AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG024296

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG024296 MtrunA17_Chr8g0387931 97.065 477 11 2 1 475 1 476 0.0 905
MsaG024296 MtrunA17_Chr8g0370431 47.126 87 40 2 257 337 29 115 1.10e-12 65.5
MsaG024296 MtrunA17_Chr3g0143991 41.111 90 50 1 255 341 35 124 3.37e-12 64.3
MsaG024296 MtrunA17_Chr7g0242251 45.205 73 37 1 261 330 47 119 6.13e-11 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG024296 AT4G11080.1 57.609 460 162 7 10 464 11 442 3.33e-163 469
MsaG024296 AT4G23800.2 57.083 480 159 9 1 467 1 446 7.70e-161 463
MsaG024296 AT4G23800.1 56.875 480 166 8 1 467 1 452 5.76e-160 461
MsaG024296 AT3G51880.4 42.857 84 44 2 251 330 38 121 7.85e-12 63.9
MsaG024296 AT3G51880.5 42.857 84 44 2 251 330 38 121 1.12e-11 63.9
MsaG024296 AT3G51880.1 42.857 84 44 2 251 330 38 121 1.12e-11 63.9
MsaG024296 AT3G51880.3 42.857 84 44 2 251 330 38 121 1.12e-11 63.9
MsaG024296 AT3G51880.2 42.857 84 44 2 251 330 38 121 1.30e-11 63.9
MsaG024296 AT4G35570.1 38.824 85 49 2 251 332 20 104 4.71e-11 60.8
MsaG024296 AT4G35570.2 38.824 85 49 2 251 332 20 104 4.71e-11 60.8
MsaG024296 AT1G20696.2 35.294 119 72 2 260 375 30 146 9.22e-11 60.5

Find 102 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAAGGACATTTCAAACATTT+TGG 0.072036 4:+98029068 MsaT024296.1:CDS
CTTCATGTTTCTGAAGTTTC+AGG 0.139396 4:-98030068 None:intergenic
TTGCTTCAAGATCTCATCTT+TGG 0.243800 4:-98028515 None:intergenic
AAATCCAGAGGCAGAATTTA+AGG 0.251785 4:+98029050 MsaT024296.1:CDS
CTTGCAATTGCTCAAGAAAA+AGG 0.274473 4:+98030092 MsaT024296.1:CDS
CTTCTTCGGCATACATGTTA+TGG 0.283880 4:+98028875 MsaT024296.1:CDS
GTTTGTAAGCCTCCATTTCT+TGG 0.287307 4:-98029996 None:intergenic
CTTCCTCTTGATTTCTTTGT+CGG 0.303855 4:-98028259 None:intergenic
CCACTCTTCAGATGTGATCT+TGG 0.324738 4:-98029818 None:intergenic
TGCTCGAAAGATCGTTCCTT+TGG 0.352886 4:-98028418 None:intergenic
GCTTGGTATTTCTCCTCATA+AGG 0.353624 4:-98029129 None:intergenic
CATCCTCATATATTCTATTC+AGG 0.354033 4:+98030217 MsaT024296.1:CDS
AAAGCTGACATAGGATGCTT+TGG 0.369497 4:-98029333 None:intergenic
CAAATCTATTGTTGCAAAGC+TGG 0.374240 4:+98030614 MsaT024296.1:CDS
GTTAGACAGATTCTCAGAAA+TGG 0.376205 4:-98028356 None:intergenic
