AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1262060

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1262060 MtrunA17_Chr4g0063371 84.082 245 16 2 1 237 1 230 1.90e-137 385
Msa1262060 MtrunA17_Chr4g0063391 66.667 210 30 2 1 170 1 210 2.73e-93 273
Msa1262060 MtrunA17_Chr4g0063361 44.583 240 60 4 1 167 1 240 6.29e-63 197
Msa1262060 MtrunA17_Chr4g0063401 44.980 249 56 6 1 169 1 248 6.17e-58 184
Msa1262060 MtrunA17_Chr3g0098251 41.477 176 50 5 31 167 15 176 2.36e-32 117
Msa1262060 MtrunA17_Chr8g0366501 36.364 110 44 1 54 137 91 200 6.53e-17 79.0
Msa1262060 MtrunA17_Chr8g0366501 34.454 119 54 4 142 238 258 374 3.11e-11 62.4
Msa1262060 MtrunA17_Chr8g0360671 58.065 62 18 1 77 130 41 102 6.88e-17 75.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1262060 AT3G19360.1 35.017 297 100 7 31 238 81 373 6.12e-45 155
Msa1262060 AT3G19360.2 35.017 297 100 7 31 238 81 373 6.12e-45 155
Msa1262060 AT2G35430.1 32.308 195 106 8 55 238 71 250 2.02e-19 84.7
Msa1262060 AT1G32360.1 33.913 115 45 2 54 137 90 204 8.50e-15 73.2

Find 61 sgRNAs with CRISPR-Local

Find 93 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCAACTAGCTTCTGCGAATT+TGG 0.155359 8_2:+64611105 None:intergenic
ATGAAGATCCTGCACAATTT+AGG 0.163729 8_2:-64610981 Msa1262060:CDS
CCAAGTATACGTTTCTTCTT+AGG 0.214369 8_2:+64609952 None:intergenic
TGAAGATCCTGCACAATTTA+GGG 0.278155 8_2:-64610980 Msa1262060:CDS
AGTCAGATCAATCGTATTTA+CGG 0.310380 8_2:-64609919 Msa1262060:CDS
GATACAGGATATTGTTCCTT+TGG 0.336419 8_2:-64610919 Msa1262060:CDS
TCAATCGTATTTACGGTGAT+TGG 0.347052 8_2:-64609912 Msa1262060:CDS
ATTTGTACTAAGTTCAGATT+TGG 0.359410 8_2:-64611192 Msa1262060:CDS
CACAATTTAGGGGCACTTAT+CGG 0.370314 8_2:-64610969 Msa1262060:CDS
AAATCAGAGTTACAAGTTCC+TGG 0.400098 8_2:-64610096 Msa1262060:intron
AATTGCAGCTTCAGCTTCAA+TGG 0.400607 8_2:+64610044 None:intergenic
CACTTTGCTCATTGTGAAGA+AGG 0.404690 8_2:-64610886 Msa1262060:intron
GACTTGCAGGGGAGGTGGTA+GGG 0.419543 8_2:+64610001 None:intergenic
TGCAAGTCAACTTGTGGAAA+AGG 0.437938 8_2:-64609986 Msa1262060:CDS
CCTAAGAAGAAACGTATACT+TGG 0.441257 8_2:-64609952 Msa1262060:CDS
AGATTTGGTGCTTGTAGAAA+CGG 0.444340 8_2:-64611177 Msa1262060:CDS
CTGAGGCGGTGACATCTTAG+AGG 0.449778 8_2:+64611344 None:intergenic
TTAGAGGTTGGAATATCATC+TGG 0.452783 8_2:+64611360 None:intergenic
