AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG043078

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG043078 MtrunA17_Chr8g0360221 98.933 375 4 0 1 375 1 375 0.0 776
MsaG043078 MtrunA17_Chr3g0140441 40.076 262 125 4 1 260 1 232 5.61e-65 206
MsaG043078 MtrunA17_Chr8g0340501 38.372 258 148 3 1 258 1 247 9.18e-50 168
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG043078 AT3G18380.1 69.637 303 76 5 1 287 1 303 2.81e-152 433
MsaG043078 AT3G18380.2 69.408 304 76 6 1 287 1 304 1.79e-150 429
MsaG043078 AT3G18380.3 69.435 301 78 6 1 287 1 301 9.45e-150 427
MsaG043078 AT1G15215.2 43.725 247 135 2 14 259 14 257 1.83e-63 204
MsaG043078 AT1G15215.4 42.979 235 128 3 14 246 14 244 1.17e-56 186
MsaG043078 AT1G15215.3 42.979 235 128 3 14 246 14 244 1.79e-56 185
MsaG043078 AT1G15215.1 35.256 156 92 4 14 167 14 162 9.99e-19 82.8

Find 90 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTTGAGTCATTATCCTTCC+TGG 0.211207 8:-34999629 None:intergenic
GAAGGCGGGGCCTCCGTTAC+TGG 0.217756 8:-34997376 None:intergenic
TGTAATCTGTAATCAGTTTC+AGG 0.218700 8:-35004464 None:intergenic
GAAACATTTGTTTGCAAAAC+AGG 0.257239 8:-35004635 None:intergenic
AAAATAAGCGATATGCTATA+AGG 0.259455 8:+34999543 MsaT043078.1:CDS
GTTCCTGCTCCTTCAGCTTC+AGG 0.261491 8:+34999665 MsaT043078.1:CDS
AAGCACTTGCAGACAAGTTT+AGG 0.288349 8:+34999283 MsaT043078.1:CDS
GGCGTGATATTTAACTTTGC+AGG 0.330713 8:-34999584 None:intergenic
CTTTCTATCATACAGACATT+TGG 0.352765 8:+35002402 MsaT043078.1:CDS
ATGGAATTTGAAGCTAAATC+TGG 0.358674 8:+35002257 MsaT043078.1:CDS
CTCGCACCATGAACATTTGC+TGG 0.369463 8:-35004548 None:intergenic
TTTCATTGCAGGTATGGAAT+TGG 0.369862 8:+34999516 MsaT043078.1:intron
GTTGAGTCATTATCCTTCCT+GGG 0.392666 8:-34999628 None:intergenic
CCAGTGAATGCGGCGGTGCT+TGG 0.419350 8:-35004737 None:intergenic
ATCTGTATAGGTAACAGAAA+TGG 0.427116 8:+34999209 MsaT043078.1:intron
GGATCCACATTCATACTTTG+TGG 0.428698 8:-35004665 None:intergenic
AAATAAGCGATATGCTATAA+GGG 0.442347 8:+34999544 MsaT043078.1:CDS
CCAAGCACCGCCGCATTCAC+TGG 0.450582 8:+35004737 MsaT043078.1:CDS
GGCTGAGTGAAACGGAAGGC+GGG 0.454503 8:-34997390 None:intergenic
GGTTACTAATCCTTCTGAAA+TGG 0.459416 8:+35004571 MsaT043078.1:CDS
TGTAATCTTGCCTTTACGAT+CGG 0.459596 8:-34999415 None:intergenic
CGCAATCTTCTGCTGATCCG+TGG 0.463686 8:-35004516 None:intergenic
GAAGCTGAAGGAGCAGGAAC+AGG 0.470238 8:-34999662 None:intergenic
GTAATCTTGCCTTTACGATC+GGG 0.473723 8:-34999414 None:intergenic
