AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG002780

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG002780 MtrunA17_Chr1g0177351 98.276 464 7 1 1 464 1 463 0.0 937
MsaG002780 MtrunA17_Chr4g0025881 59.685 444 167 8 25 461 19 457 6.90e-176 501
MsaG002780 MtrunA17_Chr3g0142581 48.986 296 137 4 127 422 89 370 2.62e-84 264
MsaG002780 MtrunA17_Chr4g0059551 44.776 67 37 0 143 209 17 83 4.21e-11 64.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG002780 AT2G36010.1 57.173 467 158 11 16 458 30 478 1.14e-173 496
MsaG002780 AT2G36010.3 56.930 469 158 12 16 458 30 480 1.76e-171 491
MsaG002780 AT5G22220.2 53.092 469 179 14 22 461 10 466 1.81e-143 419
MsaG002780 AT5G22220.3 52.790 466 182 13 22 461 10 463 9.81e-141 412
MsaG002780 AT2G36010.2 46.525 518 164 14 16 458 30 509 3.28e-134 397
MsaG002780 AT1G47870.2 47.319 317 117 7 105 420 123 390 1.85e-80 255
MsaG002780 AT1G47870.1 47.319 317 117 7 105 420 124 391 2.14e-80 254
MsaG002780 AT5G14960.1 41.304 92 49 1 136 227 6 92 1.81e-12 68.9
MsaG002780 AT3G48160.1 45.205 73 39 1 143 215 34 105 3.92e-11 65.1
MsaG002780 AT3G48160.2 45.205 73 39 1 143 215 34 105 3.99e-11 65.1

Find 122 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTTCGCTGCTGTTGATTCT+AGG 0.183439 1:+47477149 MsaT002780.1:CDS
TGTAGAATGATGCTGATTAT+TGG 0.219679 1:+47481708 MsaT002780.1:intron
AGGACATGATTTGCCTTCTT+TGG 0.234385 1:-47478428 None:intergenic
TTACCTCTTGCTTCAAGTTC+AGG 0.236533 1:+47481353 MsaT002780.1:CDS
GAGAAATTTGAAGAGATTAA+TGG 0.237066 1:+47481311 MsaT002780.1:CDS
AATCAAAATCATCTCTGATT+AGG 0.254900 1:-47481998 None:intergenic
TGTGACCGAGGAAGATATTA+AGG 0.256644 1:+47480744 MsaT002780.1:CDS
CAATTGATGTCTACCTTATC+AGG 0.299411 1:+47481129 MsaT002780.1:CDS
ATATGACATAACTAATGTTT+TGG 0.312982 1:+47478940 MsaT002780.1:CDS
ATCAAAATCATCTCTGATTA+GGG 0.322568 1:-47481997 None:intergenic
TATCTTCCTCGGTCACAAAA+AGG 0.345600 1:-47480738 None:intergenic
TAAGGGCCTACCTTGCTTCC+AGG 0.358343 1:+47480762 MsaT002780.1:CDS
AAAACTCCTTTGTCTGCAAA+AGG 0.367786 1:+47478379 MsaT002780.1:CDS
TGGTGATATCTCTTTGCTTA+AGG 0.368188 1:+47479162 MsaT002780.1:CDS
GAAGCAAGAGGTAAGCTTGC+GGG 0.386616 1:-47481344 None:intergenic
CTGATAAGGTAGACATCAAT+TGG 0.387115 1:-47481128 None:intergenic
