AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG000839

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG000839 MtrunA17_Chr1g0205751 36.103 662 389 15 14 645 39 696 6.34e-97 313
MsaG000839 MtrunA17_Chr5g0394261 37.876 631 349 15 53 649 76 697 1.37e-96 312
MsaG000839 MtrunA17_Chr7g0259851 36.068 585 340 15 97 657 123 697 1.39e-80 269
MsaG000839 MtrunA17_Chr1g0149211 27.158 475 285 21 68 494 68 529 7.57e-16 81.3
MsaG000839 MtrunA17_Chr3g0079171 28.169 284 167 13 113 368 20 294 3.53e-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
MsaG000839 AT5G13060.1 33.186 681 395 18 9 645 61 725 1.64e-86 286
MsaG000839 AT5G19330.1 35.468 609 350 15 63 637 91 690 7.79e-85 281
MsaG000839 AT5G19330.2 31.843 559 302 12 63 594 92 598 1.27e-50 186

Find 115 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTCGTTGCTCTAACATTAA+AGG 0.177108 1:-11427589 MsaT000839.1:CDS
CAAGTTGGCCAGTAAATTCT+TGG 0.274559 1:-11429981 MsaT000839.1:CDS
ATCGACTTCTGAACTTAAAT+AGG 0.307874 1:+11430200 None:intergenic
AACACGAATTGCTTTGGCTT+TGG 0.334035 1:-11430223 MsaT000839.1:CDS
ATAAGAATACTGAGCTTTCC+TGG 0.338428 1:+11431435 None:intergenic
TCATCGTCTTGCAGATAATA+AGG 0.339116 1:-11430753 MsaT000839.1:intron
TACTTAGCGTGGAAACTATA+TGG 0.342160 1:-11427635 MsaT000839.1:CDS
GACGTTATATTTCTTATTGA+AGG 0.346191 1:-11429584 MsaT000839.1:intron
TTCGTTGCTCTAACATTAAA+GGG 0.350794 1:-11427588 MsaT000839.1:CDS
CAACTATGCTAGATAGTATA+AGG 0.352751 1:-11433783 MsaT000839.1:intron
ATCCTCCTTGGAGGAGTCTC+TGG 0.355174 1:+11430578 None:intergenic
TCATTAGCGGAAAAGATTAA+TGG 0.357540 1:-11430382 MsaT000839.1:CDS
ATTAGAACCACTTCAGTTAT+CGG 0.364657 1:+11434861 None:intergenic
CTAAACTGCCACTGCGTAAG+AGG 0.378205 1:+11427303 None:intergenic
GTAAGTGCCTTTGTCAATAA+AGG 0.380566 1:+11431476 None:intergenic
ATAAAGGTATAAGACCTCTT+TGG 0.387340 1:+11431492 None:intergenic
AGCTTCCGATCCCTCCTTAG+AGG 0.391644 1:+11430018 None:intergenic
ATCGAAACAAATCAAATGCT+TGG 0.395849 1:+11430416 None:intergenic
CTCCTCCAAGGAGGATATCT+TGG 0.404179 1:-11430571 MsaT000839.1:CDS
GCTACTTGGCTCATCCTCTA+AGG 0.406347 1:-11430032 MsaT000839.1:CDS
TTAGAACCACTTCAGTTATC+GGG 0.408364 1:+11434862 None:intergenic
TTCTATATCTATCAGATTGT+AGG 0.413639 1:-11432309 MsaT000839.1:intron
CTCCTCATCATACTCTGTTA+TGG 0.426496 1:+11435093 None:intergenic
TACCTCATTAATTCTGTAAG+TGG 0.440870 1:+11431804 None:intergenic
