AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG016534

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG016534 MtrunA17_Chr3g0129881 96.429 392 12 2 1 392 1 390 0.0 780
MsaG016534 MtrunA17_Chr1g0146731 60.938 320 121 2 74 392 26 342 1.79e-138 398
MsaG016534 MtrunA17_Chr1g0146761 52.484 322 116 4 74 392 73 360 8.34e-114 336
MsaG016534 MtrunA17_Chr1g0146751 56.250 128 56 0 235 362 69 196 4.79e-44 151
MsaG016534 MtrunA17_Chr1g0146741 49.367 158 55 2 170 312 30 177 9.74e-38 134
MsaG016534 MtrunA17_Chr8g0357751 56.311 103 44 1 235 336 14 116 5.15e-33 121
MsaG016534 MtrunA17_Chr3g0129871 72.464 69 18 1 54 122 1 68 1.52e-31 114
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG016534 AT5G09790.2 65.109 321 109 2 72 392 62 379 1.78e-157 448
MsaG016534 AT5G09790.1 64.798 321 109 2 72 392 62 378 3.14e-156 445
MsaG016534 AT5G24330.1 60.377 318 123 2 76 392 34 349 3.87e-135 390

Find 110 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATGCCACCGTTCTCTAAAA+TGG 0.242537 3:-99038560 None:intergenic
CGTAGGGATTCTCTTGATTC+CGG 0.245953 3:+99036446 MsaT016534.1:CDS
TGGTGAAAGCCGGGTCTTAT+TGG 0.291905 3:+99039458 MsaT016534.1:CDS
AGAAAATTCTCCATTTCTTC+GGG 0.303724 3:+99036420 MsaT016534.1:CDS
AAGAAAATTCTCCATTTCTT+CGG 0.317251 3:+99036419 MsaT016534.1:CDS
AGGCTTTATTATGACTATAA+TGG 0.341103 3:+99039510 MsaT016534.1:CDS
TGAATCATAAACGACCATTA+AGG 0.349153 3:-99038787 None:intergenic
ATTTGCTTCAGCCTCCTATC+AGG 0.349536 3:-99038442 None:intergenic
GTAGGGATTCTCTTGATTCC+GGG 0.353728 3:+99036447 MsaT016534.1:CDS
AATAAGCTGACGTACTTTCC+AGG 0.362677 3:+99038511 MsaT016534.1:CDS
CCCTACGAAGCCCGAAGAAA+TGG 0.364855 3:-99036430 None:intergenic
GAACAATCGTGCTTCTTCTC+AGG 0.365882 3:+99036469 MsaT016534.1:CDS
AGGCCAATTCCCTCCCTTAA+TGG 0.366828 3:+99038773 MsaT016534.1:CDS
ATAAATGTCATATCTTTGAT+TGG 0.375561 3:-99038933 None:intergenic
TCTTTGTATCTTCCTTAGTA+AGG 0.376226 3:-99038719 None:intergenic
TGCTACTGCTTTAACAGCAT+TGG 0.399408 3:+99038474 MsaT016534.1:CDS
TTCTGTACCACCAGAGGTCT+TGG 0.407511 3:-99038379 None:intergenic
AGAAGAAGCACGATTGTTCC+CGG 0.418393 3:-99036465 None:intergenic
ATCGGAACTCGAACAACAAT+TGG 0.420274 3:-99036222 None:intergenic
GCAGATCTAGGAGCCATTCC+TGG 0.421695 3:-99038529 None:intergenic
CGCTTGTTAATATATATAAG+AGG 0.428689 3:+99036064 MsaT016534.1:CDS
ATGTGGGTCCGGTGAACAAC+CGG 0.439307 3:+99036143 MsaT016534.1:CDS
GGATCTTCTGTAGGAACAAA+TGG 0.446011 3:-99038421 None:intergenic
GAATCATAAACGACCATTAA+GGG 0.451048 3:-99038786 None:intergenic
TAAATGTCATATCTTTGATT+GGG 0.451435 3:-99038932 None:intergenic
GATTAAGCTTGATAGCTTGA+TGG 0.452643 3:-99035947 None:intergenic
CTCTGGTGGTACAGAAGAAA+AGG 0.456244 3:+99038386 MsaT016534.1:CDS