TTCATTACATTAGTGTATCC+AGG 0.390006 1:-47478346 None:intergenic
ATATCAAGAACAGAATATAT+TGG 0.392044 1:+47478987 MsaT002780.1:CDS
CCAGCAGGAGTGAGCGGAGA+AGG 0.392492 1:-47478583 None:intergenic
CCTCAGCACGCTTGAGCAAA+TGG 0.395797 1:-47478769 None:intergenic
TTCCCTAAACTTACTTCCTC+AGG 0.398706 1:-47480969 None:intergenic
TACCTCTTGCTTCAAGTTCA+GGG 0.401939 1:+47481354 MsaT002780.1:CDS
GTCGGAAGGTCCAGCGTTAC+CGG 0.403176 1:-47477020 None:intergenic
AATGTTTCACAAGAGTTTGC+TGG 0.409766 1:+47481476 MsaT002780.1:CDS
TTCTGACCAGCATTTGAGAT+AGG 0.420653 1:-47478457 None:intergenic
GGAAGTTGACAACCTTTCTC+TGG 0.430841 1:+47480440 MsaT002780.1:CDS
TAAAGCAGCAGAAACTTTGC+AGG 0.430868 1:+47478811 MsaT002780.1:CDS
AAACTCCTTTGTCTGCAAAA+GGG 0.431635 1:+47478380 MsaT002780.1:CDS
GCCGCCGTTGAAGCGTCATC+TGG 0.433324 1:+47477078 MsaT002780.1:CDS
ATCTGTGCTCCGGTCGGCAT+CGG 0.435761 1:-47477052 None:intergenic
GGAGATATAGAATCATTCTA+AGG 0.456891 1:+47481093 MsaT002780.1:CDS
CTCGAGAGCATTTCAAAGTC+AGG 0.458107 1:-47481923 None:intergenic
TGTCGTTATGACAGTTCCTT+AGG 0.460009 1:+47478610 MsaT002780.1:CDS
TCCTTTCCACTGCATTCAGC+AGG 0.460324 1:-47481407 None:intergenic
GTGACCGAGGAAGATATTAA+GGG 0.460410 1:+47480745 MsaT002780.1:CDS
GCATAACAGCTAATGTTGAT+TGG 0.461803 1:+47481879 MsaT002780.1:intron
CCTTCTCCGCTCACTCCTGC+TGG 0.469787 1:+47478583 MsaT002780.1:CDS
GCAAGTAGTTATACCTGATA+AGG 0.470864 1:-47481142 None:intergenic
ATGTTTCACAAGAGTTTGCT+GGG 0.474909 1:+47481477 MsaT002780.1:CDS
TGCCGACCGGAGCACAGATT+CGG 0.476300 1:+47477056 MsaT002780.1:CDS
GATGGTGCTTCCGCAATTCC+CGG 0.478589 1:-47481962 None:intergenic
ATCATTCTAAGGAGCACAAT+GGG 0.480097 1:+47481104 MsaT002780.1:CDS
GGGGAAGGGCAAACAAGTCA+AGG 0.482335 1:+47478401 MsaT002780.1:CDS
AAACTTACTTCCTCAGGATC+AGG 0.482688 1:-47480963 None:intergenic
ATTCCCGGCGATGGAGTTTG+TGG 0.483877 1:-47481947 None:intergenic
TACTCATCAGTCGGTGCAAA+CGG 0.485816 1:-47477121 None:intergenic
TGAGCAACAAGTGACAGAAA+TGG 0.489280 1:+47481382 MsaT002780.1:CDS
GCTTCCGCAATTCCCGGCGA+TGG 0.490056 1:-47481956 None:intergenic
GTCTCTGCTCTTCCAGAGAA+AGG 0.490737 1:-47480452 None:intergenic
AGCCGTTATTGTTAGATCTC+CGG 0.504106 1:+47477195 MsaT002780.1:CDS
CCAGCATTTGAGATAGGTGT+TGG 0.506282 1:-47478451 None:intergenic
