AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG020410

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG020410 MtrunA17_Chr4g0025061 71.078 529 108 7 7 506 99 611 0.0 672
MsaG020410 MtrunA17_Chr4g0025051 73.092 498 102 4 7 477 75 567 0.0 645
MsaG020410 MtrunA17_Chr4g0024391 69.495 495 117 5 39 506 1 488 0.0 620
MsaG020410 MtrunA17_Chr2g0322391 40.338 533 209 19 11 506 142 602 1.87e-77 254
MsaG020410 MtrunA17_Chr2g0288871 40.896 357 134 11 167 460 192 534 5.48e-48 174
MsaG020410 MtrunA17_Chr4g0075201 50.667 225 78 6 247 443 245 464 1.92e-47 171
MsaG020410 MtrunA17_Chr3g0099641 26.991 452 204 12 34 455 89 444 5.95e-35 136
MsaG020410 MtrunA17_Chr7g0270831 40.816 245 81 8 254 465 201 414 3.38e-33 130
MsaG020410 MtrunA17_Chr2g0302391 36.735 196 90 4 240 402 182 376 2.48e-24 105
MsaG020410 MtrunA17_Chr7g0216891 27.778 342 150 10 226 478 170 503 4.45e-19 90.5
MsaG020410 MtrunA17_Chr4g0051181 44.762 105 34 1 254 334 228 332 3.22e-14 75.1
MsaG020410 MtrunA17_Chr4g0060271 40.506 158 49 4 249 365 235 388 1.09e-12 70.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG020410 AT4G04450.2 50.628 239 81 5 248 455 177 409 7.89e-52 182
MsaG020410 AT4G04450.1 50.840 238 80 5 249 455 272 503 2.07e-51 183
MsaG020410 AT1G62300.1 44.841 252 97 6 248 458 291 541 2.63e-42 159
MsaG020410 AT4G22070.4 48.963 241 86 5 249 455 277 514 2.05e-36 142
MsaG020410 AT4G22070.3 48.963 241 86 5 249 455 277 514 2.05e-36 142
MsaG020410 AT4G22070.2 48.963 241 86 5 249 455 277 514 2.05e-36 142
MsaG020410 AT4G22070.1 48.963 241 86 5 249 455 277 514 2.05e-36 142
MsaG020410 AT4G01720.1 36.735 245 84 10 254 452 224 443 8.03e-23 102
MsaG020410 AT1G69810.1 38.554 166 71 5 240 380 174 333 4.53e-18 86.7
MsaG020410 AT1G69810.2 39.521 167 68 6 240 380 116 275 5.13e-18 85.5
MsaG020410 AT1G68150.1 35.526 152 60 3 213 326 165 316 1.79e-17 84.7
MsaG020410 AT5G15130.2 47.778 90 23 1 254 319 170 259 1.11e-16 83.2
MsaG020410 AT5G15130.1 47.778 90 23 1 254 319 212 301 1.21e-16 83.2
MsaG020410 AT1G18860.1 33.333 213 95 6 198 374 173 374 3.75e-13 72.0

Find 93 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAAGTTTCTGATGGAAAATT+TGG 0.138864 4:-51328391 MsaT020410.1:CDS