AGATGGGGCCAAGAATTTAC+TGG 0.441095 1:+11429973 None:intergenic
ATTCGTGTTTGAAAATCATT+CGG 0.442477 1:+11430237 None:intergenic
CTACTTTGAGAGCCAACGTT+TGG 0.442715 1:-11431693 MsaT000839.1:CDS
TTGAAGAGGATGGTGGACTT+AGG 0.449737 1:-11434918 MsaT000839.1:CDS
CAGGACTCGGATTGTCAAGT+TGG 0.452315 1:-11430860 MsaT000839.1:CDS
TAAATTCTTGGCCCCATCTC+CGG 0.457915 1:-11429969 MsaT000839.1:CDS
AATATTGTACCTTCCATTGT+GGG 0.461806 1:+11431636 None:intergenic
GTTAAGATCTACTGTGGGTC+TGG 0.463107 1:+11427269 None:intergenic
GATGCACAATATCATCTAGT+AGG 0.464401 1:+11433649 None:intergenic
TACTTCTTTATCAATACATC+CGG 0.470787 1:-11429945 MsaT000839.1:intron
TCGAAACAAATCAAATGCTT+GGG 0.476037 1:+11430417 None:intergenic
TGCAGATGGAATTCCATCCT+TGG 0.479025 1:-11433676 MsaT000839.1:CDS
ATCTATCAGATTGTAGGTCT+CGG 0.479989 1:-11432303 MsaT000839.1:intron
ATATTAAGAATGGCATTTCA+CGG 0.482955 1:-11435028 MsaT000839.1:intron
GAGTTGCTTACTGAGCTACT+TGG 0.486455 1:-11430046 MsaT000839.1:CDS
ATCATGTTGTCAATAAAGTC+AGG 0.495057 1:+11427353 None:intergenic
CAAGTTGGTATTGTGAATGA+AGG 0.499666 1:-11430845 MsaT000839.1:CDS
TCGAATAATAAATGCTTCAA+AGG 0.502494 1:-11429421 MsaT000839.1:CDS
TTGTTTAGATTTATTTACAC+TGG 0.503233 1:-11427909 MsaT000839.1:intron
CTTATTATGTTTCTTATCTG+AGG 0.504191 1:-11431417 MsaT000839.1:intron
ATTGACACTTGAATCATTAG+CGG 0.504484 1:-11430395 MsaT000839.1:CDS
GAGAAACTATGAAGAGTTGA+GGG 0.505799 1:-11427544 MsaT000839.1:CDS
CATTCGGCAAACTCCACATT+CGG 0.507417 1:+11430253 None:intergenic
GATAAAGAAGTAGCCGGAGA+TGG 0.508149 1:+11429956 None:intergenic
ATCCACTTACAGAATTAATG+AGG 0.509465 1:-11431806 MsaT000839.1:intron
AGTCGTGAGGATATCAATAG+AGG 0.514618 1:+11433822 None:intergenic
ATAAAGAAGTAGCCGGAGAT+GGG 0.514779 1:+11429957 None:intergenic
CATCACCAAGATATCCTCCT+TGG 0.515233 1:+11430566 None:intergenic
TTGTACCTTCCATTGTGGGT+TGG 0.521112 1:+11431640 None:intergenic
GTCTGCTAATGAAGGAGTCC+AGG 0.521443 1:-11431453 MsaT000839.1:CDS
GAATATTGTACCTTCCATTG+TGG 0.525011 1:+11431635 None:intergenic
AAGAGTAGCTTGCTTTGCGT+TGG 0.526568 1:-11433625 MsaT000839.1:CDS
CTCATCCTCTAAGGAGGGAT+CGG 0.529278 1:-11430023 MsaT000839.1:CDS
CTGTGAAAATAAGATTGCTC+AGG 0.533457 1:-11427805 MsaT000839.1:intron
TGCTGCGGCTTTATTCAAGT+TGG 0.534737 1:-11429996 MsaT000839.1:CDS
CACCAAGATATCCTCCTTGG+AGG 0.535091 1:+11430569 None:intergenic