TTTAGATGGCTAAGAAGAAC+AGG 0.380697 4:+98029962 MsaT024296.1:intron
AGCTATGATGTTGGAATCAT+TGG 0.383362 4:-98028314 None:intergenic
TTTGTAAGCCTCCATTTCTT+GGG 0.388249 4:-98029995 None:intergenic
ATAGGATGCTTTGGTTTCAA+TGG 0.388725 4:-98029324 None:intergenic
CATAATTGTACCTCTTCATA+AGG 0.394411 4:-98029868 None:intergenic
TTCCTCTTGATTTCTTTGTC+GGG 0.407431 4:-98028258 None:intergenic
TTCTTCGGCATACATGTTAT+GGG 0.422963 4:+98028876 MsaT024296.1:CDS
TGCAGACAACAAGGGTGTCT+TGG 0.424980 4:+98029392 MsaT024296.1:CDS
ATGTCCTTAAATTCTGCCTC+TGG 0.426198 4:-98029054 None:intergenic
GCAAGATCTGCTTGAGATGC+AGG 0.431264 4:+98028438 MsaT024296.1:CDS
AGCATGTTTCCTCCAACTCC+TGG 0.432342 4:-98030367 None:intergenic
TTTGGCTTTCAACAGCTCTT+CGG 0.438123 4:-98028497 None:intergenic
ATGATTGGTGCAGGTTAAGA+AGG 0.440565 4:+98029026 MsaT024296.1:intron
AGAAGCAAGGAAGAGTATAC+TGG 0.445784 4:+98030336 MsaT024296.1:CDS
TGTTCCTTGTCTTTCACCAT+AGG 0.447107 4:-98028805 None:intergenic
TGATTTCTTTGTCGGGATCT+CGG 0.448117 4:-98028251 None:intergenic
AGATGAGATCTTGAAGCAAA+AGG 0.457726 4:+98028519 MsaT024296.1:CDS
AAAAGAATTCCGATCCAAAC+AGG 0.460635 4:+98030181 MsaT024296.1:CDS
GGATGCATACAAGAAGGAAA+TGG 0.463280 4:+98030581 MsaT024296.1:CDS
AATGATTCCAACATCATAGC+TGG 0.469777 4:+98028316 MsaT024296.1:CDS
GGAGCAATATGCCCAAGAAA+TGG 0.469866 4:+98029984 MsaT024296.1:CDS
GCTTGAGATGCAGGAAAAGA+TGG 0.475770 4:+98028447 MsaT024296.1:CDS
TTAGACAGATTCTCAGAAAT+GGG 0.478209 4:-98028355 None:intergenic
ACACACTTGTTTCAATGAAG+TGG 0.480362 4:+98030392 MsaT024296.1:CDS
GAATCTGTCTAACCCTAAGA+AGG 0.489907 4:+98028366 MsaT024296.1:CDS
TCACCTGAATAGAATATATG+AGG 0.495351 4:-98030220 None:intergenic
ATGTTGGAATCATTGGTTGA+TGG 0.499815 4:-98028307 None:intergenic
CAAAGTCAATTATTACTCGT+TGG 0.500645 4:-98030646 None:intergenic
AGACAAGGAACAAGAAAAGA+AGG 0.503199 4:+98028816 MsaT024296.1:CDS
AGTATACTGGAGGAACGTCC+AGG 0.504758 4:+98030349 MsaT024296.1:CDS
CAATGTACAGAATTTGCCTA+TGG 0.505456 4:+98028789 MsaT024296.1:intron
AATTGAGGCAATGAAACTCT+TGG 0.505662 4:+98029197 MsaT024296.1:CDS
AGGAAGCAGAAAGGCTCTCA+AGG 0.506919 4:+98028276 MsaT024296.1:CDS
TGTTGGAATCATTGGTTGAT+GGG 0.514270 4:-98028306 None:intergenic