GTCTTTGAGCATCAAGGACA+TGG 0.475882 8:-35003216 None:intergenic
ATATTCAAGTTACTTCCCTT+CGG 0.477909 8:-35004807 None:intergenic
ACAAAAGCTGTTGTTCAAGC+TGG 0.478601 8:+35004701 MsaT043078.1:CDS
GACATGGGCATCAAAGTAAA+GGG 0.481099 8:-35003200 None:intergenic
CAAATGTCTGTATGATAGAA+AGG 0.481293 8:-35002401 None:intergenic
GTCAAATCAGTCCGAGGCAT+GGG 0.481986 8:-34999605 None:intergenic
GATCATCCAGCAAATGTTCA+TGG 0.483799 8:+35004542 MsaT043078.1:CDS
CGGGGCCTCCGTTACTGGGT+GGG 0.497571 8:-34997371 None:intergenic
GATTACAGTACAGATGAAAC+AGG 0.498566 8:+34999431 MsaT043078.1:CDS
GGACATGGGCATCAAAGTAA+AGG 0.499318 8:-35003201 None:intergenic
GCCAGGAAATCGTGCCGCTT+AGG 0.503677 8:+35004426 MsaT043078.1:intron
AAGGCGGGGCCTCCGTTACT+GGG 0.508017 8:-34997375 None:intergenic
CTACCTGAAGCTGAAGGAGC+AGG 0.516322 8:-34999668 None:intergenic
GAAGCTAAATCTGGAAGAGA+TGG 0.517358 8:+35002266 MsaT043078.1:CDS
CCTCGGACTGATTTGACCCC+AGG 0.520581 8:+34999611 MsaT043078.1:CDS
CAAGTTACTTCCCTTCGGCC+AGG 0.523928 8:-35004802 None:intergenic
ATACCTCGGGCTGAGTGAAA+CGG 0.535015 8:-34997398 None:intergenic
ACATTTGGAGAGCAGTGATC+CGG 0.538548 8:+35002417 MsaT043078.1:CDS
AGACGGAGGCATGATGTAAG+AGG 0.539794 8:+35003235 MsaT043078.1:CDS
TAAATATCACGCCCATGCCT+CGG 0.541650 8:+34999594 MsaT043078.1:CDS
AAACAAAGTATGAGATCACC+AGG 0.544394 8:-35003036 None:intergenic
TGCCGCTTAGGAAGATTTGT+CGG 0.552355 8:+35004438 MsaT043078.1:CDS
GCAATCTTCTGCTGATCCGT+GGG 0.554224 8:-35004515 None:intergenic
GCTGAGTGAAACGGAAGGCG+GGG 0.554948 8:-34997389 None:intergenic
GCGGGGCCTCCGTTACTGGG+TGG 0.555777 8:-34997372 None:intergenic
AGTGAATCACCCGATCGTAA+AGG 0.556434 8:+34999405 MsaT043078.1:intron
GGCTCCTGAAAATTCAGTTA+TGG 0.559539 8:+35002238 MsaT043078.1:CDS
CAGCAAATGTTCATGGTGCG+AGG 0.569607 8:+35004549 MsaT043078.1:CDS
GGTCAAATCAGTCCGAGGCA+TGG 0.569910 8:-34999606 None:intergenic
GGGCTGAGTGAAACGGAAGG+CGG 0.572841 8:-34997391 None:intergenic
GAATGTGTCGCAGTGCTCCC+TGG 0.583022 8:+35003018 MsaT043078.1:CDS
ATGGGTCGCCCACCCAGTAA+CGG 0.584649 8:+34997363 MsaT043078.1:CDS
ATTAATCCACTCATCTTCCT+CGG 0.585484 8:-35002950 None:intergenic
GCTTGAAGAACATCTCGTGC+AGG 0.588249 8:-34999264 None:intergenic
CTACTCAAAACCTGGCCGAA+GGG 0.589785 8:+35004792 MsaT043078.1:CDS
TCTACTCAAAACCTGGCCGA+AGG 0.590738 8:+35004791 MsaT043078.1:CDS
GCCTCCGTCTTTGAGCATCA+AGG 0.590882 8:-35003222 None:intergenic
TTGAGTCATTATCCTTCCTG+GGG 0.591497 8:-34999627 None:intergenic
GCAGGAACAGGAGAAGCTGT+TGG 0.594628 8:-34999650 None:intergenic
