AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG003892

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG003892 MtrunA17_Chr1g0191011 92.063 378 27 2 1 378 1 375 0.0 635
MsaG003892 MtrunA17_Chr1g0191021 32.544 338 170 11 83 374 45 370 2.47e-41 149
MsaG003892 MtrunA17_Chr7g0273821 44.444 171 76 7 74 231 42 206 2.63e-28 115
MsaG003892 MtrunA17_Chr7g0273821 40.000 115 48 5 279 375 323 434 4.25e-12 67.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG003892 AT5G28040.2 34.877 367 153 17 79 375 72 422 1.31e-43 157
MsaG003892 AT5G28040.1 34.877 367 153 17 79 375 72 422 1.31e-43 157
MsaG003892 AT3G04930.1 30.366 382 173 12 79 375 78 451 1.57e-33 130
MsaG003892 AT3G04930.2 36.612 183 89 7 79 242 78 252 9.02e-26 107
MsaG003892 AT1G11510.1 35.606 132 69 4 110 231 105 230 4.00e-13 70.5
MsaG003892 AT1G11510.2 39.394 99 53 2 134 231 109 201 5.26e-13 69.7

Find 96 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTGAATTCCACGCTGAATT+TGG 0.144423 1:+63362072 None:intergenic
TGCTTTCACCATTGGTTTCT+TGG 0.184831 1:-63362600 MsaT003892.1:CDS
TCGAAATTTCCCACAAGATT+TGG 0.203495 1:-63361937 MsaT003892.1:CDS
CGAAATTTCCCACAAGATTT+GGG 0.213735 1:-63361936 MsaT003892.1:CDS
CTTGTGGGAAATTTCGAAAA+TGG 0.256771 1:+63361943 None:intergenic
TCAATAAGATCAGGACTTTC+AGG 0.284560 1:+63361863 None:intergenic
ACCATTGTTGAAGGAACTAT+TGG 0.296222 1:-63361666 MsaT003892.1:CDS
TGAACTGTTGAAGGGATATC+TGG 0.305389 1:-63362170 MsaT003892.1:CDS
TGACACCGACCATGACGTTT+TGG 0.344618 1:-63361909 MsaT003892.1:CDS
AGAAGCTACGTAGGTTAAAA+AGG 0.350716 1:-63362033 MsaT003892.1:CDS
GGGATGAACAATGGTTAAAA+AGG 0.351704 1:-63361583 MsaT003892.1:CDS
ATTGTGAAGAAACAGATAAA+AGG 0.357039 1:-63361808 MsaT003892.1:CDS
TGGTCTTCATCCACATTGTA+TGG 0.361996 1:+63362409 None:intergenic
GCCATGGCCACCGTCACAAC+GGG 0.369780 1:+63362343 None:intergenic
TTGAATTCCACGCTGAATTT+GGG 0.371612 1:+63362073 None:intergenic
GACGCACTGGGTGGCTCTAC+TGG 0.372415 1:+63361635 None:intergenic
CTCAACAATGCTTTCACCAT+TGG 0.374554 1:-63362608 None:intergenic
CATTGTATGGACATAGAAAA+TGG 0.389529 1:+63362422 None:intergenic
TGGTGAGAAACAAGACTTCA+TGG 0.394662 1:+63361685 None:intergenic
GCCGTGTTTGTGTCATCTGC+AGG 0.398083 1:+63362316 None:intergenic