AACTGCAGATTCAGCTTCAA+TGG 0.461590 8_2:+64610068 None:intergenic
TGTCTCAAGTGGAAGGATAC+AGG 0.464303 8_2:-64610934 Msa1262060:CDS
ACAAATTGCAACTTTGCTCA+TGG 0.469357 8_2:-64611153 Msa1262060:CDS
CTGATCTGTTTGATTGAGGA+AGG 0.475163 8_2:+64611238 None:intergenic
CTCATGGGGCTGAAGAGATA+AGG 0.488249 8_2:-64611137 Msa1262060:CDS
TGTGCAAGAAGTATAGCAAT+GGG 0.488339 8_2:-64611041 Msa1262060:CDS
CAAATTGCAACTTTGCTCAT+GGG 0.490368 8_2:-64611152 Msa1262060:CDS
TGACTTGCAGGGGAGGTGGT+AGG 0.490726 8_2:+64610000 None:intergenic
GATTGAGGAAGGGTCATCCT+TGG 0.496966 8_2:+64611249 None:intergenic
AGCTTCTGCGAATTTGGAGG+TGG 0.504943 8_2:+64611111 None:intergenic
CACAAGTTGACTTGCAGGGG+AGG 0.509364 8_2:+64609993 None:intergenic
CCAAATTCGCAGAAGCTAGT+TGG 0.513477 8_2:-64611105 Msa1262060:CDS
ACTAGCTTCTGCGAATTTGG+AGG 0.524749 8_2:+64611108 None:intergenic
GGAAGGGTCATCCTTGGAGG+AGG 0.531078 8_2:+64611255 None:intergenic
GGCGGTGACATCTTAGAGGT+TGG 0.533133 8_2:+64611348 None:intergenic
AATTTACACTTATCTGCATA+GGG 0.538027 8_2:+64611009 None:intergenic
AACAATGACTTCAAAAGAGA+AGG 0.542813 8_2:-64611306 Msa1262060:CDS
CTCCCCTGCAAGTCAACTTG+TGG 0.543090 8_2:-64609992 Msa1262060:CDS
AAGTTGACTTGCAGGGGAGG+TGG 0.548779 8_2:+64609996 None:intergenic
AAATTGCAACTTTGCTCATG+GGG 0.550865 8_2:-64611151 Msa1262060:CDS
AGGAGGGCATATCAATGCAT+TGG 0.555491 8_2:+64611272 None:intergenic
TGAGGAAGGGTCATCCTTGG+AGG 0.556539 8_2:+64611252 None:intergenic
CATTGATATGCCCTCCTCCA+AGG 0.556864 8_2:-64611266 Msa1262060:CDS
GAATTTACACTTATCTGCAT+AGG 0.559420 8_2:+64611008 None:intergenic
TTTCCACAAGTTGACTTGCA+GGG 0.560920 8_2:+64609989 None:intergenic
TGGTCTGATCTGTTTGATTG+AGG 0.566957 8_2:+64611234 None:intergenic
TAAGTGCCCCTAAATTGTGC+AGG 0.568865 8_2:+64610973 None:intergenic
CTGTGCAAGAAGTATAGCAA+TGG 0.572239 8_2:-64611042 Msa1262060:CDS
CTAAGAAGAAACGTATACTT+GGG 0.583825 8_2:-64609951 Msa1262060:CDS
TTCCACAAGTTGACTTGCAG+GGG 0.588906 8_2:+64609990 None:intergenic
TCAGCTTCAATGGCTCCACC+AGG 0.589035 8_2:+64610078 None:intergenic
AGACTAAGCTGTGTCTCAAG+TGG 0.589149 8_2:-64610945 Msa1262060:CDS
ATTGTGCAGGATCTTCATGA+AGG 0.599081 8_2:+64610986 None:intergenic
TAAGCTGTGTCTCAAGTGGA+AGG 0.609632 8_2:-64610941 Msa1262060:CDS
AAAGTGACAGTTCTTTCCAA+AGG 0.613225 8_2:+64610903 None:intergenic
TGATCTGTTTGATTGAGGAA+GGG 0.618914 8_2:+64611239 None:intergenic