TTCCTCTCAGGCCCTTACTA+AGG 0.457202 3:+99038707 MsaT016534.1:intron
GACCTTGACATCAGAACACT+TGG 0.458131 3:-99036262 None:intergenic
ACCTCCTGTGTGAGCAATGT+GGG 0.458530 3:+99036127 MsaT016534.1:CDS
GCTGAGGAGGAGGAGGATTA+CGG 0.459874 3:+99036102 MsaT016534.1:CDS
CTCCACCTTCGAGGAGGAGG+AGG 0.460011 3:+99036026 MsaT016534.1:CDS
GGCTGAGTACACGGTGGCTG+AGG 0.462695 3:+99036086 MsaT016534.1:CDS
CTCCTCTTCCTCCACCTTCG+AGG 0.464032 3:+99036017 MsaT016534.1:CDS
CTCCTCGAAGGTGGAGGAAG+AGG 0.464573 3:-99036019 None:intergenic
CGACCATTAAGGGAGGGAAT+TGG 0.466483 3:-99038776 None:intergenic
TTCCTCCACCTTCGAGGAGG+AGG 0.469701 3:+99036023 MsaT016534.1:CDS
AATTTATATGCAGGGAAGGC+AGG 0.471087 3:+99039397 MsaT016534.1:intron
CCATTTCTTCGGGCTTCGTA+GGG 0.472840 3:+99036430 MsaT016534.1:CDS
CTTTGTATCTTCCTTAGTAA+GGG 0.478851 3:-99038718 None:intergenic
GGGCAAATCCACGGACCAAT+CGG 0.479975 3:-99036240 None:intergenic
TCACATAAAAGCAGCTCCTC+CGG 0.483953 3:-99036162 None:intergenic
TGATAGGAGGCTGAAGCAAA+TGG 0.484670 3:+99038444 MsaT016534.1:CDS
TCCATTTCTTCGGGCTTCGT+AGG 0.489521 3:+99036429 MsaT016534.1:CDS
TTCCTACAGAAGATCCTGAT+AGG 0.493201 3:+99038428 MsaT016534.1:CDS
AATGGCTCCGGCGACAGCTC+CGG 0.497607 3:+99035906 None:intergenic
TGTGTGAGATATGATGTTAA+TGG 0.499519 3:+99039438 MsaT016534.1:CDS
ATGGATCGATTAGCAGATCT+AGG 0.502517 3:-99038541 None:intergenic
GTCGTTTATGATTCATGCCA+AGG 0.503792 3:+99038795 MsaT016534.1:CDS
CTGTGTGAGCAATGTGGGTC+CGG 0.504059 3:+99036132 MsaT016534.1:CDS
CTCAGACAAAATGATGAGTT+GGG 0.506277 3:-99039548 None:intergenic
CACGGTGGCTGAGGAGGAGG+AGG 0.506420 3:+99036095 MsaT016534.1:CDS
CAGCTCCTCCGGTTGTTCAC+CGG 0.511216 3:-99036151 None:intergenic
GCTCAGACAAAATGATGAGT+TGG 0.512353 3:-99039549 None:intergenic
TCGGAGACGTCCAAGACCTC+TGG 0.514165 3:+99038369 MsaT016534.1:CDS
TGAGTACACGGTGGCTGAGG+AGG 0.515374 3:+99036089 MsaT016534.1:CDS
CCCCAAGTGTTCTGATGTCA+AGG 0.520959 3:+99036260 MsaT016534.1:CDS
CTCCTCCTCCTCGAAGGTGG+AGG 0.525162 3:-99036025 None:intergenic
ATGATGTTAATGGTGAAAGC+CGG 0.525411 3:+99039448 MsaT016534.1:CDS
TTTAGAGAACGGTGGCATGC+AGG 0.534531 3:+99038564 MsaT016534.1:CDS
ACCTTGACATCAGAACACTT+GGG 0.540926 3:-99036261 None:intergenic
AACAATCGTGCTTCTTCTCA+GGG 0.545517 3:+99036470 MsaT016534.1:CDS
GTACACGGTGGCTGAGGAGG+AGG 0.545768 3:+99036092 MsaT016534.1:CDS
TGATGTTAATGGTGAAAGCC+GGG 0.546415 3:+99039449 MsaT016534.1:CDS
TTCGAGTTCCGATTGGTCCG+TGG 0.546720 3:+99036232 MsaT016534.1:CDS
ACATTTATTGCTGAATACAC+TGG 0.549884 3:+99038948 MsaT016534.1:CDS
GGAGACGCCGGAGCTGTCGC+CGG 0.559953 3:-99035913 None:intergenic
ATTGTTGTTCGAGTTCCGAT+TGG 0.560719 3:+99036225 MsaT016534.1:CDS
CTCGAAGGTGGAGGAAGAGG+AGG 0.563327 3:-99036016 None:intergenic