GACTTCAGGAACACTGCTAG+TGG 0.595794 8:-35004768 None:intergenic
TGAAGTCTCTACTCAAAACC+TGG 0.601287 8:+35004784 MsaT043078.1:CDS
GGCAATGATTCCAGTGAATG+CGG 0.603755 8:-35004747 None:intergenic
CACAGTTCAAACAACAGCAA+AGG 0.607569 8:+35002214 MsaT043078.1:intron
GATTCACATGGCAGAGAGCG+CGG 0.607948 8:-35002991 None:intergenic
ATGTCCTTGATGCTCAAAGA+CGG 0.608783 8:+35003218 MsaT043078.1:CDS
AGCAAATGTTCATGGTGCGA+GGG 0.609406 8:+35004550 MsaT043078.1:CDS
GGATCAGCAGAAGATTGCGT+TGG 0.610789 8:+35004520 MsaT043078.1:CDS
AACATTCTACCTGAAGCTGA+AGG 0.613833 8:-34999674 None:intergenic
TCCACATTCATACTTTGTGG+TGG 0.615610 8:-35004662 None:intergenic
TTGGATCCGAGGAAGATGAG+TGG 0.615863 8:+35002944 MsaT043078.1:CDS
ACCACCACAAAGTATGAATG+TGG 0.618600 8:+35004661 MsaT043078.1:CDS
CTTCCGTTTCACTCAGCCCG+AGG 0.628138 8:+34997395 MsaT043078.1:CDS
AGTTCAAACAACAGCAAAGG+CGG 0.631634 8:+35002217 MsaT043078.1:intron
TGTGAATGATGCAGCACCCA+CGG 0.641428 8:+35004499 MsaT043078.1:CDS
CTATGATCACGATCAATCTG+AGG 0.641893 8:+35003282 MsaT043078.1:CDS
AATCTGGAAGAGATGGAGCA+TGG 0.658527 8:+35002273 MsaT043078.1:CDS
CTCCGACAAATCTTCCTAAG+CGG 0.665093 8:-35004440 None:intergenic
CCTGGGGTCAAATCAGTCCG+AGG 0.675720 8:-34999611 None:intergenic
TCCTTGATGCTCAAAGACGG+AGG 0.675814 8:+35003221 MsaT043078.1:CDS
GGACTGATTTGACCCCAGGA+AGG 0.679224 8:+34999615 MsaT043078.1:CDS
GGTCGCCCACCCAGTAACGG+AGG 0.681262 8:+34997366 MsaT043078.1:CDS
ACACATTCTGATGATTCACA+TGG 0.682055 8:-35003003 None:intergenic
TCTTTGAGCATCAAGGACAT+GGG 0.687814 8:-35003215 None:intergenic
CTCGGGCTGAGTGAAACGGA+AGG 0.689498 8:-34997394 None:intergenic
AATGATTCCAGTGAATGCGG+CGG 0.736741 8:-35004744 None:intergenic
AACAAAGTATGAGATCACCA+GGG 0.773298 8:-35003035 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr8 gene 34997363 35004820 34997363 ID=MsaG043078
Chr8 mRNA 34997363 35004820 34997363 ID=MsaT043078.1;Parent=MsaG043078
Chr8 exon 34997363 34997416 34997363 ID=MsaT043078.1.exon1;Parent=MsaT043078.1
Chr8 CDS 34997363 34997416 34997363 ID=cds.MsaT043078.1;Parent=MsaT043078.1
Chr8 exon 34999219 34999304 34999219 ID=MsaT043078.1.exon2;Parent=MsaT043078.1
Chr8 CDS 34999219 34999304 34999219 ID=cds.MsaT043078.1;Parent=MsaT043078.1
Chr8 exon 34999407 34999452 34999407 ID=MsaT043078.1.exon3;Parent=MsaT043078.1
Chr8 CDS 34999407 34999452 34999407 ID=cds.MsaT043078.1;Parent=MsaT043078.1
Chr8 exon 34999527 34999686 34999527 ID=MsaT043078.1.exon4;Parent=MsaT043078.1