GACAAAGATGCAAGAAAATT+TGG 0.170415 4:+51326353 None:intergenic
TCAAAACTCTGAGAGATTAA+AGG 0.182717 4:+51326527 None:intergenic
CTTTAACTTCCTTAAACTTA+TGG 0.217911 4:+51328530 None:intergenic
CCTAACTGGTCCTGACTTCT+AGG 0.238769 4:+51328127 None:intergenic
GGGTTCCTTTGTGGAGTATT+TGG 0.246074 4:+51326566 None:intergenic
GATGCTAGACCATAAGTTTA+AGG 0.248841 4:-51328539 MsaT020410.1:CDS
ATTAAGGTTAAGGAAGTTAA+AGG 0.251785 4:-51328298 MsaT020410.1:CDS
CCTGCTCTTACTTCCATTAT+TGG 0.259720 4:-51326329 MsaT020410.1:CDS
TGCTAGATTGACTACTATTA+AGG 0.263757 4:-51328314 MsaT020410.1:CDS
CATAAGTTTAAGGAAGTTAA+AGG 0.270958 4:-51328529 MsaT020410.1:CDS
TTAACTGCCCGAGCAATATT+TGG 0.271031 4:+51326395 None:intergenic
ACTGAGAATGGTGGAGTATT+GGG 0.286055 4:-51328466 MsaT020410.1:CDS
GTCTTGTTGTCTTCTGAATT+AGG 0.286460 4:+51329822 None:intergenic
CGAGCTTGAACGAAAGAAAA+TGG 0.321409 4:-51328638 MsaT020410.1:CDS
AATAAGGTTAAGGAAGTTAA+AGG 0.322766 4:-51328415 MsaT020410.1:CDS
AAAGGAGTTTGAAACTGATC+TGG 0.348918 4:+51326545 None:intergenic
AACTGATCTGGGTTCCTTTG+TGG 0.354361 4:+51326557 None:intergenic
TCTTGGATCGACTACTAATA+AGG 0.363882 4:-51328431 MsaT020410.1:CDS
ATTGACTACTATTAAGGTTA+AGG 0.375603 4:-51328308 MsaT020410.1:CDS
TGGAAAATTTAAAGAGAAAG+AGG 0.376076 4:-51328491 MsaT020410.1:CDS
GCTTCTACTGATAATAATAA+TGG 0.377183 4:-51326281 MsaT020410.1:CDS
TCAACAGCTTGGTCCCATTC+CGG 0.379544 4:-51329895 MsaT020410.1:intron
AAAGGAAAAGAATTCTTTGC+TGG 0.388151 4:-51328511 MsaT020410.1:CDS
TTTCAGATGGCTATTCTTCA+AGG 0.408471 4:-51328661 MsaT020410.1:intron
AACTGAGAATGGTGGAGTAT+TGG 0.409551 4:-51328467 MsaT020410.1:CDS
AGCTAGATCAGAAGAAACTA+TGG 0.417776 4:-51327990 MsaT020410.1:intron
CTTTGGCTGCAGTAGGTAAA+GGG 0.427084 4:+51326768 None:intergenic
CTACTAGTATTGGTAGTAAC+CGG 0.438929 4:+51329876 None:intergenic
ACCTACTGCAGCCAAAGAAA+TGG 0.440244 4:-51326762 MsaT020410.1:CDS
TAACATCTGCATTCTTACTA+AGG 0.441748 4:+51328062 None:intergenic
TCTTTGGCTGCAGTAGGTAA+AGG 0.441950 4:+51326767 None:intergenic
ATCGACTACTAATAAGGTTA+AGG 0.442162 4:-51328425 MsaT020410.1:CDS
TGCCTGAGTATGACCAATAA+TGG 0.460348 4:+51326316 None:intergenic
CCTAGAAGTCAGGACCAGTT+AGG 0.461756 4:-51328127 MsaT020410.1:CDS
GAGAAAGAGGGAACTGAGAA+TGG 0.465364 4:-51328478 MsaT020410.1:CDS