CATCATCCACATTGTCCATT+TGG 0.402335 1:+63362455 None:intergenic
TAGTAGCATTGCCATTGTTC+CGG 0.431642 1:+63361732 None:intergenic
TGAGGGATCTTGAAAGAAAT+CGG 0.433564 1:+63361974 None:intergenic
AATTCAGCGTGGAATTCAAT+AGG 0.439027 1:-63362069 MsaT003892.1:CDS
TTGTTTCTCACCATTGTTGA+AGG 0.439029 1:-63361675 MsaT003892.1:CDS
TAACAACATCGGCGACGCAC+TGG 0.453222 1:+63361622 None:intergenic
AGATCAGGACTTTCAGGAAC+AGG 0.454735 1:+63361869 None:intergenic
CAATGGGAATGTTGTCCATT+TGG 0.457011 1:+63362389 None:intergenic
CCCCGTTGTGACGGTGGCCA+TGG 0.457760 1:-63362344 MsaT003892.1:CDS
TCGCCGATGTTGTTATCGAC+AGG 0.458917 1:-63361614 MsaT003892.1:CDS
TGACAATGTTGAAGACCAAA+TGG 0.469140 1:-63362470 MsaT003892.1:CDS
TATTGACAATGTTAAGATGA+AGG 0.472539 1:-63361846 MsaT003892.1:CDS
GTCATCTGCAGGGGCAGCCA+TGG 0.473001 1:+63362327 None:intergenic
TGAAGCTACGCCACTTTGAA+TGG 0.476510 1:+63362114 None:intergenic
TCAGAAACGGCAAGTGCAAT+GGG 0.486716 1:+63362373 None:intergenic
TTAAACAATATCAGAGGCTA+TGG 0.488222 1:-63362210 MsaT003892.1:CDS
GGACGAGATTGAACTGTTGA+AGG 0.488252 1:-63362179 MsaT003892.1:CDS
TTGTGAAGAAACAGATAAAA+GGG 0.492865 1:-63361807 MsaT003892.1:CDS
AGTGGTAGTAGCCGCGGTGG+TGG 0.497730 1:+63362282 None:intergenic
AAGGAAACACAAGATGACTT+TGG 0.497734 1:-63362014 MsaT003892.1:CDS
CAATGTGGATGAAGACCAAA+TGG 0.497943 1:-63362404 MsaT003892.1:CDS
ATCAGAAACGGCAAGTGCAA+TGG 0.502613 1:+63362372 None:intergenic
TCAGATCAAGGCTAGGTTGG+AGG 0.516669 1:-63361510 MsaT003892.1:CDS
TCGAAAATGGCTTGTTCCTG+AGG 0.518443 1:+63361956 None:intergenic
TTAACATTGTCAATAAGATC+AGG 0.519347 1:+63361854 None:intergenic
GGAGGTGTATTTGAATCGGT+TGG 0.520311 1:-63361546 MsaT003892.1:CDS
GTCATTGCCCCAAATCTTGT+GGG 0.523632 1:+63361928 None:intergenic
ATGTTGTTATCGACAGGGGA+AGG 0.529112 1:-63361608 MsaT003892.1:CDS
CGAAAATGGCTTGTTCCTGA+GGG 0.533678 1:+63361957 None:intergenic
CCGTGTTTGTGTCATCTGCA+GGG 0.538021 1:+63362317 None:intergenic
AACTGGAGGTGTATTTGAAT+CGG 0.540639 1:-63361550 MsaT003892.1:CDS
GATTTCTTTCAAGATCCCTC+AGG 0.542535 1:-63361972 MsaT003892.1:CDS
TGTCATTGCCCCAAATCTTG+TGG 0.546121 1:+63361927 None:intergenic
AATCGGTTGGAGTTGTTGCA+AGG 0.547050 1:-63361533 MsaT003892.1:CDS
AACAACATCGGCGACGCACT+GGG 0.551267 1:+63361623 None:intergenic
TCCAATAGTTCCTTCAACAA+TGG 0.555130 1:+63361665 None:intergenic