CTCAACTGTTACACCGAATG+TGG 0.535467 1:-11430266 MsaT000839.1:CDS
TATAGCATTAGAATTATAAG+TGG 0.536156 1:+11432273 None:intergenic
TCTAGTAGGTGAACCAAGGA+TGG 0.539296 1:+11433663 None:intergenic
ACAAGATGTCTAGCTAAGGC+TGG 0.541047 1:+11434888 None:intergenic
CAAACGTTGGCTCTCAAAGT+AGG 0.542198 1:+11431694 None:intergenic
TAGATCATGCTTATCCAAAG+AGG 0.547059 1:-11431506 MsaT000839.1:CDS
TAATGCTATATCGTGAAGAC+AGG 0.548205 1:-11432260 MsaT000839.1:CDS
ACTATGAAGAGTTGAGGGAA+AGG 0.551507 1:-11427539 MsaT000839.1:intron
GAGTGCTATGGTTACTAAGT+CGG 0.552815 1:-11429394 MsaT000839.1:CDS
TGAGAAACTATGAAGAGTTG+AGG 0.557066 1:-11427545 MsaT000839.1:CDS
TATTGTGAATGAAGGCTTGG+TGG 0.558315 1:-11430837 MsaT000839.1:CDS
AAATTATATTCTCTGCAAGT+AGG 0.560105 1:-11430791 MsaT000839.1:CDS
TCTTATACCTTTATTGACAA+AGG 0.563122 1:-11431483 MsaT000839.1:CDS
ACGGAGCTTGTGAGATAGTG+AGG 0.567161 1:-11431854 MsaT000839.1:CDS
GCACTTACGTCTGCTAATGA+AGG 0.575276 1:-11431461 MsaT000839.1:CDS
TTCTTAATATAAAATTAGCA+CGG 0.580057 1:+11435041 None:intergenic
AATCAAATCAAGCAAATCGA+TGG 0.582383 1:+11431670 None:intergenic
TGTATTGATAAAGAAGTAGC+CGG 0.582481 1:+11429950 None:intergenic
AGCAACCAAATGATTAACTA+CGG 0.585894 1:-11435184 None:intergenic
CGCACAGAATGTACTTAGCG+TGG 0.586567 1:-11427646 MsaT000839.1:intron
GTGTACAAGTTTATCATGCT+AGG 0.592047 1:-11430607 MsaT000839.1:CDS
GGTGGAATTACTGAAGGTGT+TGG 0.593973 1:-11430819 MsaT000839.1:CDS
CAGATGATCTATAATCTAGA+CGG 0.595673 1:-11431873 MsaT000839.1:CDS
GGAGTACAGTTCAAAGATTG+AGG 0.596794 1:-11435074 MsaT000839.1:CDS
TGTGTCCCCGATAACTGAAG+TGG 0.599893 1:-11434868 MsaT000839.1:CDS
AAAGACCAACCCACAATGGA+AGG 0.601200 1:-11431645 MsaT000839.1:intron
TTTGTGGTTAAGATCTACTG+TGG 0.601353 1:+11427263 None:intergenic
TTCAAAGGTGTTGAGTGCTA+TGG 0.603447 1:-11429406 MsaT000839.1:CDS
TGGTATTGTGAATGAAGGCT+TGG 0.604614 1:-11430840 MsaT000839.1:CDS
ACTTGGCTCATCCTCTAAGG+AGG 0.604968 1:-11430029 MsaT000839.1:CDS
GGAGTCCAGAGACTCCTCCA+AGG 0.616675 1:-11430583 MsaT000839.1:CDS
GGACACAAGATGTCTAGCTA+AGG 0.619572 1:+11434884 None:intergenic
ACCTAAAATACACCATCAGA+TGG 0.619756 1:-11427330 MsaT000839.1:CDS
GGAGGGATCGGAAGCTGCTG+CGG 0.621384 1:-11430011 MsaT000839.1:CDS
TAGAACCACTTCAGTTATCG+GGG 0.625659 1:+11434863 None:intergenic
CTTGGCTCATCCTCTAAGGA+GGG 0.627160 1:-11430028 MsaT000839.1:CDS
TTGTGGTTAAGATCTACTGT+GGG 0.628036 1:+11427264 None:intergenic
