AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG016506


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG016506 MtrunA17_Chr3g0129551 98.319 357 6 0 1 357 1 357 0.0 726
MsaG016506 MtrunA17_Chr7g0255811 31.163 215 119 5 3 200 6 208 3.09e-23 100
MsaG016506 MtrunA17_Chr6g0466661 52.000 75 34 2 52 126 7 79 4.14e-13 64.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG016506 AT5G09850.1 53.804 368 144 10 1 357 1 353 1.43e-116 342
MsaG016506 AT5G09850.4 53.804 368 144 10 1 357 1 353 1.43e-116 342
MsaG016506 AT5G09850.2 53.804 368 144 10 1 357 1 353 1.43e-116 342
MsaG016506 AT5G09850.5 53.804 368 144 10 1 357 1 353 1.43e-116 342
MsaG016506 AT5G09850.3 51.632 337 140 8 1 326 1 325 3.19e-99 297
MsaG016506 AT5G05140.1 25.728 412 220 13 3 334 7 412 4.82e-21 94.4
MsaG016506 AT3G10820.1 29.500 200 117 6 1 199 8 184 4.35e-15 76.3
MsaG016506 AT3G10820.2 28.000 200 120 4 1 199 8 184 1.41e-14 75.5

Find 95 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGAGGAACTGATTTAGGTTT+TGG 0.207613 3:-98749905 None:intergenic
GCAGAGGTAGGGGCAGTAAC+TGG 0.242308 3:-98749962 None:intergenic
GACTGTTCTCTTTCTTGATT+TGG 0.252210 3:-98748744 None:intergenic
CTATTCTCACTGTGTGGATT+TGG 0.266353 3:-98749754 None:intergenic
CCTGATGATTATGCCCATTT+GGG 0.274665 3:-98749627 None:intergenic
GTTGACCTCCGTCGCAATTC+TGG 0.284508 3:-98748702 None:intergenic
TCTTTGCGAGGAACTGATTT+AGG 0.295138 3:-98749911 None:intergenic
ACCTGATGATTATGCCCATT+TGG 0.307811 3:-98749628 None:intergenic
ACACGGCGGGCGTTGACGTC+TGG 0.362780 3:+98748560 MsaT016506.1:CDS
TCAGTCTGAAGATACTTTGA+TGG 0.368003 3:+98749048 MsaT016506.1:intron
CCGCGGCGCGGTTGTCGTTC+CGG 0.369159 3:-98748778 None:intergenic
GATGGAGTTGCTACAAAATC+TGG 0.369937 3:+98749066 MsaT016506.1:CDS
CAGAGGTAGGGGCAGTAACT+GGG 0.397450 3:-98749961 None:intergenic
GGAAAGAAATTGTTGATGAT+TGG 0.408203 3:+98749417 MsaT016506.1:CDS
TTGCAGAAAACCACCCCAAA+TGG 0.410008 3:+98749613 MsaT016506.1:CDS
GTTCAGCTTCGGAGGTGTTA+CGG 0.414057 3:-98749877 None:intergenic
AACTACAAAGAGGCCGATAA+TGG 0.421647 3:+98750183 MsaT016506.1:CDS
AATCAATCACCTTCAACTCT+TGG 0.433018 3:-98749108 None:intergenic
AATCGACGAACATTGCTTGA+TGG 0.437135 3:-98749278 None:intergenic
TTTGGAGAGTACGCAAAATC+AGG 0.441104 3:-98749736 None:intergenic
TATTACATTCCAAGAGTTGA+AGG 0.441822 3:+98749099 MsaT016506.1:CDS
AGAGGTAGGGGCAGTAACTG+GGG 0.442679 3:-98749960 None:intergenic
CGCGATCTCCGTCGCTGCGC+AGG 0.445659 3:+98748597 MsaT016506.1:CDS
GAGGTAGGGGCAGTAACTGG+GGG 0.447109 3:-98749959 None:intergenic
GAAAGAAATTGTTGATGATT+GGG 0.457864 3:+98749418 MsaT016506.1:CDS
GCTGACACAGATGGGAGCTC+TGG 0.459360 3:+98749848 MsaT016506.1:intron
CCGTCGCAATTCTGGCAAAT+CGG 0.468609 3:-98748694 None:intergenic
GCTTCTAGAAGATCCTCATC+AGG 0.474811 3:+98748921 MsaT016506.1:CDS
GTTCTCAAGGAAGGCAGCAC+TGG 0.479451 3:+98750390 MsaT016506.1:CDS
CCCAAATGGGCATAATCATC+AGG 0.480623 3:+98749627 MsaT016506.1:CDS
