AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG040811

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG040811 MtrunA17_Chr5g0430431 30.542 203 94 5 36 204 71 260 4.27e-17 77.0
MsaG040811 MtrunA17_Chr2g0281511 32.692 104 67 1 98 201 19 119 1.61e-15 70.1
MsaG040811 MtrunA17_Chr2g0309121 31.731 104 67 2 98 201 19 118 1.39e-14 67.4
MsaG040811 MtrunA17_Chr6g0459981 36.111 108 63 4 97 204 59 160 8.18e-13 63.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 48 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCAAACTTATCACTTCAAAT+AGG 0.238418 7:-104069989 MsaT040811.1:CDS
TCACCTAAGTATTTCTCATT+TGG 0.308885 7:+104069963 None:intergenic
CAAACTTATCACTTCAAATA+GGG 0.313955 7:-104069988 MsaT040811.1:CDS
TTGTTTAGCACTTCCCCAAT+AGG 0.356270 7:-104070088 MsaT040811.1:intron
CAGGTTCAAGATGATGGTTT+TGG 0.363392 7:-104070354 MsaT040811.1:CDS
CAGTTGATAGATATCCTATT+GGG 0.375059 7:+104070074 None:intergenic
TCTACGGTCCTTCACGAACT+TGG 0.378944 7:+104069932 None:intergenic
ACAGGAGAGCATTACTTTGC+AGG 0.396717 7:-104070039 MsaT040811.1:CDS
ACGTCGCAGCTAAATTCAAC+TGG 0.409112 7:-104070421 MsaT040811.1:CDS
TAAGTTTGCACTCATATTCT+CGG 0.417716 7:+104070003 None:intergenic
GCAGTTGATAGATATCCTAT+TGG 0.431455 7:+104070073 None:intergenic
ACCTCCACAAAGAGGCGATT+GGG 0.431919 7:+104069867 None:intergenic
AACTATCGTTTATCCACAAC+AGG 0.438370 7:-104070719 MsaT040811.1:intron
TCAAAGATACAAGTATGTTC+TGG 0.438514 7:-104070568 MsaT040811.1:CDS
GGGAGAAACCAACACGTGTT+AGG 0.454348 7:-104070400 MsaT040811.1:CDS
TCCTCCCAATCGCCTCTTTG+TGG 0.457073 7:-104069871 MsaT040811.1:CDS
AGAAATACTTAGGTGAAGAT+TGG 0.462766 7:-104069956 MsaT040811.1:CDS
GGTTGTCCGACGCCGTCGTT+AGG 0.473479 7:-104069847 None:intergenic
GTAATGCTCTCCTGTGTGTC+GGG 0.473972 7:+104070047 None:intergenic
TCTCTTGTTGTTGTTAGCTG+TGG 0.501306 7:+104070214 None:intergenic
TATCACCTTTCCTTAGTCTA+CGG 0.505505 7:+104069916 None:intergenic
GGTCCAAATGAGAAATACTT+AGG 0.515401 7:-104069966 MsaT040811.1:CDS
CGTGTTAGGCTTGAATATAC+TGG 0.538941 7:-104070386 MsaT040811.1:CDS
TCCCAATCGCCTCTTTGTGG+AGG 0.540742 7:-104069868 MsaT040811.1:CDS
TCGTGAAGGACCGTAGACTA+AGG 0.541590 7:-104069926 MsaT040811.1:CDS
CTCATGTTACGTCTAGAACC+TGG 0.543595 7:-104070539 MsaT040811.1:CDS
TGGATGAAGTAGGAAGTTCA+AGG 0.544776 7:-104070331 MsaT040811.1:CDS
AACCTCCACAAAGAGGCGAT+TGG 0.546407 7:+104069866 None:intergenic
CTACGGTCCTTCACGAACTT+GGG 0.555110 7:+104069933 None:intergenic
TATTCAAGCCTAACACGTGT+TGG 0.559860 7:+104070392 None:intergenic
TTCAAGGGGAAATACAATCA+AGG 0.560197 7:-104070315 MsaT040811.1:CDS
AGTAATGCTCTCCTGTGTGT+CGG 0.561176 7:+104070046 None:intergenic
CAACAAGAGATGTCAAGTAA+TGG 0.569998 7:-104070201 MsaT040811.1:intron
TGGATAAACGATAGTTTCGA+AGG 0.578245 7:+104070726 None:intergenic
GGATGAAGTAGGAAGTTCAA+GGG 0.592041 7:-104070330 MsaT040811.1:CDS
TAATATCCTAACGACGGCGT+CGG 0.594754 7:+104069841 None:intergenic
AAACTTATCACTTCAAATAG+GGG 0.599416 7:-104069987 MsaT040811.1:CDS
TCCACAAAGAGGCGATTGGG+AGG 0.627150 7:+104069870 None:intergenic
CGTCGCAGCTAAATTCAACT+GGG 0.629434 7:-104070420 MsaT040811.1:CDS
GTCGGACAACCTCCACAAAG+AGG 0.652676 7:+104069859 None:intergenic
CAACTGCTTACCCGACACAC+AGG 0.661269 7:-104070057 MsaT040811.1:CDS
AGTTGATAGATATCCTATTG+GGG 0.667078 7:+104070075 None:intergenic
AAACTATAATATCCTAACGA+CGG 0.670619 7:+104069835 None:intergenic
AAGGACCGTAGACTAAGGAA+AGG 0.676015 7:-104069921 MsaT040811.1:CDS
AGATTGGCCCAAGTTCGTGA+AGG 0.684958 7:-104069940 MsaT040811.1:CDS
TAGTTTCGAAGGAATTCACG+AGG 0.691303 7:+104070737 None:intergenic
GATGAAGTAGGAAGTTCAAG+GGG 0.704354 7:-104070329 MsaT040811.1:CDS
AGTTTCGAAGGAATTCACGA+GGG 0.714111 7:+104070738 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr7 gene 104069848 104070783 104069848 ID=MsaG040811
Chr7 mRNA 104069848 104070783 104069848 ID=MsaT040811.1;Parent=MsaG040811
Chr7 exon 104069848 104070102 104069848 ID=MsaT040811.1.exon4;Parent=MsaT040811.1
Chr7 CDS 104069848 104070102 104069848 ID=cds.MsaT040811.1;Parent=MsaT040811.1
Chr7 exon 104070202 104070444 104070202 ID=MsaT040811.1.exon3;Parent=MsaT040811.1
Chr7 CDS 104070202 104070444 104070202 ID=cds.MsaT040811.1;Parent=MsaT040811.1
Chr7 exon 104070535 104070590 104070535 ID=MsaT040811.1.exon2;Parent=MsaT040811.1
Chr7 CDS 104070535 104070590 104070535 ID=cds.MsaT040811.1;Parent=MsaT040811.1
Chr7 exon 104070720 104070783 104070720 ID=MsaT040811.1.exon1;Parent=MsaT040811.1
Chr7 CDS 104070720 104070783 104070720 ID=cds.MsaT040811.1;Parent=MsaT040811.1
Gene Sequence

