AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0380015073.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380015073.01.T01 MTR_2g064650 60.256 78 30 1 3 80 19 95 3.00e-25 91.3
MsG0380015073.01.T01 MTR_2g064650 60.256 78 30 1 3 80 19 95 5.11e-25 90.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 15 sgRNAs with CRISPR-Local

Find 43 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAATACAATGTTAATGTTGA+TGG 0.341072 3:+64788313 MsG0380015073.01.T01:CDS
CATTGTATTTGTGCACAAAC+TGG 0.367675 3:-64788300 None:intergenic
TGCTGAAGATTCTAATCTTT+AGG 0.380047 3:-64788355 None:intergenic
ATTAAGATAGACACACCTTA+TGG 0.402984 3:+64787867 MsG0380015073.01.T01:CDS
TAATCTTTAGGCTCGTAGAT+AGG 0.422803 3:-64788343 None:intergenic
ATAGACACACCTTATGGAAC+TGG 0.470237 3:+64787873 MsG0380015073.01.T01:CDS
GATAGTATGTCTGCTATAGT+TGG 0.498336 3:-64787901 None:intergenic
AACTCTGAAAGGAATTGAAA+GGG 0.509933 3:-64787823 None:intergenic
TTGGCATTACCAGTTCCATA+AGG 0.512086 3:-64787882 None:intergenic
ATGGCTGAGAAGTCTTCAGT+TGG 0.518069 3:+64787789 MsG0380015073.01.T01:CDS
CAACTCTGAAAGGAATTGAA+AGG 0.520151 3:-64787824 None:intergenic
CCTTTCAGAGTTGTGTCCAG+TGG 0.522178 3:+64787834 MsG0380015073.01.T01:CDS
CTTAATCTTCATGACACCAC+TGG 0.533138 3:-64787850 None:intergenic
CCACTGGACACAACTCTGAA+AGG 0.551600 3:-64787834 None:intergenic
CTGAAAGGAATTGAAAGGGA+AGG 0.594918 3:-64787819 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATACAATGTTAATGTTGA+TGG + Chr3:64788313-64788332 MsG0380015073.01.T01:CDS 20.0%
!!! ATGCTTTTGTTAAAAAACAA+AGG + Chr3:64788260-64788279 MsG0380015073.01.T01:CDS 20.0%
!!! TGCTTTTGTTAAAAAACAAA+GGG + Chr3:64788261-64788280 MsG0380015073.01.T01:CDS 20.0%
! AACAACTGCAAATAAAAGAA+AGG + Chr3:64788184-64788203 MsG0380015073.01.T01:intron 25.0%
! TGTTAAAAAACAAAGGGAAA+GGG + Chr3:64788267-64788286 MsG0380015073.01.T01:CDS 25.0%
! TTGTTAAAAAACAAAGGGAA+AGG + Chr3:64788266-64788285 MsG0380015073.01.T01:CDS 25.0%
AAAAATAGAAAACCTCGACA+TGG + Chr3:64788212-64788231 MsG0380015073.01.T01:intron 30.0%
ATTAAGATAGACACACCTTA+TGG + Chr3:64787867-64787886 MsG0380015073.01.T01:CDS 30.0%
! AACTCTGAAAGGAATTGAAA+GGG - Chr3:64787826-64787845 None:intergenic 30.0%
! CTATGATTTTGTGAATGAGT+TGG - Chr3:64788139-64788158 None:intergenic 30.0%
! TGTTTCTGTTGTTACATTCT+AGG + Chr3:64788087-64788106 MsG0380015073.01.T01:intron 30.0%
!! TGTTACATTCTAGGATTAGT+TGG + Chr3:64788096-64788115 MsG0380015073.01.T01:intron 30.0%
!! TTGTGAATGAGTTGGTTATT+GGG - Chr3:64788131-64788150 None:intergenic 30.0%
!! TTTGTGAATGAGTTGGTTAT+TGG - Chr3:64788132-64788151 None:intergenic 30.0%
AAACTCTCGCCAAAAAATCA+AGG + Chr3:64788023-64788042 MsG0380015073.01.T01:intron 35.0%
AACAACAGAAACAGTTGCAA+TGG - Chr3:64788080-64788099 None:intergenic 35.0%
AACTCTCGCCAAAAAATCAA+GGG + Chr3:64788024-64788043 MsG0380015073.01.T01:intron 35.0%
CATTGTATTTGTGCACAAAC+TGG - Chr3:64788303-64788322 None:intergenic 35.0%