AGGTAGGGGCAGTAACTGGG+GGG 0.499817 3:-98749958 None:intergenic
TTTCCTTCAGACTGCGGCGT+CGG 0.501959 3:-98748817 None:intergenic
ATCAAGCAATGTTCGTCGAT+TGG 0.507263 3:+98749280 MsaT016506.1:CDS
AAGAGGGAAAAGCACTCTCA+TGG 0.508075 3:+98749457 MsaT016506.1:CDS
TGCAGAAAACCACCCCAAAT+GGG 0.518736 3:+98749614 MsaT016506.1:CDS
CCTTCAGACTGCGGCGTCGG+AGG 0.522259 3:-98748814 None:intergenic
GGCTTGCTGCTGCAAGAAAA+CGG 0.522716 3:+98750151 MsaT016506.1:CDS
TGTCGTTCCGGACTCAGACT+AGG 0.527954 3:-98748766 None:intergenic
CCTAAGTCAAAAGCAAAGAA+TGG 0.530585 3:+98750338 MsaT016506.1:CDS
ATAACGCCGGTGAGCTAAAG+AGG 0.531488 3:+98748620 MsaT016506.1:CDS
GCAAAGAACAATTCAGGTGA+TGG 0.534043 3:+98750301 MsaT016506.1:CDS
GAACAGTCCTAGTCTGAGTC+CGG 0.534784 3:+98748759 MsaT016506.1:CDS
CCTCCGACGCCGCAGTCTGA+AGG 0.534970 3:+98748814 MsaT016506.1:CDS
AAAGGTGGTGGCAGTTCTCA+AGG 0.538937 3:+98750377 MsaT016506.1:CDS
TTTGTGTAGGAAACTGACAT+AGG 0.539813 3:+98749227 MsaT016506.1:intron
TTTGCAAAGCACAAAGGTGG+TGG 0.542006 3:+98750365 MsaT016506.1:CDS
CATTCTGAGGAGCAGAGGTA+GGG 0.542374 3:-98749973 None:intergenic
ATTCTGAGGAGCAGAGGTAG+GGG 0.547934 3:-98749972 None:intergenic
GGTAGGGGCAGTAACTGGGG+GGG 0.560913 3:-98749957 None:intergenic
TTGTGTAGGAAACTGACATA+GGG 0.564467 3:+98749228 MsaT016506.1:intron
GGCGTTATCCTGCGCAGCGA+CGG 0.566982 3:-98748605 None:intergenic
GTGAAGCAGAATCCACAAAG+AGG 0.569929 3:+98749440 MsaT016506.1:CDS
TTTGGAGGTGGGTCTTTGCG+AGG 0.573343 3:-98749923 None:intergenic
ATGATTATGCCCATTTGGGG+TGG 0.576734 3:-98749623 None:intergenic
AGAGGGAAAAGCACTCTCAT+GGG 0.577480 3:+98749458 MsaT016506.1:CDS
GAGGAGAAGAGACGGAATCG+TGG 0.579304 3:+98748639 MsaT016506.1:CDS
ATTCAAAACCGTACATTCTG+AGG 0.580864 3:-98749986 None:intergenic
ACATTCTGAGGAGCAGAGGT+AGG 0.580912 3:-98749974 None:intergenic
AGCTTCGGAGGTGTTACGGT+CGG 0.581005 3:-98749873 None:intergenic
GAGCTAAAGAGGAGAAGAGA+CGG 0.582096 3:+98748631 MsaT016506.1:CDS
CGATCTATATTACACACGGC+GGG 0.584757 3:+98748547 MsaT016506.1:CDS
GAACGACAACCGCGCCGCGG+CGG 0.588629 3:+98748781 MsaT016506.1:CDS
TCTTCTCCTCTTTAGCTCAC+CGG 0.592478 3:-98748626 None:intergenic
TCATCAAACAAACCACCGTA+AGG 0.594373 3:-98748868 None:intergenic
GATGAGGAGATAGATCCTTA+CGG 0.597718 3:+98748853 MsaT016506.1:CDS
CCGCCGTGTGTAATATAGAT+CGG 0.605511 3:-98748546 None:intergenic
TAATTAAACAAAACCTGATG+AGG 0.606618 3:-98748934 None:intergenic
TACTTTGCAAAGCACAAAGG+TGG 0.607829 3:+98750362 MsaT016506.1:CDS
AAACGAAGACGGTGAAGATG+AGG 0.609578 3:+98748837 MsaT016506.1:CDS
GAAGAAGCTCCGCCGCGGCG+CGG 0.611025 3:-98748790 None:intergenic
CTGCGCAGCGACGGAGATCG+CGG 0.611264 3:-98748596 None:intergenic
CCGATTTGCCAGAATTGCGA+CGG 0.612546 3:+98748694 MsaT016506.1:CDS
TGAAGCAGAATCCACAAAGA+GGG 0.616018 3:+98749441 MsaT016506.1:CDS
CGGAAATCGTCCAAATCCAT+CGG 0.620451 3:-98748526 None:intergenic
GTGGTGGCAGTTCTCAAGGA+AGG 0.622677 3:+98750381 MsaT016506.1:CDS
