AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG009934

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG009934 MtrunA17_Chr2g0318721 84.472 322 17 11 1 312 1 299 1.21e-160 449
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 60 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTCTCACTGTTTCAGCTTA+TGG 0.159665 2:+66412379 MsaT009934.1:CDS
CACCAATTGTGGGAAATTTC+AGG 0.195712 2:-66412336 None:intergenic
TTATTCTGATTCTGATTGTT+AGG 0.266258 2:-66410817 None:intergenic
TGTGGGAAATTTCAGGTTCT+TGG 0.268740 2:-66412329 None:intergenic
GGTTGAGAGTGATGAAGATT+TGG 0.342640 2:-66410943 None:intergenic
GAAGGTTGAGGTTGAGGTTG+AGG 0.345487 2:-66411779 None:intergenic
AGAACAGAAGGTTGAGGTTG+AGG 0.346254 2:-66411785 None:intergenic
AGCTCTTTAGAAGGCTCAAA+AGG 0.358727 2:-66410910 None:intergenic
GGTGGTGGTAACTATGGATA+TGG 0.361187 2:+66410856 MsaT009934.1:CDS
AGTGTTATTGTTATTGTTGT+TGG 0.365355 2:-66410725 None:intergenic
AACCTGAAATTTCCCACAAT+TGG 0.372059 2:+66412334 MsaT009934.1:CDS
TCAACTCCTACACCTCTTAG+TGG 0.420541 2:-66410526 None:intergenic
ATCAGAATCAGAATAACAAC+AGG 0.420921 2:+66410824 MsaT009934.1:CDS
ATTGAAGAGAGCTCTTTAGA+AGG 0.427011 2:-66410919 None:intergenic
TGAGGTTGAGGTTGAGGTTG+AGG 0.427504 2:-66411773 None:intergenic
AGAAGCAGCTTCACCAATTG+TGG 0.451010 2:-66412347 None:intergenic
TCATGAACATGATGATGATT+AGG 0.458805 2:-66411731 None:intergenic
GTTGTTGGTGGTGGTAACTA+TGG 0.459219 2:+66410850 MsaT009934.1:CDS
GCTTGCTCAAACGTTGGTGC+TGG 0.461104 2:+66410784 MsaT009934.1:CDS
GAGAGGAGCTAGAAACCCTT+TGG 0.463191 2:+66411700 MsaT009934.1:CDS
AGGTTGTTGCTGTGCATAGG+AGG 0.469491 2:+66412224 MsaT009934.1:CDS
ACCTTGAGGCAAAGATCAAA+AGG 0.476163 2:-66410964 None:intergenic
GTTAGAGAAGCAGAGGATAG+AGG 0.478278 2:+66410552 MsaT009934.1:CDS
GAAGCAGAGGATAGAGGCAT+TGG 0.478285 2:+66410558 MsaT009934.1:CDS
GGTAACTATGGATATGGATC+TGG 0.489747 2:+66410862 MsaT009934.1:CDS
GTTGGAGCTTGCTCAAACGT+TGG 0.497141 2:+66410778 MsaT009934.1:CDS
TCAGAAAACACGTTTGAATG+AGG 0.499550 2:+66411664 MsaT009934.1:intron
AGGAGGGGAAGTTCTTCATC+AGG 0.500625 2:+66412241 MsaT009934.1:CDS
TCATCAAGATTGTGATGAGT+TGG 0.506524 2:-66411818 None:intergenic
AACAGGGTCGTTGTTGGTGG+TGG 0.507033 2:+66410841 MsaT009934.1:CDS
AATAACAACAGGGTCGTTGT+TGG 0.507101 2:+66410835 MsaT009934.1:CDS
TTTGAGCAAGCTCCAACAAA+AGG 0.507919 2:-66410772 None:intergenic
GCTCAAACGTTGGTGCTGGA+TGG 0.518767 2:+66410788 MsaT009934.1:CDS
CTAGAAACCCTTTGGAGGCA+TGG 0.527762 2:+66411708 MsaT009934.1:CDS
GAGGAGAGTAATGTAATGAG+AGG 0.529842 2:+66411683 MsaT009934.1:CDS
TGATGTTGAGGAAACTGAAA+TGG 0.535711 2:-66410673 None:intergenic
CTCACTGTTTCAGCTTATGG+TGG 0.545279 2:+66412382 MsaT009934.1:CDS
AACAACAGGGTCGTTGTTGG+TGG 0.551873 2:+66410838 MsaT009934.1:CDS
AAGTTCTTCATCAGGAGGGA+AGG 0.555848 2:+66412249 MsaT009934.1:CDS
TTGAACAGTTAGAGAAGCAG+AGG 0.558284 2:+66410545 MsaT009934.1:CDS
GATTAGGCCATGCCTCCAAA+GGG 0.558465 2:-66411715 None:intergenic
GGATAAGCAGAAAGAACAGA+AGG 0.566886 2:-66411797 None:intergenic
GCTCTTTAGAAGGCTCAAAA+GGG 0.569253 2:-66410909 None:intergenic
TGATTAGGCCATGCCTCCAA+AGG 0.575637 2:-66411716 None:intergenic
GGTTGTTGCTGTGCATAGGA+GGG 0.577962 2:+66412225 MsaT009934.1:CDS
ATTTGCTGTTGATGATGTTG+AGG 0.585953 2:-66410685 None:intergenic
TTGGTGAGAAAAGCTGAAGC+TGG 0.589265 2:+66410577 MsaT009934.1:CDS
GTTGTTGATGAGGATGATCA+AGG 0.590020 2:-66410612 None:intergenic
TTGTGTTGTAAAGTGTGTGG+AGG 0.590206 2:+66412204 MsaT009934.1:intron
GCAGAAAGAACAGAAGGTTG+AGG 0.592292 2:-66411791 None:intergenic
AGGAGCTAGAAACCCTTTGG+AGG 0.592534 2:+66411703 MsaT009934.1:CDS
AAAAGCTGTTGTTGTTGATG+AGG 0.593088 2:-66410622 None:intergenic
TGGAGGTTGTTGCTGTGCAT+AGG 0.593913 2:+66412221 MsaT009934.1:CDS
GTTGTTGCTGTGCATAGGAG+GGG 0.608997 2:+66412226 MsaT009934.1:CDS
GAAGCAGCTTCACCAATTGT+GGG 0.613866 2:-66412346 None:intergenic
GGAAACTGAAATGGCCCAGT+TGG 0.639292 2:-66410664 None:intergenic
AACTCATCACAATCTTGATG+AGG 0.642648 2:+66411820 MsaT009934.1:CDS
AGGGGAAGTTCTTCATCAGG+AGG 0.645014 2:+66412244 MsaT009934.1:CDS
GGGGAAGTTCTTCATCAGGA+GGG 0.656793 2:+66412245 MsaT009934.1:CDS
TCAGAATCAGAATAACAACA+GGG 0.760807 2:+66410825 MsaT009934.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr2 gene 66410460 66412456 66410460 ID=MsaG009934
Chr2 mRNA 66410460 66412456 66410460 ID=MsaT009934.1;Parent=MsaG009934
Chr2 exon 66410460 66410984 66410460 ID=MsaT009934.1.exon1;Parent=MsaT009934.1
Chr2 CDS 66410460 66410984 66410460 ID=cds.MsaT009934.1;Parent=MsaT009934.1
Chr2 exon 66411668 66411841 66411668 ID=MsaT009934.1.exon2;Parent=MsaT009934.1
Chr2 CDS 66411668 66411841 66411668 ID=cds.MsaT009934.1;Parent=MsaT009934.1
Chr2 exon 66412217 66412456 66412217 ID=MsaT009934.1.exon3;Parent=MsaT009934.1
Chr2 CDS 66412217 66412456 66412217 ID=cds.MsaT009934.1;Parent=MsaT009934.1
Gene Sequence