TTGTAAAGACCAACCCACAA+TGG 0.630882 1:-11431649 MsaT000839.1:CDS
ACGTTGGCTCTCAAAGTAGG+TGG 0.633070 1:+11431697 None:intergenic
GCAAATCGATGGCCAAACGT+TGG 0.640110 1:+11431681 None:intergenic
ATCATCTAGTAGGTGAACCA+AGG 0.648799 1:+11433659 None:intergenic
TAAAGAAGTAGCCGGAGATG+GGG 0.655484 1:+11429958 None:intergenic
TACAAGTTTATCATGCTAGG+TGG 0.658188 1:-11430604 MsaT000839.1:CDS
GAACCATGAAAATGCTACAC+AGG 0.659261 1:-11433589 MsaT000839.1:intron
ATATCCTCACGACTCTTGCG+AGG 0.664239 1:-11433813 MsaT000839.1:CDS
GTAAGAGGTGTACCATCTGA+TGG 0.669881 1:+11427318 None:intergenic
TACCATAACAGAGTATGATG+AGG 0.683678 1:-11435095 MsaT000839.1:CDS
GCTTGTGAGATAGTGAGGAG+AGG 0.683896 1:-11431849 MsaT000839.1:CDS
TTGTCCTCGCAAGAGTCGTG+AGG 0.687559 1:+11433809 None:intergenic
GAGGATGGTGGACTTAGGTG+TGG 0.697058 1:-11434913 MsaT000839.1:CDS
AGGCTTGGTGGAATTACTGA+AGG 0.698166 1:-11430825 MsaT000839.1:CDS
GTCCAGAGACTCCTCCAAGG+AGG 0.702113 1:-11430580 MsaT000839.1:CDS
ATGGTACACCTCTTACGCAG+TGG 0.704422 1:-11427311 MsaT000839.1:CDS
TGGAAACACATATGTCAGTG+TGG 0.704970 1:-11427889 MsaT000839.1:CDS
CAGGCAACTTCACAACTCTG+TGG 0.728431 1:-11432241 MsaT000839.1:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr1 gene 11427277 11435197 11427277 ID=MsaG000839
Chr1 mRNA 11427277 11435197 11427277 ID=MsaT000839.1;Parent=MsaG000839
Chr1 exon 11427277 11427379 11427277 ID=MsaT000839.1.exon19;Parent=MsaT000839.1
Chr1 CDS 11427277 11427379 11427277 ID=cds.MsaT000839.1;Parent=MsaT000839.1
Chr1 exon 11427540 11427661 11427540 ID=MsaT000839.1.exon18;Parent=MsaT000839.1
Chr1 CDS 11427540 11427661 11427540 ID=cds.MsaT000839.1;Parent=MsaT000839.1
Chr1 exon 11427806 11427923 11427806 ID=MsaT000839.1.exon17;Parent=MsaT000839.1
Chr1 CDS 11427806 11427923 11427806 ID=cds.MsaT000839.1;Parent=MsaT000839.1
Chr1 exon 11428015 11428075 11428015 ID=MsaT000839.1.exon16;Parent=MsaT000839.1
Chr1 CDS 11428015 11428075 11428015 ID=cds.MsaT000839.1;Parent=MsaT000839.1
Chr1 exon 11429382 11429468 11429382 ID=MsaT000839.1.exon15;Parent=MsaT000839.1
Chr1 CDS 11429382 11429468 11429382 ID=cds.MsaT000839.1;Parent=MsaT000839.1
Chr1 exon 11429585 11429651 11429585 ID=MsaT000839.1.exon14;Parent=MsaT000839.1
Chr1 CDS 11429585 11429651 11429585 ID=cds.MsaT000839.1;Parent=MsaT000839.1
Chr1 exon 11429946 11430073 11429946 ID=MsaT000839.1.exon13;Parent=MsaT000839.1