CTGGAGGAACGTCCAGGAGT+TGG 0.521217 4:+98030355 MsaT024296.1:CDS
CATAACATGTATGCCGAAGA+AGG 0.530436 4:-98028874 None:intergenic
TCTTGTTTACTAATGATAGG+AGG 0.532413 4:+98029358 MsaT024296.1:CDS
CAAGAAGAACAAGAAAGAGA+AGG 0.537336 4:+98029299 MsaT024296.1:CDS
TGCAAATCTTATGAAGGAAG+AGG 0.537954 4:+98030038 MsaT024296.1:CDS
GAGGAACGTCCAGGAGTTGG+AGG 0.538510 4:+98030358 MsaT024296.1:CDS
TGTTATGGGTCAAAGATCAA+TGG 0.542670 4:+98028890 MsaT024296.1:CDS
ATGATTCCAACATCATAGCT+GGG 0.548826 4:+98028317 MsaT024296.1:CDS
GGCAATGAAACTCTTGGAAG+AGG 0.550214 4:+98029203 MsaT024296.1:CDS
TGGCAAAGCATCTGAAGCAA+TGG 0.552222 4:+98030560 MsaT024296.1:CDS
CTTCGGTCTTCTCTTTCTCG+AGG 0.553334 4:-98028480 None:intergenic
AGCTATTCTTGCAGACAACA+AGG 0.554530 4:+98029383 MsaT024296.1:CDS
AATAGAATATATGAGGATGC+AGG 0.554919 4:-98030213 None:intergenic
CTTGTTTACTAATGATAGGA+GGG 0.555181 4:+98029359 MsaT024296.1:CDS
GTTGGAATCATTGGTTGATG+GGG 0.557105 4:-98028305 None:intergenic
GTTTATGCAATTCAAACAAG+AGG 0.559702 4:+98029263 MsaT024296.1:CDS
GTGAGGAAGATAAACAATTG+TGG 0.559951 4:+98030535 MsaT024296.1:CDS
GGGACTAAATGGAAGACAGT+TGG 0.560896 4:+98029090 MsaT024296.1:CDS
GAAGATAAACAATTGTGGAA+TGG 0.568238 4:+98030540 MsaT024296.1:CDS
AAAGAAACAACAAAAGCCAA+AGG 0.574463 4:+98028402 MsaT024296.1:CDS
AGAAGAGAAGAAGCCTTATG+AGG 0.578854 4:+98029116 MsaT024296.1:CDS
ATCCCGACAAAGAAATCAAG+AGG 0.579809 4:+98028256 MsaT024296.1:CDS
ATGAACTAACTAACCATGGT+GGG 0.581194 4:-98028604 None:intergenic
ACAGAAGCAGAAGACTGCTA+TGG 0.587399 4:+98029227 MsaT024296.1:CDS
GAAATCAAGAGGAAGCAGAA+AGG 0.590805 4:+98028267 MsaT024296.1:CDS
CCAAGATCACATCTGAAGAG+TGG 0.592813 4:+98029818 MsaT024296.1:CDS
GGAGGCTGCAAATCTTATGA+AGG 0.596196 4:+98030032 MsaT024296.1:CDS
TGCCTCCCCAGCTATGATGT+TGG 0.596788 4:-98028323 None:intergenic
AGCAATGGATGCATACAAGA+AGG 0.597525 4:+98030575 MsaT024296.1:CDS
AGACAACAAGGGTGTCTTGG+AGG 0.604107 4:+98029395 MsaT024296.1:CDS
TGCATACAAGAAGGAAATGG+AGG 0.608817 4:+98030584 MsaT024296.1:CDS
TTCCATGCAGCAAAGAAGCA+AGG 0.615026 4:+98030323 MsaT024296.1:intron
GAAAGAATTCAAACCCACCA+TGG 0.617162 4:+98028591 MsaT024296.1:CDS
CGGGATCTCGGCAACTACGT+CGG 0.621564 4:-98028239 None:intergenic
ACTTGTTTCAATGAAGTGGA+AGG 0.625574 4:+98030396 MsaT024296.1:CDS