ATGGCAATGCTACTAGCATA+CGG 0.556871 1:-63361724 MsaT003892.1:CDS
TGGCAATGCTACTAGCATAC+GGG 0.563532 1:-63361723 MsaT003892.1:CDS
CGCCGATGTTGTTATCGACA+GGG 0.567511 1:-63361613 MsaT003892.1:CDS
AGCCATGGCCACCGTCACAA+CGG 0.580091 1:+63362342 None:intergenic
TGTTATCGACAGGGGAAGGG+AGG 0.580249 1:-63361604 MsaT003892.1:CDS
GTTATCGACAGGGGAAGGGA+GGG 0.582470 1:-63361603 MsaT003892.1:CDS
CAATGTGGATGATGACGAAA+AGG 0.583654 1:-63362446 MsaT003892.1:CDS
GACTTTGGACAAAGGCAAAG+AGG 0.584181 1:-63361999 MsaT003892.1:CDS
GTTGTTGCAAGGTCAGATCA+AGG 0.586461 1:-63361522 MsaT003892.1:CDS
GACAAAATCCAAGAAACCAA+TGG 0.589116 1:+63362592 None:intergenic
TCAGAGGCTATGGACAAAGC+AGG 0.591463 1:-63362200 MsaT003892.1:CDS
TACGTAGCTTCTCAACAAGC+TGG 0.592388 1:+63362044 None:intergenic
AGGTCAGATCAAGGCTAGGT+TGG 0.595411 1:-63361513 MsaT003892.1:CDS
TTCTTCTTCGGATGACGAAG+AGG 0.605501 1:+63362555 None:intergenic
TGTTGTTATCGACAGGGGAA+GGG 0.605894 1:-63361607 MsaT003892.1:CDS
GAAATTTCCCACAAGATTTG+GGG 0.610345 1:-63361935 MsaT003892.1:CDS
GCAAATACTACCATTCAAAG+TGG 0.615727 1:-63362124 MsaT003892.1:CDS
CTGGATTACATTAAACAGCA+AGG 0.616623 1:-63362151 MsaT003892.1:CDS
GACGAGATTGAACTGTTGAA+GGG 0.620700 1:-63362178 MsaT003892.1:CDS
CACAAGATGACTTTGGACAA+AGG 0.621465 1:-63362007 MsaT003892.1:CDS
AACATCCAAAACGTCATGGT+CGG 0.630878 1:+63361904 None:intergenic
AAGGAGGATTCTGGAACTGG+AGG 0.638141 1:-63361564 MsaT003892.1:CDS
CGTGTTTGTGTCATCTGCAG+GGG 0.638603 1:+63362318 None:intergenic
CATCAACATCCAAAACGTCA+TGG 0.640991 1:+63361900 None:intergenic
CCCTGCAGATGACACAAACA+CGG 0.644402 1:-63362317 MsaT003892.1:CDS
TGCAAGGTCAGATCAAGGCT+AGG 0.648837 1:-63361517 MsaT003892.1:CDS
GGCAATGCTACTAGCATACG+GGG 0.651150 1:-63361722 MsaT003892.1:CDS
TGTTATAGTGGTAGTAGCCG+CGG 0.655252 1:+63362276 None:intergenic
GGGAAGGGAGGGATGAACAA+TGG 0.657732 1:-63361592 MsaT003892.1:CDS
GCCGATGTTGTTATCGACAG+GGG 0.669203 1:-63361612 MsaT003892.1:CDS
TCCCCTGTCGATAACAACAT+CGG 0.673860 1:+63361611 None:intergenic
CATGGCCACCGTCACAACGG+GGG 0.676320 1:+63362345 None:intergenic
CCATGGCCACCGTCACAACG+GGG 0.678792 1:+63362344 None:intergenic
ACGGTGTTAAACAATATCAG+AGG 0.680774 1:-63362216 MsaT003892.1:CDS
AGTTATTCCCAAATTCAGCG+TGG 0.688982 1:-63362080 MsaT003892.1:CDS