Chr1 CDS 11429946 11430073 11429946 ID=cds.MsaT000839.1;Parent=MsaT000839.1
Chr1 exon 11430172 11430295 11430172 ID=MsaT000839.1.exon12;Parent=MsaT000839.1
Chr1 CDS 11430172 11430295 11430172 ID=cds.MsaT000839.1;Parent=MsaT000839.1
Chr1 exon 11430378 11430440 11430378 ID=MsaT000839.1.exon11;Parent=MsaT000839.1
Chr1 CDS 11430378 11430440 11430378 ID=cds.MsaT000839.1;Parent=MsaT000839.1
Chr1 exon 11430567 11430635 11430567 ID=MsaT000839.1.exon10;Parent=MsaT000839.1
Chr1 CDS 11430567 11430635 11430567 ID=cds.MsaT000839.1;Parent=MsaT000839.1
Chr1 exon 11430754 11430879 11430754 ID=MsaT000839.1.exon9;Parent=MsaT000839.1
Chr1 CDS 11430754 11430879 11430754 ID=cds.MsaT000839.1;Parent=MsaT000839.1
Chr1 exon 11431418 11431525 11431418 ID=MsaT000839.1.exon8;Parent=MsaT000839.1
Chr1 CDS 11431418 11431525 11431418 ID=cds.MsaT000839.1;Parent=MsaT000839.1
Chr1 exon 11431646 11431721 11431646 ID=MsaT000839.1.exon7;Parent=MsaT000839.1
Chr1 CDS 11431646 11431721 11431646 ID=cds.MsaT000839.1;Parent=MsaT000839.1
Chr1 exon 11431807 11431898 11431807 ID=MsaT000839.1.exon6;Parent=MsaT000839.1
Chr1 CDS 11431807 11431898 11431807 ID=cds.MsaT000839.1;Parent=MsaT000839.1
Chr1 exon 11432242 11432316 11432242 ID=MsaT000839.1.exon5;Parent=MsaT000839.1
Chr1 CDS 11432242 11432316 11432242 ID=cds.MsaT000839.1;Parent=MsaT000839.1
Chr1 exon 11433590 11433701 11433590 ID=MsaT000839.1.exon4;Parent=MsaT000839.1
Chr1 CDS 11433590 11433701 11433590 ID=cds.MsaT000839.1;Parent=MsaT000839.1
Chr1 exon 11433784 11433941 11433784 ID=MsaT000839.1.exon3;Parent=MsaT000839.1
Chr1 CDS 11433784 11433941 11433784 ID=cds.MsaT000839.1;Parent=MsaT000839.1
Chr1 exon 11434830 11434948 11434830 ID=MsaT000839.1.exon2;Parent=MsaT000839.1
Chr1 CDS 11434830 11434948 11434830 ID=cds.MsaT000839.1;Parent=MsaT000839.1
Chr1 exon 11435029 11435197 11435029 ID=MsaT000839.1.exon1;Parent=MsaT000839.1
Chr1 CDS 11435029 11435197 11435029 ID=cds.MsaT000839.1;Parent=MsaT000839.1
Gene Sequence

>MsaT000839.1

ATGATTAACTACGGTAATAGAAATACTCGAAGTCTTGATGATGACGATGTTCGCTCGTTTACAGAATTTCTGAATGATGTTACCATAACAGAGTATGATGAGGAGTACAGTTCAAAGATTGAGGAGTTCAAGAACCGTGCTAATTTTATATTAAGAATGGCATTTCACGGAAGAATTTTGAAGAGGATGGTGGACTTAGGTGTGGTTCCAGCCTTAGCTAGACATCTTGTGTCCCCGATAACTGAAGTGGTTCTAATAACTCTAAGAGCACTGAAGAATTTTGCTAAGCAATATCAAGAGCAATTTGATGAGACTCGTGCTGTATCACAAATAATTAATTTTTTAAACAATAGTCAAAATGAAGCAAAACACAGTTTGATTTACTCCTCTATTGATATCCTCACGACTCTTGCGAGGACAAGCACAACTATGCTAGATAGTATAAGGATTGCAGATGGAATTCCATCCTTGGTTCACCTACTAGATGATATTGTGCATCAAAGAGTAGCTTGCTTTGCGTTGGAAGTCCTTTCCACGAACCATGAAAATGCTACACAGATTGTAGGTCTCGGTGCTGTTCCACTTATAATTCTAATGCTATATCGTGAAGACAGGCAACTTCACAACTCTGTGTTTCAGATGATCTATAATCTAGACGGAGCTTGTGAGATAGTGAGGAGAGGTTATCTTGTTGAAGCTTTTCATCCACTTACAGAATTAATGAGCTCCACCTACTTTGAGAGCCAACGTTTGGCCATCGATTTGCTTGATTTGATTGTAAAGACCAACCCACAATGGAAGATCATGCTTATCCAAAGAGGTCTTATACCTTTATTGACAAAGGCACTTACGTCTGCTAATGAAGGAGTCCAGGAAAGCTCAGTATTCTTATTATGTTTCTTATCTGAGGACTCGGATTGTCAAGTTGGTATTGTGAATGAAGGCTTGGTGGAATTACTGAAGGTGTTGGACACAAAATTATATTCTCTGCAAGTAGGTGCTGCTTTTACTCTTCATCGTCTTGCAGATAATAAGGACAATGTGTACAAGTTTATCATGCTAGGTGGAGTCCAGAGACTCCTCCAAGGAGGATATCTTGGTGATACCCAAGCATTTGATTTGTTTCGATTGACACTTGAATCATTAGCGGAAAAGATTAATGGACATGTACTAACTCAACTGTTACACCGAATGTGGAGTTTGCCGAATGATTTTCAAACACGAATTGCTTTGGCTTTGGCCTATTTAAGTTCAGAAGTCGATAGCAAAAGAATTTTTATCGATAGCTATGGTCTTGAGTTGCTTACTGAGCTACTTGGCTCATCCTCTAAGGAGGGATCGGAAGCTGCTGCGGCTTTATTCAAGTTGGCCAGTAAATTCTTGGCCCCATCTCCGGCTACTTCTTTATCAATACATCCGGGCAAATATAGAGAGAGTTTTGCTGATACTGATGGAAAAATGTCAGACGTTATATTTCTTATTGAAGGCAAACTGCTGTATGCACATAAATCTCGAATAATAAATGCTTCAAAGGTGTTGAGTGCTATGGTTACTAAGTCGGAGTCTTTTGTGACGGGCACTGCACACGTAGTGATCACTGAAGTGAAATATAAAGTTTTTGAAAGGATATTGAGATTTATTTACACTGGAAACACATATGTCAGTGTGGATACTGCTAGAGAACTTTTTGAAGCTGCTAGTTATTTTGATTTAGCAGAACTAATGAAACTCTGTGAAAATAAGATTGCTCAGAATGTACTTAGCGTGGAAACTATATGGCTTTTATATGAAGCTGCTGAAGCTTTCGTTGCTCTAACATTAAAGGGTCACTGTATCATGTTTGCATTGAGAAACTATGAAGAGTTGAGGGAAAGGAAACCTGACTTTATTGACAACATGATACCTAAAATACACCATCAGATGGTACACCTCTTACGCAGTGGCAGTTTAGATTGTGCGCGTCCAGACCCACAGTAG
Protein sequence

>MsaT000839.1

MINYGNRNTRSLDDDDVRSFTEFLNDVTITEYDEEYSSKIEEFKNRANFILRMAFHGRILKRMVDLGVVPALARHLVSPITEVVLITLRALKNFAKQYQEQFDETRAVSQIINFLNNSQNEAKHSLIYSSIDILTTLARTSTTMLDSIRIADGIPSLVHLLDDIVHQRVACFALEVLSTNHENATQIVGLGAVPLIILMLYREDRQLHNSVFQMIYNLDGACEIVRRGYLVEAFHPLTELMSSTYFESQRLAIDLLDLIVKTNPQWKIMLIQRGLIPLLTKALTSANEGVQESSVFLLCFLSEDSDCQVGIVNEGLVELLKVLDTKLYSLQVGAAFTLHRLADNKDNVYKFIMLGGVQRLLQGGYLGDTQAFDLFRLTLESLAEKINGHVLTQLLHRMWSLPNDFQTRIALALAYLSSEVDSKRIFIDSYGLELLTELLGSSSKEGSEAAAALFKLASKFLAPSPATSLSIHPGKYRESFADTDGKMSDVIFLIEGKLLYAHKSRIINASKVLSAMVTKSESFVTGTAHVVITEVKYKVFERILRFIYTGNTYVSVDTARELFEAASYFDLAELMKLCENKIAQNVLSVETIWLLYEAAEAFVALTLKGHCIMFALRNYEELRERKPDFIDNMIPKIHHQMVHLLRSGSLDCARPDPQ*