AATCTGTCTAACCCTAAGAA+GGG 0.626603 4:+98028367 MsaT024296.1:CDS
CAAACTGAAGAAAGATGAGG+AGG 0.628380 4:+98030014 MsaT024296.1:CDS
TTATTTGCAAGTAATTACAA+AGG 0.633815 4:+98029164 MsaT024296.1:CDS
TTACAAACTGAAGAAAGATG+AGG 0.634789 4:+98030011 MsaT024296.1:CDS
GCAATATGCCCAAGAAATGG+AGG 0.637518 4:+98029987 MsaT024296.1:CDS
AGCAAGGAAGAGTATACTGG+AGG 0.646246 4:+98030339 MsaT024296.1:CDS
AATGAACTAACTAACCATGG+TGG 0.650169 4:-98028605 None:intergenic
ATTTATATAGGATATGAGTG+AGG 0.652499 4:+98030518 MsaT024296.1:intron
GATGAAGAACTCGAGAATCG+TGG 0.659301 4:+98028541 MsaT024296.1:CDS
TTTGCCTATGGTGAAAGACA+AGG 0.660185 4:+98028801 MsaT024296.1:CDS
GGTCAAAGATCAATGGCATG+AGG 0.662193 4:+98028897 MsaT024296.1:CDS
TTCCAACATCATAGCTGGGG+AGG 0.663327 4:+98028321 MsaT024296.1:CDS
GGTTAAGAAGGAAAATCCAG+AGG 0.669344 4:+98029038 MsaT024296.1:intron
TGATTCCAACATCATAGCTG+GGG 0.673997 4:+98028318 MsaT024296.1:CDS
AGAACTCGAGAATCGTGGCA+AGG 0.678863 4:+98028546 MsaT024296.1:CDS
GCTATTCTTGCAGACAACAA+GGG 0.690298 4:+98029384 MsaT024296.1:CDS
TTAGATGGCTAAGAAGAACA+GGG 0.692791 4:+98029963 MsaT024296.1:intron
TCAGAAGAAGAAACATAACA+AGG 0.711427 4:+98030155 MsaT024296.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr4 gene 98028235 98030656 98028235 ID=MsaG024296
Chr4 mRNA 98028235 98030656 98028235 ID=MsaT024296.1;Parent=MsaG024296
Chr4 exon 98028235 98028612 98028235 ID=MsaT024296.1.exon1;Parent=MsaT024296.1
Chr4 CDS 98028235 98028612 98028235 ID=cds.MsaT024296.1;Parent=MsaT024296.1
Chr4 exon 98028799 98028918 98028799 ID=MsaT024296.1.exon2;Parent=MsaT024296.1
Chr4 CDS 98028799 98028918 98028799 ID=cds.MsaT024296.1;Parent=MsaT024296.1
Chr4 exon 98029039 98029416 98029039 ID=MsaT024296.1.exon3;Parent=MsaT024296.1
Chr4 CDS 98029039 98029416 98029039 ID=cds.MsaT024296.1;Parent=MsaT024296.1
Chr4 exon 98029814 98029879 98029814 ID=MsaT024296.1.exon4;Parent=MsaT024296.1
Chr4 CDS 98029814 98029879 98029814 ID=cds.MsaT024296.1;Parent=MsaT024296.1
Chr4 exon 98029967 98030238 98029967 ID=MsaT024296.1.exon5;Parent=MsaT024296.1
Chr4 CDS 98029967 98030238 98029967 ID=cds.MsaT024296.1;Parent=MsaT024296.1
Chr4 exon 98030333 98030417 98030333 ID=MsaT024296.1.exon6;Parent=MsaT024296.1