GAAGGGTCATCCTTGGAGGA+GGG 0.622595 8_2:+64611256 None:intergenic
AATATCATCTGGAAAAGCCA+TGG 0.624162 8_2:+64611371 None:intergenic
TTCAATGAAGAGAACTGAGG+CGG 0.637828 8_2:+64611330 None:intergenic
GAAGATCCTGCACAATTTAG+GGG 0.650410 8_2:-64610979 Msa1262060:CDS
CAAGAAGTATAGCAATGGGG+AGG 0.680526 8_2:-64611037 Msa1262060:CDS
TCAGAGTTACAAGTTCCTGG+TGG 0.718686 8_2:-64610093 Msa1262060:intron
GTGCAAGAAGTATAGCAATG+GGG 0.763140 8_2:-64611040 Msa1262060:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GACAATTTTTTTTAAATATA+AGG + chr8_2:64611024-64611043 None:intergenic 10.0%
!!! TTTTTTTAAATATAAGGTCT+AGG + chr8_2:64611018-64611037 None:intergenic 15.0%
!!! CAATAACTCATTTTGATTAT+TGG - chr8_2:64610409-64610428 Msa1262060:intron 20.0%
!! AGTAATCATACATTAGAATA+AGG + chr8_2:64610655-64610674 None:intergenic 20.0%
!! AATGTATGATTACTATTGTA+TGG - chr8_2:64610661-64610680 Msa1262060:intron 20.0%
!!! TACTATAATTTCTAGTAGTT+TGG - chr8_2:64610731-64610750 Msa1262060:intron 20.0%
!!! TTATAACAATTGCAACTTTT+TGG - chr8_2:64611105-64611124 Msa1262060:CDS 20.0%
! ATTTGTACTAAGTTCAGATT+TGG - chr8_2:64610077-64610096 Msa1262060:CDS 25.0%
!!! ATTTTTTTAACTTCGTTGCA+CGG + chr8_2:64610191-64610210 None:intergenic 25.0%
! AATTTACACTTATCTGCATA+GGG + chr8_2:64610263-64610282 None:intergenic 25.0%
!!! CTCATTTTGATTATTGGTTT+TGG - chr8_2:64610415-64610434 Msa1262060:intron 25.0%
! ATCATACATTAGAATAAGGA+TGG + chr8_2:64610651-64610670 None:intergenic 25.0%
!! AAATTCCACAGTTTTACATT+TGG - chr8_2:64610703-64610722 Msa1262060:intron 25.0%
!! ACTTTAAGAAGAAACAAGTT+TGG + chr8_2:64610806-64610825 None:intergenic 25.0%
!! TTAAAGTTTCTGCTGATTAT+TGG - chr8_2:64610819-64610838 Msa1262060:intron 25.0%
!! TTTTTCAATGAAGAGAACTG+AGG + chr8_2:64609945-64609964 None:intergenic 30.0%
AACAATGACTTCAAAAGAGA+AGG - chr8_2:64609963-64609982 Msa1262060:CDS 30.0%
! TTCGTGTTTTGTAGAAAATG+TGG + chr8_2:64610058-64610077 None:intergenic 30.0%
GAATTTACACTTATCTGCAT+AGG + chr8_2:64610264-64610283 None:intergenic 30.0%
!!! TTTGAATGTGTGTCATTTTG+TGG - chr8_2:64610563-64610582 Msa1262060:intron 30.0%
TCTTACCAAATGTAAAACTG+TGG + chr8_2:64610711-64610730 None:intergenic 30.0%
GATGAACATAATACAATAGC+TGG + chr8_2:64610779-64610798 None:intergenic 30.0%
CCTCAAAATTATTGATGAGT+CGG + chr8_2:64610860-64610879 None:intergenic 30.0%