>MsaT040811.1

ATGCAAAGCAACAAGCTACTATACCCTCGTGAATTCCTTCGAAACTATCGTTTATCCACAACAGTCAAAGATACAAGTATGTTCTGGATTCTTCTCATGTTACGTCTAGAACCTGGAAAAGACGTCGCAGCTAAATTCAACTGGGAGAAACCAACACGTGTTAGGCTTGAATATACTGGCGCTTTTAACAGGTTCAAGATGATGGTTTTGGTGGATGAAGTAGGAAGTTCAAGGGGAAATACAATCAAGGAAGAAGTTATTGATTCTGATTCTGAAGATGATTGTGTAGAAATCGATTATGATCATTTTGAGAGGAATGTCACTTATGCCACAGCTAACAACAACAAGAGATGTCAAGTAATGCACTTCCCCAATAGGATATCTATCAACTGCTTACCCGACACACAGGAGAGCATTACTTTGCAGGATGTGCATAATCTCCGAGAATATGAGTGCAAACTTATCACTTCAAATAGGGGTCCAAATGAGAAATACTTAGGTGAAGATTGGCCCAAGTTCGTGAAGGACCGTAGACTAAGGAAAGGTGATAAGTTGATATTTGATCTTTGTGCTCCTCCCAATCGCCTCTTTGTGGAGGTTGTCCGACGCCGTCGTTAG
Protein sequence

>MsaT040811.1

MQSNKLLYPREFLRNYRLSTTVKDTSMFWILLMLRLEPGKDVAAKFNWEKPTRVRLEYTGAFNRFKMMVLVDEVGSSRGNTIKEEVIDSDSEDDCVEIDYDHFERNVTYATANNNKRCQVMHFPNRISINCLPDTQESITLQDVHNLREYECKLITSNRGPNEKYLGEDWPKFVKDRRLRKGDKLIFDLCAPPNRLFVEVVRRRR*