AACTCCTTTGTCTGCAAAAG+GGG 0.506592 1:+47478381 MsaT002780.1:CDS
GGAATTGAATCTTCTACGCC+TGG 0.513959 1:+47479130 MsaT002780.1:CDS
AAGGTCATAAAGCGGAAGAA+TGG 0.515250 1:+47478280 MsaT002780.1:intron
CAGCAGGAGTGAGCGGAGAA+GGG 0.521252 1:-47478582 None:intergenic
TGAGAAGAGAGCAGAGCTTG+AGG 0.521585 1:-47481437 None:intergenic
CGTGGCTCGCCGATGCCGAC+CGG 0.525876 1:+47477043 MsaT002780.1:CDS
AACTCCATCGCCGGGAATTG+CGG 0.529034 1:+47481952 MsaT002780.1:CDS
GGCCGAATCTGTGCTCCGGT+CGG 0.529279 1:-47477058 None:intergenic
AGTCGGTGCAAACGGTGGCT+TGG 0.531462 1:-47477113 None:intergenic
CGGCATCGGCGAGCCACGGT+CGG 0.533060 1:-47477038 None:intergenic
GAGGCCACAAACTCCATCGC+CGG 0.533964 1:+47481943 MsaT002780.1:CDS
AAGTCAAGGGCATCCAAAGA+AGG 0.536537 1:+47478415 MsaT002780.1:CDS
AGGCCACAAACTCCATCGCC+GGG 0.537724 1:+47481944 MsaT002780.1:CDS
CGGTCGGCATCGGCGAGCCA+CGG 0.539391 1:-47477042 None:intergenic
CACCGGAGATCTAACAATAA+CGG 0.545488 1:-47477197 None:intergenic
ATCGGCGAGCCACGGTCGGA+AGG 0.546657 1:-47477034 None:intergenic
CTATACTATAGGTGCAAAAG+AGG 0.547054 1:+47478912 MsaT002780.1:intron
AAGCAAGAGGTAAGCTTGCG+GGG 0.551818 1:-47481343 None:intergenic
AGCAGGAGTGAGCGGAGAAG+GGG 0.552395 1:-47478581 None:intergenic
TTGCTCAAGCGTGCTGAGGA+TGG 0.554722 1:+47478773 MsaT002780.1:CDS
CAAAAGTCAAGTAACAGCCC+TGG 0.555813 1:+47478328 MsaT002780.1:CDS
ATCTTCTACGCCTGGTAATG+TGG 0.558876 1:+47479138 MsaT002780.1:CDS
AGAGACTAGATGATCAGATA+AGG 0.559999 1:+47480469 MsaT002780.1:CDS
CGGCGGCCGAATCTGTGCTC+CGG 0.564361 1:-47477062 None:intergenic
TCATAACGACAGCTACCAGC+AGG 0.570121 1:-47478598 None:intergenic
TAGGCCCTTAATATCTTCCT+CGG 0.571156 1:-47480749 None:intergenic
CCAACACCTATCTCAAATGC+TGG 0.572738 1:+47478451 MsaT002780.1:CDS
GACCCTGAACTTGAAGCAAG+AGG 0.573741 1:-47481356 None:intergenic
GCATTTGAGATAGGTGTTGG+AGG 0.574157 1:-47478448 None:intergenic
TCATTACATTAGTGTATCCA+GGG 0.578943 1:-47478345 None:intergenic
ACAGCTAATGTTGATTGGAG+TGG 0.580563 1:+47481884 MsaT002780.1:intron
AACGCCAGATGACGCTTCAA+CGG 0.580618 1:-47477082 None:intergenic
AAGTTAGCATAACAGATATG+TGG 0.583522 1:+47481747 MsaT002780.1:CDS
AAAGAACTCACCTGGAAGCA+AGG 0.584852 1:-47480772 None:intergenic