CCGTACATTCTGAGGAGCAG+AGG 0.628754 3:-98749978 None:intergenic
CTGATGATTATGCCCATTTG+GGG 0.635715 3:-98749626 None:intergenic
CAGTCTGAAGGAAACGAAGA+CGG 0.636870 3:+98748826 MsaT016506.1:CDS
ATTTGCCAGAATTGCGACGG+AGG 0.638773 3:+98748697 MsaT016506.1:CDS
GCGTCTCTACGCTGCCACCA+CGG 0.639790 3:+98748663 MsaT016506.1:CDS
GGTTACTTTGCAAAGCACAA+AGG 0.645193 3:+98750359 MsaT016506.1:CDS
AAGACCCACCTCCAAAACCA+AGG 0.647167 3:+98749930 MsaT016506.1:CDS
GGAGTTGCTACAAAATCTGG+TGG 0.648131 3:+98749069 MsaT016506.1:CDS
TGTAGGAAACTGACATAGGG+AGG 0.652621 3:+98749231 MsaT016506.1:intron
CCGGAACGACAACCGCGCCG+CGG 0.654440 3:+98748778 MsaT016506.1:CDS
GTCGCTGCGCAGGATAACGC+CGG 0.655654 3:+98748607 MsaT016506.1:CDS
GCTTCAAGCGAACTACAAAG+AGG 0.673966 3:+98750173 MsaT016506.1:CDS
TCTTCGTTTCCTTCAGACTG+CGG 0.687107 3:-98748823 None:intergenic
GAGGAGAAGAAGCTCCGCCG+CGG 0.688012 3:-98748795 None:intergenic
TTTCCGATCTATATTACACA+CGG 0.691280 3:+98748543 MsaT016506.1:CDS
AATCGGAGTAACCTCCGTGG+TGG 0.706021 3:-98748677 None:intergenic
GAGGAGATAGATCCTTACGG+TGG 0.724438 3:+98748856 MsaT016506.1:CDS
CCGATCTATATTACACACGG+CGG 0.755687 3:+98748546 MsaT016506.1:CDS
GCAAATCGGAGTAACCTCCG+TGG 0.764862 3:-98748680 None:intergenic
TCTCTACGCTGCCACCACGG+AGG 0.775314 3:+98748666 MsaT016506.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr3 gene 98748529 98750415 98748529 ID=MsaG016506
Chr3 mRNA 98748529 98750415 98748529 ID=MsaT016506.1;Parent=MsaG016506
Chr3 exon 98748529 98748942 98748529 ID=MsaT016506.1.exon1;Parent=MsaT016506.1
Chr3 CDS 98748529 98748942 98748529 ID=cds.MsaT016506.1;Parent=MsaT016506.1
Chr3 exon 98749052 98749120 98749052 ID=MsaT016506.1.exon2;Parent=MsaT016506.1
Chr3 CDS 98749052 98749120 98749052 ID=cds.MsaT016506.1;Parent=MsaT016506.1
Chr3 exon 98749236 98749318 98749236 ID=MsaT016506.1.exon3;Parent=MsaT016506.1
Chr3 CDS 98749236 98749318 98749236 ID=cds.MsaT016506.1;Parent=MsaT016506.1
Chr3 exon 98749412 98749479 98749412 ID=MsaT016506.1.exon4;Parent=MsaT016506.1
Chr3 CDS 98749412 98749479 98749412 ID=cds.MsaT016506.1;Parent=MsaT016506.1
Chr3 exon 98749596 98749648 98749596 ID=MsaT016506.1.exon5;Parent=MsaT016506.1
Chr3 CDS 98749596 98749648 98749596 ID=cds.MsaT016506.1;Parent=MsaT016506.1
Chr3 exon 98749733 98749766 98749733 ID=MsaT016506.1.exon6;Parent=MsaT016506.1
Chr3 CDS 98749733 98749766 98749733 ID=cds.MsaT016506.1;Parent=MsaT016506.1
Chr3 exon 98749858 98749994 98749858 ID=MsaT016506.1.exon7;Parent=MsaT016506.1
Chr3 CDS 98749858 98749994 98749858 ID=cds.MsaT016506.1;Parent=MsaT016506.1
Chr3 exon 98750111 98750204 98750111 ID=MsaT016506.1.exon8;Parent=MsaT016506.1
Chr3 CDS 98750111 98750204 98750111 ID=cds.MsaT016506.1;Parent=MsaT016506.1
Chr3 exon 98750294 98750415 98750294 ID=MsaT016506.1.exon9;Parent=MsaT016506.1
Chr3 CDS 98750294 98750415 98750294 ID=cds.MsaT016506.1;Parent=MsaT016506.1
Gene Sequence