TATAGTGGTAGTAGCCGCGG+TGG 0.689187 1:+63362279 None:intergenic
TGAAGACCAAATGGACAATG+TGG 0.693003 1:-63362461 MsaT003892.1:CDS
AACATCGGCGACGCACTGGG+TGG 0.698538 1:+63361626 None:intergenic
AACAAACACAGCCACCACCG+CGG 0.714798 1:-63362293 MsaT003892.1:CDS
AGCTTGTTGAGAAGCTACGT+AGG 0.743250 1:-63362042 MsaT003892.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr1 gene 63361487 63362623 63361487 ID=MsaG003892
Chr1 mRNA 63361487 63362623 63361487 ID=MsaT003892.1;Parent=MsaG003892
Chr1 exon 63361487 63362623 63361487 ID=MsaT003892.1.exon1;Parent=MsaT003892.1
Chr1 CDS 63361487 63362623 63361487 ID=cds.MsaT003892.1;Parent=MsaT003892.1
Gene Sequence

>MsaT003892.1

ATGCTTTCACCATTGGTTTCTTGGATTTTGTCAACATCATCATCTTCCTCTTCGTCATCCGAAGAAGAAGAAGAAGAAGAAGAAAGTCTTGACATTAACAATGACGAAGCAGACTGTGAAAACTTTGAAAATGACAATGTTGAAGACCAAATGGACAATGTGGATGATGACGAAAAGGACCATTTTCTATGTCCATACAATGTGGATGAAGACCAAATGGACAACATTCCCATTGCACTTGCCGTTTCTGATGCATCCCCCGTTGTGACGGTGGCCATGGCTGCCCCTGCAGATGACACAAACACGGCAACAAACACAGCCACCACCGCGGCTACTACCACTATAACAACACGCTCAAAACGACAATATAACAAAAAGTATTCAGACGGTGTTAAACAATATCAGAGGCTATGGACAAAGCAGGACGAGATTGAACTGTTGAAGGGATATCTGGATTACATTAAACAGCAAGGAAGAGCAAATACTACCATTCAAAGTGGCGTAGCTTCATTCTATGATCAAGTTATTCCCAAATTCAGCGTGGAATTCAATAGGAACCAGCTTGTTGAGAAGCTACGTAGGTTAAAAAGGAAACACAAGATGACTTTGGACAAAGGCAAAGAGGTTCCGATTTCTTTCAAGATCCCTCAGGAACAAGCCATTTTCGAAATTTCCCACAAGATTTGGGGCAATGACACCGACCATGACGTTTTGGATGTTGATGAATCAAGACCTGTTCCTGAAAGTCCTGATCTTATTGACAATGTTAAGATGAAGGATGAAGATGTTGACAATTGTGAAGAAACAGATAAAAGGGTGCACAAGCGTGTGAAGATAACAACAGATGACGACGTGAACACAAAAAATGACCGGAACAATGGCAATGCTACTAGCATACGGGGCTTCATTGAAGAAACCATGAAGTCTTGTTTCTCACCATTGTTGAAGGAACTATTGGATGATGTTCCAGTAGAGCCACCCAGTGCGTCGCCGATGTTGTTATCGACAGGGGAAGGGAGGGATGAACAATGGTTAAAAAGGAGGATTCTGGAACTGGAGGTGTATTTGAATCGGTTGGAGTTGTTGCAAGGTCAGATCAAGGCTAGGTTGGAGGAGTTAAAGTCTAGCTTAGATTGA
Protein sequence

>MsaT003892.1

MLSPLVSWILSTSSSSSSSSEEEEEEEESLDINNDEADCENFENDNVEDQMDNVDDDEKDHFLCPYNVDEDQMDNIPIALAVSDASPVVTVAMAAPADDTNTATNTATTAATTTITTRSKRQYNKKYSDGVKQYQRLWTKQDEIELLKGYLDYIKQQGRANTTIQSGVASFYDQVIPKFSVEFNRNQLVEKLRRLKRKHKMTLDKGKEVPISFKIPQEQAIFEISHKIWGNDTDHDVLDVDESRPVPESPDLIDNVKMKDEDVDNCEETDKRVHKRVKITTDDDVNTKNDRNNGNATSIRGFIEETMKSCFSPLLKELLDDVPVEPPSASPMLLSTGEGRDEQWLKRRILELEVYLNRLELLQGQIKARLEELKSSLD*