CAAGGAAAGAGTGTTCTTGC+GGG 0.472692 4:+51326659 None:intergenic
GCTATCATTGTGATTTCCTT+CGG 0.473387 4:+51326247 None:intergenic
ACAAGATCTTTGCATTGCCT+TGG 0.476445 4:+51328211 None:intergenic
TGGTTGCTCAGTCCGAAAAC+AGG 0.478137 4:-51327781 MsaT020410.1:intron
AATGAGAAAACCTAGAAGTC+AGG 0.488123 4:-51328137 MsaT020410.1:CDS
GTATAATCAAGTGTAATAGT+TGG 0.498502 4:+51326596 None:intergenic
TTGGGGCCGAGGAAAGATCT+TGG 0.508825 4:-51328448 MsaT020410.1:CDS
ATGGTGGAGAATCAATGAAA+AGG 0.509688 4:-51328348 MsaT020410.1:CDS
ATTGTAATCACAACTTATGA+AGG 0.509853 4:-51326803 MsaT020410.1:CDS
AAGCATCGAGGTTGCTTCGA+AGG 0.510775 4:-51328092 MsaT020410.1:CDS
AAAGAGGGAACTGAGAATGG+TGG 0.516698 4:-51328475 MsaT020410.1:CDS
TAGCAGTACCAAATATTGCT+CGG 0.517614 4:-51326403 MsaT020410.1:CDS
TTCCATTATTGGTCATACTC+AGG 0.517830 4:-51326318 MsaT020410.1:CDS
AAGGAGTTTGAAACTGATCT+GGG 0.518182 4:+51326546 None:intergenic
GTAATAGTTGGAAACGAAGC+AGG 0.518849 4:+51326608 None:intergenic
TAGTAGTGATCAATCTATGA+TGG 0.520634 4:-51329859 MsaT020410.1:CDS
TAATAACATTACCTCCCTCT+TGG 0.525706 4:+51329800 None:intergenic
GTTAAAGGACAAGTTTCTGA+TGG 0.527289 4:-51328400 MsaT020410.1:CDS
AAAATTTGGATTAGCAGCAA+TGG 0.542627 4:+51326367 None:intergenic
GTATTGGTAGTAACCGGAAT+GGG 0.543800 4:+51329882 None:intergenic
AGCAGTACCAAATATTGCTC+GGG 0.548717 4:-51326402 MsaT020410.1:CDS
GGTACTGCTAATAATTGTGA+AGG 0.548903 4:+51326416 None:intergenic
AGATTGATCACTACTAGTAT+TGG 0.549551 4:+51329866 None:intergenic
CAGAAGACAACAAGACCAAG+AGG 0.560043 4:-51329815 MsaT020410.1:CDS
AATAACAATGGTAATATCAC+AGG 0.561708 4:-51326203 MsaT020410.1:CDS
TATCGTTGCAGCATGGCCCA+TGG 0.571602 4:-51327801 MsaT020410.1:CDS
CCAATAATGGAAGTAAGAGC+AGG 0.573308 4:+51326329 None:intergenic
ATGGTGGAGTATTGGGGCCG+AGG 0.574560 4:-51328459 MsaT020410.1:CDS
TAGCAACACTAATGATCAGA+AGG 0.581418 4:-51326180 MsaT020410.1:CDS
GCCATTTCTTTGGCTGCAGT+AGG 0.583103 4:+51326761 None:intergenic
GGAAAATTTAAAGAGAAAGA+GGG 0.583274 4:-51328490 MsaT020410.1:CDS
AGCAACAATAATGTCACAGA+AGG 0.584455 4:-51326227 MsaT020410.1:CDS
ACAAGGAAAGAGTGTTCTTG+CGG 0.592338 4:+51326658 None:intergenic
GTACTGCTAATAATTGTGAA+GGG 0.593217 4:+51326417 None:intergenic
ATGGTGGAGAGTTGGTGCCA+AGG 0.595504 4:-51328228 MsaT020410.1:CDS