CCCCTCCTCCTCCTCGAAGG+TGG 0.568245 3:-99036028 None:intergenic
CAACCTCACCTGAATGGCTC+CGG 0.568822 3:+99035894 None:intergenic
ATGCTGTTAAAGCAGTAGCA+AGG 0.571401 3:-99038471 None:intergenic
TGCTGTTAAAGCAGTAGCAA+GGG 0.574924 3:-99038470 None:intergenic
CCACCTTCGAGGAGGAGGAG+GGG 0.583605 3:+99036028 MsaT016534.1:CDS
TCCACCTTCGAGGAGGAGGA+GGG 0.584045 3:+99036027 MsaT016534.1:CDS
CTTTAGATGCTATGAAGCGT+CGG 0.589068 3:+99038350 MsaT016534.1:intron
ATTCCCCTCCTCCTCCTCGA+AGG 0.589669 3:-99036031 None:intergenic
CTTGATAGCTTGATGGAAGA+CGG 0.590190 3:-99035940 None:intergenic
GCTTGTTAATATATATAAGA+GGG 0.591764 3:+99036065 MsaT016534.1:CDS
GCTGACGTACTTTCCAGGAA+TGG 0.592256 3:+99038516 MsaT016534.1:CDS
CTCCTATCAGGATCTTCTGT+AGG 0.592606 3:-99038430 None:intergenic
GAACACTTGGGGCAAATCCA+CGG 0.593747 3:-99036249 None:intergenic
GAAGACGGCGATGGAGACGC+CGG 0.596034 3:-99035925 None:intergenic
CCTTGACATCAGAACACTTG+GGG 0.598005 3:-99036260 None:intergenic
ATATAAGAGGGCTGAGTACA+CGG 0.598652 3:+99036077 MsaT016534.1:CDS
AACATTGCTCGCTTCATCAG+TGG 0.600548 3:+99039083 MsaT016534.1:CDS
AGCTTGATGGAAGACGGCGA+TGG 0.603823 3:-99035934 None:intergenic
TTATGTGACAAATGTGACAA+TGG 0.612992 3:+99036177 MsaT016534.1:CDS
TGTGAGGTGCATGGGTGCGG+CGG 0.615402 3:-99035969 None:intergenic
GCTACTCGAGATATTTCCAA+GGG 0.615468 3:+99039483 MsaT016534.1:CDS
CTCTTCCTCCACCTTCGAGG+AGG 0.618161 3:+99036020 MsaT016534.1:CDS
TGCTACTCGAGATATTTCCA+AGG 0.618331 3:+99039482 MsaT016534.1:CDS
TCGTTTATGATTCATGCCAA+GGG 0.622600 3:+99038796 MsaT016534.1:CDS
CGGACCCACATTGCTCACAC+AGG 0.629732 3:-99036131 None:intergenic
CATAAACGACCATTAAGGGA+GGG 0.633637 3:-99038782 None:intergenic
CTACAGAAGATCCTGATAGG+AGG 0.635132 3:+99038431 MsaT016534.1:CDS
TCATAAACGACCATTAAGGG+AGG 0.648173 3:-99038783 None:intergenic
ACCCACATTGCTCACACAGG+AGG 0.655882 3:-99036128 None:intergenic
GAGTAGCAACCAATAAGACC+CGG 0.658883 3:-99039467 None:intergenic
GACCTCCTGTGTGAGCAATG+TGG 0.660393 3:+99036126 MsaT016534.1:CDS
TGGTACAGAAGAAAAGGAGA+AGG 0.674031 3:+99038392 MsaT016534.1:CDS
GAGACGTCCAAGACCTCTGG+TGG 0.674893 3:+99038372 MsaT016534.1:CDS
TGGGTCCGGTGAACAACCGG+AGG 0.676363 3:+99036146 MsaT016534.1:CDS
GCAATGTAGCTATACTGTGG+AGG 0.683236 3:+99038902 MsaT016534.1:intron
TACTCGAGATATTTCCAAGG+GGG 0.699750 3:+99039485 MsaT016534.1:CDS
GTTATCTGTGCTGATAAACG+TGG 0.699829 3:+99039059 MsaT016534.1:CDS
TGCATAGCTATGACTAAACG+AGG 0.704634 3:+99038753 MsaT016534.1:CDS
CTACTCGAGATATTTCCAAG+GGG 0.743213 3:+99039484 MsaT016534.1:CDS
TATGCAATGTAGCTATACTG+TGG 0.744881 3:+99038899 MsaT016534.1:intron
TAAGAGGGCTGAGTACACGG+TGG 0.812154 3:+99036080 MsaT016534.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr3 gene 99035907 99039569 99035907 ID=MsaG016534