ATATCACCATCCACATTACC+AGG 0.586810 1:-47479148 None:intergenic
GCCAGATGACGCTTCAACGG+CGG 0.590423 1:-47477079 None:intergenic
ATACTTACATCAGCATCTGA+AGG 0.592246 1:-47481518 None:intergenic
TACTATAGGTGCAAAAGAGG+AGG 0.592536 1:+47478915 MsaT002780.1:intron
AAAGTATGATACTCATCAGT+CGG 0.596002 1:-47477130 None:intergenic
AACGCTGGACCTTCCGACCG+TGG 0.596010 1:+47477025 MsaT002780.1:CDS
AACGGCTTCATTGACATGAT+CGG 0.597493 1:-47477179 None:intergenic
CAGCTACCAGCAGGAGTGAG+CGG 0.598273 1:-47478589 None:intergenic
CTCAGGATCAGGAACTTCCA+AGG 0.601233 1:-47480952 None:intergenic
TCTACGCCTGGTAATGTGGA+TGG 0.603037 1:+47479142 MsaT002780.1:CDS
CTTGGAAGTTCCTGATCCTG+AGG 0.604439 1:+47480953 MsaT002780.1:CDS
AGCTCCGCATGGAACCACCT+TGG 0.605657 1:+47480935 MsaT002780.1:CDS
TCCACCGTAACCGTAATGTC+CGG 0.609815 1:+47477001 None:intergenic
AATGGAATGAATGAAAGTGA+AGG 0.612614 1:+47478298 MsaT002780.1:CDS
CTGACTTTGAAATGCTCTCG+AGG 0.615106 1:+47481924 MsaT002780.1:CDS
AACTCACCTGGAAGCAAGGT+AGG 0.616174 1:-47480768 None:intergenic
TACTTACATCAGCATCTGAA+GGG 0.619198 1:-47481517 None:intergenic
TCTCCGCTGTAGTTCGTCAA+CGG 0.627564 1:-47481075 None:intergenic
CCATTTGCTCAAGCGTGCTG+AGG 0.631281 1:+47478769 MsaT002780.1:CDS
ATAGCAATCAAAGCTCCGCA+TGG 0.631816 1:+47480924 MsaT002780.1:CDS
AATCATTCTAAGGAGCACAA+TGG 0.638536 1:+47481103 MsaT002780.1:CDS
AGCAAGAGGTAAGCTTGCGG+GGG 0.640114 1:-47481342 None:intergenic
GTTTCACAAGAGTTTGCTGG+GGG 0.641606 1:+47481479 MsaT002780.1:CDS
ACTCCTTTGTCTGCAAAAGG+GGG 0.643497 1:+47478382 MsaT002780.1:CDS
ACCTGCTGAATGCAGTGGAA+AGG 0.654494 1:+47481406 MsaT002780.1:CDS
GCAAGAGGTAAGCTTGCGGG+GGG 0.656380 1:-47481341 None:intergenic
GGGAAGGGCAAACAAGTCAA+GGG 0.657296 1:+47478402 MsaT002780.1:CDS
TGAAGCAAGAGGTAAGCTTG+CGG 0.662777 1:-47481345 None:intergenic
ATGGTACCTGCTGAATGCAG+TGG 0.669987 1:+47481401 MsaT002780.1:CDS
TCATCAGTCGGTGCAAACGG+TGG 0.672671 1:-47477118 None:intergenic
TTAGGGTTAGCTACAGTCGA+TGG 0.674010 1:-47481980 None:intergenic
AGGCCGTTGACGAACTACAG+CGG 0.677542 1:+47481072 MsaT002780.1:intron
TGTTTCACAAGAGTTTGCTG+GGG 0.692916 1:+47481478 MsaT002780.1:CDS
TAATGTTGATTGGAGTGGAG+TGG 0.694763 1:+47481889 MsaT002780.1:CDS
ACTTCCAAGGTGGTTCCATG+CGG 0.714996 1:-47480939 None:intergenic