AAGAGTCAGAACAATATACA+TGG + chr8_2:64611134-64611153 None:intergenic 30.0%
!!! AGGGTTTGTTGAATTTTCTA+TGG + chr8_2:64611252-64611271 None:intergenic 30.0%
CTAAGAAGAAACGTATACTT+GGG - chr8_2:64611318-64611337 Msa1262060:CDS 30.0%
AGTCAGATCAATCGTATTTA+CGG - chr8_2:64611350-64611369 Msa1262060:CDS 30.0%
TTAGAGGTTGGAATATCATC+TGG + chr8_2:64609912-64609931 None:intergenic 35.0%
TGATCTGTTTGATTGAGGAA+GGG + chr8_2:64610033-64610052 None:intergenic 35.0%
!! AGATTTGGTGCTTGTAGAAA+CGG - chr8_2:64610092-64610111 Msa1262060:CDS 35.0%
ACAAATTGCAACTTTGCTCA+TGG - chr8_2:64610116-64610135 Msa1262060:intron 35.0%
CAAATTGCAACTTTGCTCAT+GGG - chr8_2:64610117-64610136 Msa1262060:intron 35.0%
AAATTGCAACTTTGCTCATG+GGG - chr8_2:64610118-64610137 Msa1262060:intron 35.0%
! TGTGCAAGAAGTATAGCAAT+GGG - chr8_2:64610228-64610247 Msa1262060:intron 35.0%
ATGAAGATCCTGCACAATTT+AGG - chr8_2:64610288-64610307 Msa1262060:intron 35.0%
TGAAGATCCTGCACAATTTA+GGG - chr8_2:64610289-64610308 Msa1262060:intron 35.0%
GATACAGGATATTGTTCCTT+TGG - chr8_2:64610350-64610369 Msa1262060:intron 35.0%
AAAGTGACAGTTCTTTCCAA+AGG + chr8_2:64610369-64610388 None:intergenic 35.0%
!! TTGACAAAGCAAGTTCTGAA+TGG - chr8_2:64610616-64610635 Msa1262060:intron 35.0%
! CCGACTCATCAATAATTTTG+AGG - chr8_2:64610857-64610876 Msa1262060:intron 35.0%
TGTTCTGACTCTTGAAGTAT+TGG - chr8_2:64611141-64611160 Msa1262060:CDS 35.0%
AAATCAGAGTTACAAGTTCC+TGG - chr8_2:64611173-64611192 Msa1262060:CDS 35.0%
CCAAGTATACGTTTCTTCTT+AGG + chr8_2:64611320-64611339 None:intergenic 35.0%
CCTAAGAAGAAACGTATACT+TGG - chr8_2:64611317-64611336 Msa1262060:CDS 35.0%
TCAATCGTATTTACGGTGAT+TGG - chr8_2:64611357-64611376 Msa1262060:CDS 35.0%
TTCAATGAAGAGAACTGAGG+CGG + chr8_2:64609942-64609961 None:intergenic 40.0%
CTGATCTGTTTGATTGAGGA+AGG + chr8_2:64610034-64610053 None:intergenic 40.0%
TGGTCTGATCTGTTTGATTG+AGG + chr8_2:64610038-64610057 None:intergenic 40.0%
! CTGTGCAAGAAGTATAGCAA+TGG - chr8_2:64610227-64610246 Msa1262060:intron 40.0%
! GTGCAAGAAGTATAGCAATG+GGG - chr8_2:64610229-64610248 Msa1262060:intron 40.0%
ATTGTGCAGGATCTTCATGA+AGG + chr8_2:64610286-64610305 None:intergenic 40.0%
GAAGATCCTGCACAATTTAG+GGG - chr8_2:64610290-64610309 Msa1262060:intron 40.0%
!! CACAATTTAGGGGCACTTAT+CGG - chr8_2:64610300-64610319 Msa1262060:intron 40.0%
CACTTTGCTCATTGTGAAGA+AGG - chr8_2:64610383-64610402 Msa1262060:intron 40.0%