Chr8 CDS 34999527 34999686 34999527 ID=cds.MsaT043078.1;Parent=MsaT043078.1
Chr8 exon 35002219 35002294 35002219 ID=MsaT043078.1.exon5;Parent=MsaT043078.1
Chr8 CDS 35002219 35002294 35002219 ID=cds.MsaT043078.1;Parent=MsaT043078.1
Chr8 exon 35002387 35002438 35002387 ID=MsaT043078.1.exon6;Parent=MsaT043078.1
Chr8 CDS 35002387 35002438 35002387 ID=cds.MsaT043078.1;Parent=MsaT043078.1
Chr8 exon 35002919 35003062 35002919 ID=MsaT043078.1.exon7;Parent=MsaT043078.1
Chr8 CDS 35002919 35003062 35002919 ID=cds.MsaT043078.1;Parent=MsaT043078.1
Chr8 exon 35003184 35003303 35003184 ID=MsaT043078.1.exon8;Parent=MsaT043078.1
Chr8 CDS 35003184 35003303 35003184 ID=cds.MsaT043078.1;Parent=MsaT043078.1
Chr8 exon 35004431 35004820 35004431 ID=MsaT043078.1.exon9;Parent=MsaT043078.1
Chr8 CDS 35004431 35004820 35004431 ID=cds.MsaT043078.1;Parent=MsaT043078.1
Gene Sequence

>MsaT043078.1

ATGGGTCGCCCACCCAGTAACGGAGGCCCCGCCTTCCGTTTCACTCAGCCCGAGGTAACAGAAATGGAAGCTATTCTATCAGAACACAACAATGCAATGCCTGCACGAGATGTTCTTCAAGCACTTGCAGACAAGTTTAGTGAATCACCCGATCGTAAAGGCAAGATTACAGTACAGATGAAACAGGTATGGAATTGGTTTCAAAATAAGCGATATGCTATAAGGGCTAAATCTAGTAAGACTCCTGCAAAGTTAAATATCACGCCCATGCCTCGGACTGATTTGACCCCAGGAAGGATAATGACTCAACCAACAGCTTCTCCTGTTCCTGCTCCTTCAGCTTCAGTTCAAACAACAGCAAAGGCGGCTCCTGAAAATTCAGTTATGGAATTTGAAGCTAAATCTGGAAGAGATGGAGCATGGTATGATGTGGCTACCTTTCTATCATACAGACATTTGGAGAGCAGTGATCCGGAAGTGCTAGTGCGTTTTGCTGGTTTTGGATCCGAGGAAGATGAGTGGATTAATGTGCGAAAAAATGTCAGGCCGCGCTCTCTGCCATGTGAATCATCAGAATGTGTCGCAGTGCTCCCTGGTGATCTCATACTTTGTTTTCAGGAGGGTAAAGAGCAAGCCCTTTACTTTGATGCCCATGTCCTTGATGCTCAAAGACGGAGGCATGATGTAAGAGGTTGTCGCTGTAGATTTTTGGTTCGCTATGATCACGATCAATCTGAGGAAATCGTGCCGCTTAGGAAGATTTGTCGGAGACCTGAAACTGATTACAGATTACATCAACTTCATGCTGTGAATGATGCAGCACCCACGGATCAGCAGAAGATTGCGTTGGATCATCCAGCAAATGTTCATGGTGCGAGGGTTACTAATCCTTCTGAAATGGTGCAAAAGCAGCAGCAGATTGCAAATATTCATATAGTAACACCTGTTTTGCAAACAAATGTTTCTATACCACCACAAAGTATGAATGTGGATCCAACGAAAGCTGAAACAAAAGCTGTTGTTCAAGCTGGAAATTCTGTCACTCCAAGCACCGCCGCATTCACTGGAATCATTGCCACTAGCAGTGTTCCTGAAGTCTCTACTCAAAACCTGGCCGAAGGGAAGTAA
Protein sequence

>MsaT043078.1

MGRPPSNGGPAFRFTQPEVTEMEAILSEHNNAMPARDVLQALADKFSESPDRKGKITVQMKQVWNWFQNKRYAIRAKSSKTPAKLNITPMPRTDLTPGRIMTQPTASPVPAPSASVQTTAKAAPENSVMEFEAKSGRDGAWYDVATFLSYRHLESSDPEVLVRFAGFGSEEDEWINVRKNVRPRSLPCESSECVAVLPGDLILCFQEGKEQALYFDAHVLDAQRRRHDVRGCRCRFLVRYDHDQSEEIVPLRKICRRPETDYRLHQLHAVNDAAPTDQQKIALDHPANVHGARVTNPSEMVQKQQQIANIHIVTPVLQTNVSIPPQSMNVDPTKAETKAVVQAGNSVTPSTAAFTGIIATSSVPEVSTQNLAEGK*