CTGAGAATGGTGGAGTATTG+GGG 0.595747 4:-51328465 MsaT020410.1:CDS
TTCAAACTTAATAGGTACAA+AGG 0.595754 4:-51326844 MsaT020410.1:intron
GTCGATCCAAGATCTTTCCT+CGG 0.596268 4:+51328442 None:intergenic
AGTATTGGTAGTAACCGGAA+TGG 0.599485 4:+51329881 None:intergenic
GCATCAACATCAAGCAATGG+TGG 0.602123 4:-51326701 MsaT020410.1:CDS
ACTTGAGAATGGTGGAGAGT+TGG 0.607530 4:-51328236 MsaT020410.1:CDS
ATTAACTAGAGTTGAAGCCA+TGG 0.607847 4:+51330346 None:intergenic
TTGAGGGATCAAAGAAGCTG+AGG 0.622461 4:+51326499 None:intergenic
AAGTCAGGACCAGTTAGGAT+CGG 0.622675 4:-51328122 MsaT020410.1:CDS
AATGGCAACAATGTCACCGA+AGG 0.626879 4:-51326263 MsaT020410.1:CDS
TGGCTGCAGTAGGTAAAGGG+TGG 0.628113 4:+51326771 None:intergenic
ATCTTAGTATCGTTGCAGCA+TGG 0.634470 4:-51327808 MsaT020410.1:intron
GTCACAGAAGGCAATAACAA+TGG 0.641704 4:-51326215 MsaT020410.1:CDS
TCAGCATCAACATCAAGCAA+TGG 0.645156 4:-51326704 MsaT020410.1:CDS
AGACAACAAGACCAAGAGGG+AGG 0.676991 4:-51329811 MsaT020410.1:intron
AATCTCCAAATACTCCACAA+AGG 0.678231 4:-51326571 MsaT020410.1:CDS
AGAAGACAACAAGACCAAGA+GGG 0.683090 4:-51329814 MsaT020410.1:CDS
GTTGAAATACTTGAAGAACA+AGG 0.687606 4:+51326641 None:intergenic
TTTCTCGAAACACATCCGCA+TGG 0.694478 4:+51328564 None:intergenic
TGATAATGTTGAGACAACAT+TGG 0.697860 4:-51328035 MsaT020410.1:CDS
GAACAGATTACAATACCATG+CGG 0.758838 4:-51328579 MsaT020410.1:CDS
ATCGGCGATGAAAAGCATCG+AGG 0.778036 4:-51328104 MsaT020410.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr4 gene 51326175 51330366 51326175 ID=MsaG020410
Chr4 mRNA 51326175 51330366 51326175 ID=MsaT020410.1;Parent=MsaG020410
Chr4 exon 51326175 51326852 51326175 ID=MsaT020410.1.exon5;Parent=MsaT020410.1
Chr4 CDS 51326175 51326852 51326175 ID=cds.MsaT020410.1;Parent=MsaT020410.1
Chr4 exon 51327782 51327823 51327782 ID=MsaT020410.1.exon4;Parent=MsaT020410.1
Chr4 CDS 51327782 51327823 51327782 ID=cds.MsaT020410.1;Parent=MsaT020410.1
Chr4 exon 51327991 51328677 51327991 ID=MsaT020410.1.exon3;Parent=MsaT020410.1
Chr4 CDS 51327991 51328677 51327991 ID=cds.MsaT020410.1;Parent=MsaT020410.1
Chr4 exon 51329812 51329910 51329812 ID=MsaT020410.1.exon2;Parent=MsaT020410.1
Chr4 CDS 51329812 51329910 51329812 ID=cds.MsaT020410.1;Parent=MsaT020410.1
Chr4 exon 51330352 51330366 51330352 ID=MsaT020410.1.exon1;Parent=MsaT020410.1