GGTGGTGTAAGGTCATAAAG+CGG 0.723032 1:+47478272 MsaT002780.1:intron
AGGATCAGGAACTTCCAAGG+TGG 0.735853 1:-47480949 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr1 gene 47477016 47482012 47477016 ID=MsaG002780
Chr1 mRNA 47477016 47482012 47477016 ID=MsaT002780.1;Parent=MsaG002780
Chr1 exon 47477016 47477216 47477016 ID=MsaT002780.1.exon1;Parent=MsaT002780.1
Chr1 CDS 47477016 47477216 47477016 ID=cds.MsaT002780.1;Parent=MsaT002780.1
Chr1 exon 47478283 47478472 47478283 ID=MsaT002780.1.exon2;Parent=MsaT002780.1
Chr1 CDS 47478283 47478472 47478283 ID=cds.MsaT002780.1;Parent=MsaT002780.1
Chr1 exon 47478578 47478631 47478578 ID=MsaT002780.1.exon3;Parent=MsaT002780.1
Chr1 CDS 47478578 47478631 47478578 ID=cds.MsaT002780.1;Parent=MsaT002780.1
Chr1 exon 47478747 47478832 47478747 ID=MsaT002780.1.exon4;Parent=MsaT002780.1
Chr1 CDS 47478747 47478832 47478747 ID=cds.MsaT002780.1;Parent=MsaT002780.1
Chr1 exon 47478923 47479011 47478923 ID=MsaT002780.1.exon5;Parent=MsaT002780.1
Chr1 CDS 47478923 47479011 47478923 ID=cds.MsaT002780.1;Parent=MsaT002780.1
Chr1 exon 47479129 47479183 47479129 ID=MsaT002780.1.exon6;Parent=MsaT002780.1
Chr1 CDS 47479129 47479183 47479129 ID=cds.MsaT002780.1;Parent=MsaT002780.1
Chr1 exon 47480438 47480490 47480438 ID=MsaT002780.1.exon7;Parent=MsaT002780.1
Chr1 CDS 47480438 47480490 47480438 ID=cds.MsaT002780.1;Parent=MsaT002780.1
Chr1 exon 47480574 47480624 47480574 ID=MsaT002780.1.exon8;Parent=MsaT002780.1
Chr1 CDS 47480574 47480624 47480574 ID=cds.MsaT002780.1;Parent=MsaT002780.1
Chr1 exon 47480735 47480783 47480735 ID=MsaT002780.1.exon9;Parent=MsaT002780.1
Chr1 CDS 47480735 47480783 47480735 ID=cds.MsaT002780.1;Parent=MsaT002780.1
Chr1 exon 47480912 47480977 47480912 ID=MsaT002780.1.exon10;Parent=MsaT002780.1
Chr1 CDS 47480912 47480977 47480912 ID=cds.MsaT002780.1;Parent=MsaT002780.1
Chr1 exon 47481074 47481150 47481074 ID=MsaT002780.1.exon11;Parent=MsaT002780.1
Chr1 CDS 47481074 47481150 47481074 ID=cds.MsaT002780.1;Parent=MsaT002780.1
Chr1 exon 47481301 47481532 47481301 ID=MsaT002780.1.exon12;Parent=MsaT002780.1
Chr1 CDS 47481301 47481532 47481301 ID=cds.MsaT002780.1;Parent=MsaT002780.1
Chr1 exon 47481713 47481779 47481713 ID=MsaT002780.1.exon13;Parent=MsaT002780.1