CTTATTTGACCGCGGTATTA+AGG + chr8_2:64610928-64610947 None:intergenic 40.0%
CTTAATACCGCGGTCAAATA+AGG - chr8_2:64610926-64610945 Msa1262060:CDS 40.0%
! GCATTAACCTTATTTGACCG+CGG + chr8_2:64610936-64610955 None:intergenic 40.0%
ATCATACACTCGCACACAAA+TGG + chr8_2:64611046-64611065 None:intergenic 40.0%
AACTGCAGATTCAGCTTCAA+TGG + chr8_2:64611204-64611223 None:intergenic 40.0%
AATTGCAGCTTCAGCTTCAA+TGG + chr8_2:64611228-64611247 None:intergenic 40.0%
!! TTTCCACAAGTTGACTTGCA+GGG + chr8_2:64611283-64611302 None:intergenic 40.0%
!!! TTTTCCACAAGTTGACTTGC+AGG + chr8_2:64611284-64611303 None:intergenic 40.0%
TGCAAGTCAACTTGTGGAAA+AGG - chr8_2:64611283-64611302 Msa1262060:CDS 40.0%
! AGGAGGGCATATCAATGCAT+TGG + chr8_2:64610000-64610019 None:intergenic 45.0%
! ACTAGCTTCTGCGAATTTGG+AGG + chr8_2:64610164-64610183 None:intergenic 45.0%
! CCAACTAGCTTCTGCGAATT+TGG + chr8_2:64610167-64610186 None:intergenic 45.0%
CCAAATTCGCAGAAGCTAGT+TGG - chr8_2:64610164-64610183 Msa1262060:intron 45.0%
! CAAGAAGTATAGCAATGGGG+AGG - chr8_2:64610232-64610251 Msa1262060:intron 45.0%
TAAGTGCCCCTAAATTGTGC+AGG + chr8_2:64610299-64610318 None:intergenic 45.0%
AGACTAAGCTGTGTCTCAAG+TGG - chr8_2:64610324-64610343 Msa1262060:intron 45.0%
TAAGCTGTGTCTCAAGTGGA+AGG - chr8_2:64610328-64610347 Msa1262060:intron 45.0%
TGTCTCAAGTGGAAGGATAC+AGG - chr8_2:64610335-64610354 Msa1262060:intron 45.0%
CGGTATTAAGGATCGTGACA+TGG + chr8_2:64610916-64610935 None:intergenic 45.0%
TGTCACGATCCTTAATACCG+CGG - chr8_2:64610916-64610935 Msa1262060:CDS 45.0%
TCAGAGTTACAAGTTCCTGG+TGG - chr8_2:64611176-64611195 Msa1262060:CDS 45.0%
!! TTCCACAAGTTGACTTGCAG+GGG + chr8_2:64611282-64611301 None:intergenic 45.0%
CATTGATATGCCCTCCTCCA+AGG - chr8_2:64610003-64610022 Msa1262060:CDS 50.0%
GATTGAGGAAGGGTCATCCT+TGG + chr8_2:64610023-64610042 None:intergenic 50.0%
CTCATGGGGCTGAAGAGATA+AGG - chr8_2:64610132-64610151 Msa1262060:intron 50.0%
AGCTTCTGCGAATTTGGAGG+TGG + chr8_2:64610161-64610180 None:intergenic 50.0%
GGCGGTGACATCTTAGAGGT+TGG + chr8_2:64609924-64609943 None:intergenic 55.0%
CTGAGGCGGTGACATCTTAG+AGG + chr8_2:64609928-64609947 None:intergenic 55.0%
GAAGGGTCATCCTTGGAGGA+GGG + chr8_2:64610016-64610035 None:intergenic 55.0%
TGAGGAAGGGTCATCCTTGG+AGG + chr8_2:64610020-64610039 None:intergenic 55.0%
