__chr4 40.70 Mbp_chr4_40698878 CAAGTTCAATGACCACAGGGCACTAACCCTGAGGCCTAAGGCAGCCAGGGGAGATTCAAATCTGGAGCAAAACAATGCAT
GGG
mm4__chr8 51.41 Mbp_chr8_51408556 CTCGGTAACCCCTCAGCATCCTAGTGCCAGGGTCCCCCAGGACCTTAGGCAGCCAGTGGCTGTAGGTGATGTGCTGCAGC
TCCGCGCCCACGATCTTCCTGGCTTCCTGGTAAACCGT
mm4__chr4 8.38 Mbp_chr4_8384463 CGGGCAGTGAATTCTCTTGCTCGGAATGCGGCTGCTGGCGGCCTGAGGACACACCCAGCGTCAACAACCTCTGTCCTCAA
GACTCTCCCAGAATCCTGGGTCACCACGGCCTTTCCATGTGCCTCACACCAGAAGGACTC
mm4__chr20 62.95 Mbp_chr20_62945192 CTCTGGCACTCGCTGAAGAATCTGGAAGGTTGCGGTTTGCTCTTCCAGTGTTCGGGGGCCTCTGGCTGCTGAAGGATTCG
G
TCTACCACGGAGGGCTGTGCTGTTAGGCTGCATCCCACTCAAAA
mm4__chr6 125.96 Mbp_chr6_125956946 GGCGACGTCTCGAGGTAAAACGGAGGAGGTGCGGGACGCGGAGACTGCGCGGGCCCGGTAGCCCTGGANNNNNNNNNNNN
NNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNAACAGGTGAACCGCAGCG
mm4__chr2 96.89 Mbp_chr2_96891703 CACCAACAGCAGCTCTCTCAGCCTCTTCCCAGAGGGAGAGGCTGGGCCAAGGCCTGAGGCAGCCAGAGGAGGTGGGGAAG
GAGCTGGGCAGAAGTGTTT
mm4__chr21 33.10 Mbp_chr21_33101787 CTCAAGTGGGAGCTGAAGGGACTTGGGAGCGAGGACGCCGGAGGGATGAGAGGCGCCTGGGCCGGTTCCTTAGGCAACCA
GTGG
CCCGTGGGCCTCCATAACTCTGCCCAGAGGCTGACAGCTCCCATTCAT
mm4__chr11 1.28 Mbp_chr11_1276307 GCAGCAGGAGAGACGGACGGCAGCCTCCGGCGGGCGAAGGACCCGGCTTCAGATGCCCGCTGGCTGGCAATCAGGCAGAG
CCTGGCCAACCGTGCCAGGCCCCCTTCCTCACTCCAGGTGTGGGTTCATTCTGCC
mm4__chr10 87.10 Mbp_chr10_87095463 GGGTCATGTGAGTCACGGGCGCCCCTCCTTTCCGCCCGCGCGCCCTCGGAACGGGCGGCCCACCCTGGCCTGTCCTCTGG
CGGCCTCAGGCCGGGG
CCGGGCGTGCAGGGGCTGACACGTGGGCAGGAAA
mm4__chr19 39.36 Mbp_chr19_39355529 AGACCTGAGCCCAGTAGGTTCAATGGGTCTTTGTATGAAGTTCTCAGTCCGGGGAACCTTAGTCCTTTGGCAGCCAGAGG
GGGATGGAGCTGAATGTGGT
mm3__chr6 9.05 Mbp_chr6_9050342 TCAGAGAGCTCCCATCTCCCACTGTGTGCAGCTGAGTTCCAAGCACTCCTGGCGGCATAATGACTGGGACAAAGATATTT
CCTGCAGTTGTCAATGGTGC
mm4__chr4 71.71 Mbp_chr4_71714482 ACCTAGCAACTTTAGGAGCACTCCAAGACCTGAGGCTGCCAGGGGTGTTGAGGAAACCAGAAAAGAGTATAGCTATCCCC
TTATTGAGTCAACA
mm4__chr20 62.96 Mbp_chr20_62963019 CTAGGGCTAAGGCAGACACCCAGGAAGACCTGCTGGGCACAGGTCAAGGCAGGGTGCAGGAGCAGCCGAGTCTTTGGGTG
GCCAGGGG
GCTCTGGAGGAGGCCGTGTGGAGGGTCGTTCAGAACGCGGTTCTCAAAGGTG
mm4__chr2 239.11 Mbp_chr2_239111613 CACAGACACGGGGAAGGTGGCAGACGCGGGTGAGGACTGCGCCCGGGACAGAGGCCTGTGGCCGCCGAAGGACACGGGGA
TGCCGGCGGCCTCCATGGACGCCTGGTAGTTCCTCAGCTG