Chr1 CDS 47481713 47481779 47481713 ID=cds.MsaT002780.1;Parent=MsaT002780.1
Chr1 exon 47481888 47482012 47481888 ID=MsaT002780.1.exon14;Parent=MsaT002780.1
Chr1 CDS 47481888 47482012 47481888 ID=cds.MsaT002780.1;Parent=MsaT002780.1
Gene Sequence

>MsaT002780.1

ATGTCCGGTAACGCTGGACCTTCCGACCGTGGCTCGCCGATGCCGACCGGAGCACAGATTCGGCCGCCGTTGAAGCGTCATCTGGCGTTTGTTTCGACCAAGCCACCGTTTGCACCGACTGATGAGTATCATACTTTCGCTGCTGTTGATTCTAGGAAAGTCGCCGATCATGTCAATGAAGCCGTTATTGTTAGATCTCCGGTCATAAAGCGGAAGAATGGAATGAATGAAAGTGAAGGAGACTCGCAAAAGTCAAGTAACAGCCCTGGATACACTAATGTAATGAACAGCCCCTTCAAAACTCCTTTGTCTGCAAAAGGGGGAAGGGCAAACAAGTCAAGGGCATCCAAAGAAGGCAAATCATGTCCTCCAACACCTATCTCAAATGCTGGTTCCCCTTCTCCGCTCACTCCTGCTGGTAGCTGTCGTTATGACAGTTCCTTAGGTCTCTTGACAAAAAAGTTCATCCATTTGCTCAAGCGTGCTGAGGATGGTATTCTTGACTTAAATAAAGCAGCAGAAACTTTGCAGGTGCAAAAGAGGAGGATATATGACATAACTAATGTTTTGGAAGGCATTGGTCTCATCGAAAAGAATATCAAGAACAGAATATATTGGAAAGGAATTGAATCTTCTACGCCTGGTAATGTGGATGGTGATATCTCTTTGCTTAAGTCGGAAGTTGACAACCTTTCTCTGGAAGAGCAGAGACTAGATGATCAGATAAGGGAAATGCAAGAAAGACTGAGAAGTTTGAGCGAAGATGAAAACAACCAGAAGTTCCTTTTTGTGACCGAGGAAGATATTAAGGGCCTACCTTGCTTCCAGAATGAAACTTTGATAGCAATCAAAGCTCCGCATGGAACCACCTTGGAAGTTCCTGATCCTGAGGAAGCCGTTGACGAACTACAGCGGAGATATAGAATCATTCTAAGGAGCACAATGGGTCCAATTGATGTCTACCTTATCAGTCAATTTGAAGAGAAATTTGAAGAGATTAATGGTGCTGAGCCCCCCGCAAGCTTACCTCTTGCTTCAAGTTCAGGGTCTAATGAGCAACAAGTGACAGAAATGGTACCTGCTGAATGCAGTGGAAAGGAACTTGAACCTCAAGCTCTGCTCTCTTCTCAGACATATTCTGATTTAAATGTTTCACAAGAGTTTGCTGGGGGAATGATGAAGATTGTCCCTTCAGATGCTGATAATGATGCTGATTATTGGCTTCTATCAGATGCTGAAGTTAGCATAACAGATATGTGGAGAACAGATTCTAATGTTGATTGGAGTGGAGTGGACATGCTTCATCCTGACTTTGAAATGCTCTCGAGGCCACAAACTCCATCGCCGGGAATTGCGGAAGCACCATCGACTGTAGCTAACCCTAATCAGAGATGA
Protein sequence

>MsaT002780.1

MSGNAGPSDRGSPMPTGAQIRPPLKRHLAFVSTKPPFAPTDEYHTFAAVDSRKVADHVNEAVIVRSPVIKRKNGMNESEGDSQKSSNSPGYTNVMNSPFKTPLSAKGGRANKSRASKEGKSCPPTPISNAGSPSPLTPAGSCRYDSSLGLLTKKFIHLLKRAEDGILDLNKAAETLQVQKRRIYDITNVLEGIGLIEKNIKNRIYWKGIESSTPGNVDGDISLLKSEVDNLSLEEQRLDDQIREMQERLRSLSEDENNQKFLFVTEEDIKGLPCFQNETLIAIKAPHGTTLEVPDPEEAVDELQRRYRIILRSTMGPIDVYLISQFEEKFEEINGAEPPASLPLASSSGSNEQQVTEMVPAECSGKELEPQALLSSQTYSDLNVSQEFAGGMMKIVPSDADNDADYWLLSDAEVSITDMWRTDSNVDWSGVDMLHPDFEMLSRPQTPSPGIAEAPSTVANPNQR*