>MsaT016506.1

ATGGATTTGGACGATTTCCGATCTATATTACACACGGCGGGCGTTGACGTCTGGATGTTCATCGACACCGCGATCTCCGTCGCTGCGCAGGATAACGCCGGTGAGCTAAAGAGGAGAAGAGACGGAATCGTGGAGCGTCTCTACGCTGCCACCACGGAGGTTACTCCGATTTGCCAGAATTGCGACGGAGGTCAACGTCTTGTGACAAACGATAACCAAATCAAGAAAGAGAACAGTCCTAGTCTGAGTCCGGAACGACAACCGCGCCGCGGCGGAGCTTCTTCTCCTCCGACGCCGCAGTCTGAAGGAAACGAAGACGGTGAAGATGAGGAGATAGATCCTTACGGTGGTTTGTTTGATGATGAACAGAAGAAGATTCTAGAGATTAAAGAGCTTCTAGAAGATCCTCATCAGTCTGAAGATACTTTGATGGAGTTGCTACAAAATCTGGTGGATATTGATATTACATTCCAAGAGTTGAAGGAAACTGACATAGGGAGGAACGTGAATCAGTTGCGAAAACATCCATCAAGCAATGTTCGTCGATTGGTGAAGCTACTTGTCAAGAAGTGGAAAGAAATTGTTGATGATTGGGTGAAGCAGAATCCACAAAGAGGGAAAAGCACTCTCATGGCTGATGGAGACTCTCCTTTGCAGAAAACCACCCCAAATGGGCATAATCATCAGATTCCTGATTTTGCGTACTCTCCAAATCCACACAATGGGAGCTCTGGTTCCGACCGTAACACCTCCGAAGCTGAACCAAAACCAAAACCTAAATCAGTTCCTCGCAAAGACCCACCTCCAAAACCAAGGCCATCCCCCCCAGTTACTGCCCCTACCTCTGCTCCTCAGAATAGACAGAGAGAACAGAAAGAGAGCAATTTTGATGCAGAGAGGCTTGCTGCTGCAAGAAAACGGCTTCAAGCGAACTACAAAGAGGCCGATAATGCAAAAAAGCAAAGAACAATTCAGGTGATGGACATACATGAGTTACCTAAGTCAAAAGCAAAGAATGGTTACTTTGCAAAGCACAAAGGTGGTGGCAGTTCTCAAGGAAGGCAGCACTGGTGA

Protein sequence

>MsaT016506.1

MDLDDFRSILHTAGVDVWMFIDTAISVAAQDNAGELKRRRDGIVERLYAATTEVTPICQNCDGGQRLVTNDNQIKKENSPSLSPERQPRRGGASSPPTPQSEGNEDGEDEEIDPYGGLFDDEQKKILEIKELLEDPHQSEDTLMELLQNLVDIDITFQELKETDIGRNVNQLRKHPSSNVRRLVKLLVKKWKEIVDDWVKQNPQRGKSTLMADGDSPLQKTTPNGHNHQIPDFAYSPNPHNGSSGSDRNTSEAEPKPKPKSVPRKDPPPKPRPSPPVTAPTSAPQNRQREQKESNFDAERLAAARKRLQANYKEADNAKKQRTIQVMDIHELPKSKAKNGYFAKHKGGGSSQGRQHW*