>MsaT009934.1

ATGGCCTCTGCCTCTGAAAACCAAGCAAAAAACAAAGGGAGAAAAAATGGTAAAGCACCAAAAAAACCACTAAGAGGTGTAGGAGTTGAACAGTTAGAGAAGCAGAGGATAGAGGCATTGGTGAGAAAAGCTGAAGCTGGTACATTACTTCACCTTGATCATCCTCATCAACAACAACAGCTTTTGAAGTATGGTGCATTTTCACCAACTGGGCCATTTCAGTTTCCTCAACATCATCAACAGCAAATGATGATGAATGAAAACACCAACAACAATAACAATAACACTGTTTTTGTTGGTTCTGGTTATGTTCCTTTTGTTGGAGCTTGCTCAAACGTTGGTGCTGGATGGATTGTTCCTAACAATCAGAATCAGAATAACAACAGGGTCGTTGTTGGTGGTGGTAACTATGGATATGGATCTGGTTCACTACTTTGTAGTAGTAGAAACCCTTTTGAGCCTTCTAAAGAGCTCTCTTCAATGCCAAATCTTCATCACTCTCAACCTTTTGATCTTTGCCTCAAGAAAACACGTTTGAATGAGGAGAGTAATGTAATGAGAGGAGCTAGAAACCCTTTGGAGGCATGGCCTAATCATCATCATGTTCATGATTTTCTTGGAGGATATGTGCCTCAACCTCAACCTCAACCTCAACCTTCTGTTCTTTCTGCTTATCCAACTCATCACAATCTTGATGAGTGTGTGGAGGTTGTTGCTGTGCATAGGAGGGGAAGTTCTTCATCAGGAGGGAAGGACAAAGTTTTCATGGAGTATGATTTTTTTCATGAAAAAGATGGAAGAGACACTTCTTCCAAGAACCTGAAATTTCCCACAATTGGTGAAGCTGCTTCTTCTTCTTTATCTCTCACTGTTTCAGCTTATGGTGGAGATACTGCTACTACTGATCTTAGTTCTATTGATTTGTCTCTTAAGCTTTGA
Protein sequence

>MsaT009934.1

MASASENQAKNKGRKNGKAPKKPLRGVGVEQLEKQRIEALVRKAEAGTLLHLDHPHQQQQLLKYGAFSPTGPFQFPQHHQQQMMMNENTNNNNNNTVFVGSGYVPFVGACSNVGAGWIVPNNQNQNNNRVVVGGGNYGYGSGSLLCSSRNPFEPSKELSSMPNLHHSQPFDLCLKKTRLNEESNVMRGARNPLEAWPNHHHVHDFLGGYVPQPQPQPQPSVLSAYPTHHNLDECVEVVAVHRRGSSSSGGKDKVFMEYDFFHEKDGRDTSSKNLKFPTIGEAASSSLSLTVSAYGGDTATTDLSSIDLSLKL*