mm4__chr12 48.08 Mbp_chr12_48080987 CTCCACTGACCCAACCTGTGGCCTGGAGGGCTGTTTGGAAGGGTAAAATTGCCCAAGCAACCCCCAGTCCTCAGGCTGGC
AGAGG
AGGCAAAAGAAGGAAGGCTGAGTGGTCC
mm4__chr7 54.70 Mbp_chr7_54697856 CACTTACGCGGGTCAGGACCCGTGTCCTTAGTCCCACAGAGGGACGGGACGGGCAGCAGGTGCGGTGGGTCGCCTAGCAG
CTGAGGAGCTGGCGGTAAC
mm4__chr6 168.07 Mbp_chr6_168073381 GAGTCTGACACAGGAAGCCCCAGATCCACACCTGCCCTCAGGGGCTCATGGTGTCCACTCAGGGTCCCCTGGGGGACTCA
GGACTGGG
TCTAAATGCATGAGGTCACATCAGAAAGGCTGGCC
mm4__chr20 62.33 Mbp_chr20_62328812 CTCTGGCACCAACTCCCTGCCACTGGGCGCCCAAGGACTGGGGTACTCACGCCTGCAGTTGGGGAAGCCCCAGTATCCGG
TGGCACAGCGGGAGCAGTCACGGCCAATGACATGGGCATGGCAG
mm4__chr2 34.37 Mbp_chr2_34368486 AGAACCCTCCTGTGTGCATGTTGGTCAAGCTGCAGGGCTCCCTCCCCTGTGGTTAGCTTATGGCCCTCTGGAGGCCTATT
GAATCGG
AGCTAGGTCTGGCTCTGCAAGGTTTCCTGCCCCTCAGCTAG
mm4__chr2 20.53 Mbp_chr2_20525357 CTGCAGGGTCAGATGTGGAGTGTCCCCTGCAGGCCTGAGGACTCAGCACTAGTGAAGGGCTCTCAGCAGCTTGCTCAACA
GGCACTGTCCCCTGGGATGTTGGTTTGT
mm4__chr19 5.88 Mbp_chr19_5876669 GCTGGGTGGGTGATAAAGCTGTCAGCCTGCTGGAAATTTCTCTCCCCTTGGGGCCTAAGGGCTGGGAGCCAAGGGCAGCT
GCCGCTCAGGAGGAGGGAGAAGGC
mm4__chr17 18.85 Mbp_chr17_18850909 CAGGAAGCAAAGCCACCAAGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCTAGGAGGTGCTTCCAGTGA
AGGGGGAAGGAAAAACTGCTTGCAGGACAGTGGCATAGG
mm4__chr16 271.75 Kbp_chr16_271750 GCCCCTTCTTCCAATCAGGGATCTTTCGAGGAGACCTCTGGGGGCCTAAGGTCTGGCGATCTGTGGAATATTCCACGGAA
CCTCAGGTT
mm4__chr15 83.65 Mbp_chr15_83654414 GTCTCCAAGCAGAGTCGGGGCGTGCCACGCGGGCCCCAGGGGGCCTCAGGACTGGGGTGCTCCTCACTGCTGGGCACCTC
GGGTCGGGCGCGCTTCGTGCCGTCCCGGAAGGTTCAGGGAGAGTC
mm4__chr11 65.00 Mbp_chr11_64996966 ACAGAGGTGCATGGCTTAGGCGGGGGAGCAGAGTGGTCCCTCAGCAGCTGTGACTTCCCAGTGCCCTCTGGAGGCCTAAG
GAAGTGG
CAGCTCTTTAAATCCCCAGTGGCCACTCCGCCCCCAGAGGGCCAAGTTTCAGT
mm4__chr10 113.09 Mbp_chr10_113087620 AAATGCAGAGTGGGAGGCTCTGCTTGCCAGACGGAGACCTTAGACCTCCAGGGGTGGAGAACGGAGTACTTCCTCTGGTG
CTCGGCTTCCCTTCCTGGGGGCAGATCTCTCAGCTTC
mm4__chr1 94.54 Mbp_chr1_94541354 AAAACTCTCCAGCGGAAGGGGCAGCGGGGTCTGGGGCGCCAACTCCCTCCCTGCAACTCCCGCCGGCGCCCGACGGACTC
GG
TTCATTCAAGCCGGGCTGG
mm3__chr20 50.25 Mbp_chr20_50246450 CCCACTGACCGGTTTTGGATGTAGTTGGAGATGGAACTGGCCCTCTAGGCTTTGTCCCCTGGAGGCCTAGGGACTCTGTC
TTCAGGGCAGTGCTGGCTGTCACTTTGGCCCAGCCCCTCTGGCTTCCTGGTTGTGAG

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.