Chr3 mRNA 99035907 99039569 99035907 ID=MsaT016534.1;Parent=MsaG016534
Chr3 exon 99035907 99036297 99035907 ID=MsaT016534.1.exon1;Parent=MsaT016534.1
Chr3 CDS 99035907 99036297 99035907 ID=cds.MsaT016534.1;Parent=MsaT016534.1
Chr3 exon 99036408 99036491 99036408 ID=MsaT016534.1.exon2;Parent=MsaT016534.1
Chr3 CDS 99036408 99036491 99036408 ID=cds.MsaT016534.1;Parent=MsaT016534.1
Chr3 exon 99038356 99038585 99038356 ID=MsaT016534.1.exon3;Parent=MsaT016534.1
Chr3 CDS 99038356 99038585 99038356 ID=cds.MsaT016534.1;Parent=MsaT016534.1
Chr3 exon 99038717 99038817 99038717 ID=MsaT016534.1.exon4;Parent=MsaT016534.1
Chr3 CDS 99038717 99038817 99038717 ID=cds.MsaT016534.1;Parent=MsaT016534.1
Chr3 exon 99038911 99039123 99038911 ID=MsaT016534.1.exon5;Parent=MsaT016534.1
Chr3 CDS 99038911 99039123 99038911 ID=cds.MsaT016534.1;Parent=MsaT016534.1
Chr3 exon 99039410 99039569 99039410 ID=MsaT016534.1.exon6;Parent=MsaT016534.1
Chr3 CDS 99039410 99039569 99039410 ID=cds.MsaT016534.1;Parent=MsaT016534.1
Gene Sequence

>MsaT016534.1

ATGGCTCCGGCGACAGCTCCGGCGTCTCCATCGCCGTCTTCCATCAAGCTATCAAGCTTAATCCGCCGCACCCATGCACCTCACAAAATTCAAAAGAAGCTGTCATACTCCTCCTCTTCCTCCACCTTCGAGGAGGAGGAGGGGAATAAGTTACTATCGCTTGTTAATATATATAAGAGGGCTGAGTACACGGTGGCTGAGGAGGAGGAGGATTACGGTGACCTCCTGTGTGAGCAATGTGGGTCCGGTGAACAACCGGAGGAGCTGCTTTTATGTGACAAATGTGACAATGGTTTTCATATGAAATGTGTCAGACCAATTGTTGTTCGAGTTCCGATTGGTCCGTGGATTTGCCCCAAGTGTTCTGATGTCAAGGTCAAGAAACTCAAAAAGCTTTCTCAGAAGAAAATTCTCCATTTCTTCGGGCTTCGTAGGGATTCTCTTGATTCCGGGAACAATCGTGCTTCTTCTCAGGATGCTATGAAGCGTCGGAGACGTCCAAGACCTCTGGTGGTACAGAAGAAAAGGAGAAGGCTTTTACCATTTGTTCCTACAGAAGATCCTGATAGGAGGCTGAAGCAAATGGCTTCCCTTGCTACTGCTTTAACAGCATTGGATATAGAGTTCAGTAATAAGCTGACGTACTTTCCAGGAATGGCTCCTAGATCTGCTAATCGATCCATTTTAGAGAACGGTGGCATGCAGGCCCTTACTAAGGAAGATACAAAGACCTTAAAACACTGCATAGCTATGACTAAACGAGGCCAATTCCCTCCCTTAATGGTCGTTTATGATTCATGCCAAGGCTATACTGTGGAGGCTGATAGCCCAATCAAAGATATGACATTTATTGCTGAATACACTGGCGATGTTGATTATATAAAGAAGCGAGAATCTGATGATTGTGACAGTATGATGACACTGATTATTGCAGCAAAAGCTGCTGACAGTCTTGTTATCTGTGCTGATAAACGTGGAAACATTGCTCGCTTCATCAGTGGCATCAACAATCATACTCAGGAAGGCAGGAAGAAGCAGAACTGTAAATGTGTGAGATATGATGTTAATGGTGAAAGCCGGGTCTTATTGGTTGCTACTCGAGATATTTCCAAGGGGGAGAGGCTTTATTATGACTATAATGGTTATGTGCATGAATACCCAACTCATCATTTTGTCTGA
Protein sequence

>MsaT016534.1

MAPATAPASPSPSSIKLSSLIRRTHAPHKIQKKLSYSSSSSTFEEEEGNKLLSLVNIYKRAEYTVAEEEEDYGDLLCEQCGSGEQPEELLLCDKCDNGFHMKCVRPIVVRVPIGPWICPKCSDVKVKKLKKLSQKKILHFFGLRRDSLDSGNNRASSQDAMKRRRRPRPLVVQKKRRRLLPFVPTEDPDRRLKQMASLATALTALDIEFSNKLTYFPGMAPRSANRSILENGGMQALTKEDTKTLKHCIAMTKRGQFPPLMVVYDSCQGYTVEADSPIKDMTFIAEYTGDVDYIKKRESDDCDSMMTLIIAAKAADSLVICADKRGNIARFISGINNHTQEGRKKQNCKCVRYDVNGESRVLLVATRDISKGERLYYDYNGYVHEYPTHHFV*