Chr4 CDS 98030333 98030417 98030333 ID=cds.MsaT024296.1;Parent=MsaT024296.1
Chr4 exon 98030528 98030656 98030528 ID=MsaT024296.1.exon7;Parent=MsaT024296.1
Chr4 CDS 98030528 98030656 98030528 ID=cds.MsaT024296.1;Parent=MsaT024296.1
Gene Sequence

>MsaT024296.1

ATGGCCGACGTAGTTGCCGAGATCCCGACAAAGAAATCAAGAGGAAGCAGAAAGGCTCTCAAGGAGAAAACCCCATCAACCAATGATTCCAACATCATAGCTGGGGAGGCAGCTATTTCTCCCATTTCTGAGAATCTGTCTAACCCTAAGAAGGGAAAAGCTGCATCAAAGAAACAACAAAAGCCAAAGGAACGATCTTTCGAGCAAGATCTGCTTGAGATGCAGGAAAAGATGGAGCAGTTGCGCCTCGAGAAAGAGAAGACCGAAGAGCTGTTGAAAGCCAAAGATGAGATCTTGAAGCAAAAGGATGAAGAACTCGAGAATCGTGGCAAGGAGCTTAAGAAATTGCAGAAATTGAAAGAATTCAAACCCACCATGAATTTGCCTATGGTGAAAGACAAGGAACAAGAAAAGAAGGAAAAGAAAAAGAATGGGTGCCCTGAGAAAAAAAGGCCTTCTTCGGCATACATGTTATGGGTCAAAGATCAATGGCATGAGGTTAAGAAGGAAAATCCAGAGGCAGAATTTAAGGACATTTCAAACATTTTGGGGACTAAATGGAAGACAGTTGGTGAAGAAGAGAAGAAGCCTTATGAGGAGAAATACCAAGCTGAAAAAGAGGCTTATTTGCAAGTAATTACAAAGGAAAAACGTGAAATTGAGGCAATGAAACTCTTGGAAGAGGAACAGAAGCAGAAGACTGCTATGGAATTACTTGAACAGTTTATGCAATTCAAACAAGAGGCAGAAAAAGAGAGCAAGAAGAACAAGAAAGAGAAGGATCCATTGAAACCAAAGCATCCTATGTCAGCTTTTTTCTTGTTTACTAATGATAGGAGGGCAGCTATTCTTGCAGACAACAAGGGTGTCTTGGAGGTTTCCAAGATCACATCTGAAGAGTGGAAAAACATGACAGAAGAACAAAAAAGGCCTTATGAAGAGATGGCTAAGAAGAACAGGGAGCAATATGCCCAAGAAATGGAGGCTTACAAACTGAAGAAAGATGAGGAGGCTGCAAATCTTATGAAGGAAGAGGAAGAACACCTGAAACTTCAGAAACATGAAGCCTTGCAATTGCTCAAGAAAAAGGAAAAAACTGAAAACATGATCAAGGAAACAAAATTGAATCGTCAGAAGAAGAAACATAACAAGGAAGAAAAGAATTCCGATCCAAACAGGCCTAAAAGACCTGCATCCTCATATATTCTATTCAGCAAAGAAGCAAGGAAGAGTATACTGGAGGAACGTCCAGGAGTTGGAGGAAACATGCTTAACACACTTGTTTCAATGAAGTGGAAGGATATGAGTGAGGAAGATAAACAATTGTGGAATGGCAAAGCATCTGAAGCAATGGATGCATACAAGAAGGAAATGGAGGAATACAACAAATCTATTGTTGCAAAGCTGGAGCAGAAAACCAACGAGTAA
Protein sequence

>MsaT024296.1

MADVVAEIPTKKSRGSRKALKEKTPSTNDSNIIAGEAAISPISENLSNPKKGKAASKKQQKPKERSFEQDLLEMQEKMEQLRLEKEKTEELLKAKDEILKQKDEELENRGKELKKLQKLKEFKPTMNLPMVKDKEQEKKEKKKNGCPEKKRPSSAYMLWVKDQWHEVKKENPEAEFKDISNILGTKWKTVGEEEKKPYEEKYQAEKEAYLQVITKEKREIEAMKLLEEEQKQKTAMELLEQFMQFKQEAEKESKKNKKEKDPLKPKHPMSAFFLFTNDRRAAILADNKGVLEVSKITSEEWKNMTEEQKRPYEEMAKKNREQYAQEMEAYKLKKDEEAANLMKEEEEHLKLQKHEALQLLKKKEKTENMIKETKLNRQKKKHNKEEKNSDPNRPKRPASSYILFSKEARKSILEERPGVGGNMLNTLVSMKWKDMSEEDKQLWNGKASEAMDAYKKEMEEYNKSIVAKLEQKTNE*