GATAGTATGTCTGCTATAGT+TGG - Chr3:64787904-64787923 None:intergenic 35.0%
TAATCTTTAGGCTCGTAGAT+AGG - Chr3:64788346-64788365 None:intergenic 35.0%
! CAACTCTGAAAGGAATTGAA+AGG - Chr3:64787827-64787846 None:intergenic 35.0%
!! AAAATCAAGGGTATCGTCAA+TGG + Chr3:64788036-64788055 MsG0380015073.01.T01:intron 35.0%
!! TCATGCTCTTCTGCTTTTAA+CGG + Chr3:64788000-64788019 MsG0380015073.01.T01:intron 35.0%
!!! TGACGATACCCTTGATTTTT+TGG - Chr3:64788035-64788054 None:intergenic 35.0%
AAACAGTTGCAATGGAAGAG+AGG - Chr3:64788072-64788091 None:intergenic 40.0%
ATAGACACACCTTATGGAAC+TGG + Chr3:64787873-64787892 MsG0380015073.01.T01:CDS 40.0%
CTGAAAGGAATTGAAAGGGA+AGG - Chr3:64787822-64787841 None:intergenic 40.0%
CTTAATCTTCATGACACCAC+TGG - Chr3:64787853-64787872 None:intergenic 40.0%
GCTAAGACTTCTTTGTCTTC+TGG - Chr3:64787970-64787989 None:intergenic 40.0%
TGCAATGGAAGAGAGGTAAA+TGG - Chr3:64788065-64788084 None:intergenic 40.0%
TTGGCATTACCAGTTCCATA+AGG - Chr3:64787885-64787904 None:intergenic 40.0%
ATGGCTGAGAAGTCTTCAGT+TGG + Chr3:64787789-64787808 MsG0380015073.01.T01:CDS 45.0%
CATTAGAGAGAACCATGTCG+AGG - Chr3:64788227-64788246 None:intergenic 45.0%
CTCGACATGGTTCTCTCTAA+TGG + Chr3:64788225-64788244 MsG0380015073.01.T01:intron 45.0%
! AAGCAGAAGAGCATGAGATG+AGG - Chr3:64787996-64788015 None:intergenic 45.0%
CAGTGAGGATTGTTGCTGGA+AGG - Chr3:64787930-64787949 None:intergenic 50.0%
CCACTGGACACAACTCTGAA+AGG - Chr3:64787837-64787856 None:intergenic 50.0%
CCTTTCAGAGTTGTGTCCAG+TGG + Chr3:64787834-64787853 MsG0380015073.01.T01:CDS 50.0%
GAGGATTGTTGCTGGAAGGA+CGG - Chr3:64787926-64787945 None:intergenic 50.0%
GTCTTCTGGTGAGAGAGCAA+CGG - Chr3:64787956-64787975 None:intergenic 50.0%
GTGGCAGTGAGGATTGTTGC+TGG - Chr3:64787934-64787953 None:intergenic 55.0%
TTCTGGTGAGAGAGCAACGG+TGG - Chr3:64787953-64787972 None:intergenic 55.0%
AGAGAGCAACGGTGGCAGTG+AGG - Chr3:64787945-64787964 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
Chr3 gene 64787789 64788366 64787789 ID=MsG0380015073.01;Name=MsG0380015073.01
Chr3 mRNA 64787789 64788366 64787789 ID=MsG0380015073.01.T01;Parent=MsG0380015073.01;Name=MsG0380015073.01.T01;_AED=0.47;_eAED=0.48;_QI=0|0|0|1|0|0|2|0|80
Chr3 exon 64787789 64787909 64787789 ID=MsG0380015073.01.T01:exon:6998;Parent=MsG0380015073.01.T01
Chr3 exon 64788245 64788366 64788245 ID=MsG0380015073.01.T01:exon:6999;Parent=MsG0380015073.01.T01
Chr3 CDS 64787789 64787909 64787789 ID=MsG0380015073.01.T01:cds;Parent=MsG0380015073.01.T01
Chr3 CDS 64788245 64788366 64788245 ID=MsG0380015073.01.T01:cds;Parent=MsG0380015073.01.T01
Gene Sequence

>MsG0380015073.01.T01

ATGGCTGAGAAGTCTTCAGTTGGAGAATTTCCTTCCCTTTCAATTCCTTTCAGAGTTGTGTCCAGTGGTGTCATGAAGATTAAGATAGACACACCTTATGGAACTGGTAATGCCAACTATATGGATTATGAACTTGATGCTTTTGTTAAAAAACAAAGGGAAAGGGTGTTTAATTACCAGTTTGTGCACAAATACAATGTTAATGTTGATGGATACAATCCTATCTACGAGCCTAAAGATTAG
Protein sequence

>MsG0380015073.01.T01

MAEKSSVGEFPSLSIPFRVVSSGVMKIKIDTPYGTGNANYMDYELDAFVKKQRERVFNYQFVHKYNVNVDGYNPIYEPKD*