! AAGGTCTAGGACCACGACTG+TGG + chr8_2:64611005-64611024 None:intergenic 55.0%
TCAGCTTCAATGGCTCCACC+AGG + chr8_2:64611194-64611213 None:intergenic 55.0%
!! AAGTTGACTTGCAGGGGAGG+TGG + chr8_2:64611276-64611295 None:intergenic 55.0%
!! CACAAGTTGACTTGCAGGGG+AGG + chr8_2:64611279-64611298 None:intergenic 55.0%
CTCCCCTGCAAGTCAACTTG+TGG - chr8_2:64611277-64611296 Msa1262060:CDS 55.0%
GGAAGGGTCATCCTTGGAGG+AGG + chr8_2:64610017-64610036 None:intergenic 60.0%
GTACGTCTCAGCCACAGTCG+TGG - chr8_2:64610991-64611010 Msa1262060:CDS 60.0%
GACTTGCAGGGGAGGTGGTA+GGG + chr8_2:64611271-64611290 None:intergenic 60.0%
! TGACTTGCAGGGGAGGTGGT+AGG + chr8_2:64611272-64611291 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr8_2 gene 64609900 64611391 64609900 ID=Msa1262060;Name=Msa1262060
chr8_2 mRNA 64609900 64611391 64609900 ID=Msa1262060-mRNA-1;Parent=Msa1262060;Name=Msa1262060-mRNA-1;_AED=0.05;_eAED=0.05;_QI=0|0|0|1|1|1|2|0|238
chr8_2 exon 64610887 64611391 64610887 ID=Msa1262060-mRNA-1:exon:20910;Parent=Msa1262060-mRNA-1
chr8_2 exon 64609900 64610111 64609900 ID=Msa1262060-mRNA-1:exon:20909;Parent=Msa1262060-mRNA-1
chr8_2 CDS 64610887 64611391 64610887 ID=Msa1262060-mRNA-1:cds;Parent=Msa1262060-mRNA-1
chr8_2 CDS 64609900 64610111 64609900 ID=Msa1262060-mRNA-1:cds;Parent=Msa1262060-mRNA-1
Gene Sequence

>Msa1262060

ATGGCTTTTCCAGATGATATTCCAACCTCTAAGATGTCACCGCCTCAGTTCTCTTCATTGAAAAACAATGACTTCAAAAGAGAAGGAACTTCTCATTCCAATGCATTGATATGCCCTCCTCCAAGGATGACCCTTCCTCAATCAAACAGATCAGACCACATTTTCTACAAAACACGAATTTGTACTAAGTTCAGATTTGGTGCTTGTAGAAACGGAACAAATTGCAACTTTGCTCATGGGGCTGAAGAGATAAGGAAACCACCTCCAAATTCGCAGAAGCTAGTTGGTCCGTGCAACGAAGTTAAAAAAATCATAAACAAGATGAAACTGTGCAAGAAGTATAGCAATGGGGAGGAATGTCCCTATGCAGATAAGTGTAAATTCCTTCATGAAGATCCTGCACAATTTAGGGGCACTTATCGGAAGACTAAGCTGTGTCTCAAGTGGAAGGATACAGGATATTGTTCCTTTGGAAAGAACTGTCACTTTGCTCATTGTGAAGAAGAGTTACAAGTTCCTGGTGGAGCCATTGAAGCTGAATCTGCAGTTGCCATTGAAGCTGAAGCTGCAATTACCATAGAAAATTCAACAAACCCTACCACCTCCCCTGCAAGTCAACTTGTGGAAAAGGAAGAAGAGCAGCCTAAGAAGAAACGTATACTTGGGTTGAAATTCAGTCAGATCAATCGTATTTACGGTGATTGGATTGACGATTGA
Protein sequence

>Msa1262060

MAFPDDIPTSKMSPPQFSSLKNNDFKREGTSHSNALICPPPRMTLPQSNRSDHIFYKTRICTKFRFGACRNGTNCNFAHGAEEIRKPPPNSQKLVGPCNEVKKIINKMKLCKKYSNGEECPYADKCKFLHEDPAQFRGTYRKTKLCLKWKDTGYCSFGKNCHFAHCEEELQVPGGAIEAESAVAIEAEAAITIENSTNPTTSPASQLVEKEEEQPKKKRILGLKFSQINRIYGDWIDD*