Chr4 CDS 51330352 51330366 51330352 ID=cds.MsaT020410.1;Parent=MsaT020410.1
Gene Sequence

>MsaT020410.1

ATGGCTTCAACTCTACTTGGTCCCATTCCGGTTACTACCAATACTAGTAGTGATCAATCTATGATGGATGATTGCATTCTACCTAATTCAGAAGACAACAAGACCAAGAGGGAGATGGCTATTCTTCAAGGCGAGCTTGAACGAAAGAAAATGGAGAACTGTAGATTAAAATTGATGTATGATCAACTTAGAACAGATTACAATACCATGCGGATGTGTTTCGAGAAAGTGATGCTAGACCATAAGTTTAAGGAAGTTAAAGGAAAAGAATTCTTTGCTGGAAAATTTAAAGAGAAAGAGGGAACTGAGAATGGTGGAGTATTGGGGCCGAGGAAAGATCTTGGATCGACTACTAATAAGGTTAAGGAAGTTAAAGGACAAGTTTCTGATGGAAAATTTGGACACAAAAAGAGAATAAAGAATGGTGGAGAATCAATGAAAAGGAAATTTGTTGATGCTAGATTGACTACTATTAAGGTTAAGGAAGTTAAAGGAAAAGAAGTTTTTAATGGAAAATGTGACAAGAAAAAGAGACTTGAGAATGGTGGAGAGTTGGTGCCAAGGCAATGCAAAGATCTTGTGTTGCTTACTAATGCTGAGACTGCGATAGATCATGAAGCTTGTTCCTCATCAATGAGAAAACCTAGAAGTCAGGACCAGTTAGGATCGGCGATGAAAAGCATCGAGGTTGCTTCGAAGGAGTTAGTCCTTAGTAAGAATGCAGATGTTAATGTTGATAATGTTGAGACAACATTGGTGAAAGCAAGAGTTTCTATTAGAGCTAGATCAGAAGAAACTATGTATCGTTGCAGCATGGCCCATGGTTGCTCAGTCCGAAAACAGGTACAAAGGTGTGCTCTTGACAGAACAATTGTAATCACAACTTATGAAGGAAATCACAGCCACCCTTTACCTACTGCAGCCAAAGAAATGGCAAAAACAACTTCAGCAGCTGCAAAGATGCTTCTTTCAGCATCAACATCAAGCAATGGTGGACAATTTAATGAAAATTTACCCGCAAGAACACTCTTTCCTTGTTCTTCAAGTATTTCAACTATCTCAGCTCCTGCTTCGTTTCCAACTATTACACTTGATTATACTCAATCTCCAAATACTCCACAAAGGAACCCAGATCAGTTTCAAACTCCTTTAATCTCTCAGAGTTTTGAAAATTCCTCAGCTTCTTTGATCCCTCAAATACCTAATCAAAACCAATCAAAATTTTCTGGACTACAAATGTCAAAATATGCAGCTAGCCCTTCACAATTATTAGCAGTACCAAATATTGCTCGGGCAGTTAATGCTGCCATTGCTGCTAATCCAAATTTTCTTGCATCTTTGTCACCTGCTCTTACTTCCATTATTGGTCATACTCAGGCAAACAACAACACTGCTTCTACTGATAATAATAATGGCAACAATGTCACCGAAGGAAATCACAATGATAGCAACAATAATGTCACAGAAGGCAATAACAATGGTAATATCACAGGTAGCAACACTAATGATCAGAAGGAATAA
Protein sequence

>MsaT020410.1

MASTLLGPIPVTTNTSSDQSMMDDCILPNSEDNKTKREMAILQGELERKKMENCRLKLMYDQLRTDYNTMRMCFEKVMLDHKFKEVKGKEFFAGKFKEKEGTENGGVLGPRKDLGSTTNKVKEVKGQVSDGKFGHKKRIKNGGESMKRKFVDARLTTIKVKEVKGKEVFNGKCDKKKRLENGGELVPRQCKDLVLLTNAETAIDHEACSSSMRKPRSQDQLGSAMKSIEVASKELVLSKNADVNVDNVETTLVKARVSIRARSEETMYRCSMAHGCSVRKQVQRCALDRTIVITTYEGNHSHPLPTAAKEMAKTTSAAAKMLLSASTSSNGGQFNENLPARTLFPCSSSISTISAPASFPTITLDYTQSPNTPQRNPDQFQTPLISQSFENSSASLIPQIPNQNQSKFSGLQMSKYAASPSQLLAVPNIARAVNAAIAANPNFLASLSPALTSIIGHTQANNNTASTDNNNGNNVTEGNHNDSNNNVTEGNNNGNITGSNTNDQKE*