AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0480020584.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0480020584.01.T01 MTR_4g051622 92.500 80 6 0 1 80 41 120 4.23e-47 154
MsG0480020584.01.T01 MTR_4g051622 100.000 29 0 0 81 109 272 300 4.51e-12 61.2
MsG0480020584.01.T01 MTR_4g051645 69.512 82 25 0 1 82 44 125 9.53e-37 127
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0480020584.01.T01 AT5G22140 66.234 77 26 0 1 77 49 125 4.02e-29 107
MsG0480020584.01.T01 AT3G44190 59.740 77 31 0 1 77 49 125 1.32e-27 103
MsG0480020584.01.T01 AT5G22140 66.197 71 24 0 7 77 1 71 1.77e-26 100
MsG0480020584.01.T01 AT3G44190 59.155 71 29 0 7 77 1 71 5.59e-25 95.9

Find 23 sgRNAs with CRISPR-Local

Find 65 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TATCAATAGTTTCAGATTCT+TGG 0.196415 4:-44082031 None:intergenic
CATTGCTTACCTCCTTTGTA+TGG 0.232892 4:-44081255 None:intergenic
TTCAGATTCAGTTATGTTGA+TGG 0.355713 4:-44081133 None:intergenic
GATTATCTTGTTATCGCAAC+TGG 0.394119 4:+44081189 MsG0480020584.01.T01:CDS
AGGAGCGAAAGAACGTAAAT+AGG 0.428077 4:+44082059 MsG0480020584.01.T01:CDS
AATCTGAAACTATTGATAGA+AGG 0.453316 4:+44082036 MsG0480020584.01.T01:CDS
TGCGATAACAAGATAATCAT+AGG 0.469385 4:-44081184 None:intergenic
ATTGCTTACCTCCTTTGTAT+GGG 0.475555 4:-44081254 None:intergenic
CATAGAGAATATTTCACAAA+AGG 0.477184 4:+44081090 MsG0480020584.01.T01:CDS
GATCACTGTCCTTTCTGCGA+AGG 0.531450 4:-44081064 None:intergenic
CATTGCTCTCAAACTTGCCA+TGG 0.533350 4:-44081031 None:intergenic
TCTGAAGTCTTCACTGCTGA+TGG 0.538947 4:+44081150 MsG0480020584.01.T01:CDS
ACTGTCCTTTCTGCGAAGGA+TGG 0.552774 4:-44081060 None:intergenic
GGCAAGTTTGAGAGCAATGG+TGG 0.563002 4:+44081035 MsG0480020584.01.T01:CDS
TGGAGCCATCCTTCGCAGAA+AGG 0.564663 4:+44081055 MsG0480020584.01.T01:CDS
CATGGCAAGTTTGAGAGCAA+TGG 0.565499 4:+44081032 None:intergenic
CTGAAACTATTGATAGAAGG+AGG 0.602874 4:+44082039 MsG0480020584.01.T01:CDS
GATAATCATAGGTGATCTGA+CGG 0.632076 4:-44081173 None:intergenic
GAAAGACTTGACCCATACAA+AGG 0.638978 4:+44081243 MsG0480020584.01.T01:CDS
TGATGGCACTTGATATAACA+AGG 0.655923 4:-44081116 None:intergenic
AAACAAGGAGTGTATGCACA+AGG 0.668753 4:+44081991 MsG0480020584.01.T01:CDS
AGACTTGACCCATACAAAGG+AGG 0.683399 4:+44081246 MsG0480020584.01.T01:CDS
AATGTTACAGGAAATAAACA+AGG 0.690970 4:+44081976 MsG0480020584.01.T01:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGAAATTGAAATAATGTTAC+AGG + Chr4:44081964-44081983 MsG0480020584.01.T01:intron 20.0%
!!! AAACTTTTTGAAAGATGATT+TGG + Chr4:44081529-44081548 MsG0480020584.01.T01:intron 20.0%
! AATGTTACAGGAAATAAACA+AGG + Chr4:44081976-44081995 MsG0480020584.01.T01:intron 25.0%
! CATAGAGAATATTTCACAAA+AGG + Chr4:44081090-44081109 MsG0480020584.01.T01:CDS 25.0%
! TATCAATAGTTTCAGATTCT+TGG - Chr4:44082034-44082053 None:intergenic 25.0%
! TGGAATTGTTAATAATTGCA+TGG - Chr4:44081319-44081338 None:intergenic 25.0%
!! AATCTGAAACTATTGATAGA+AGG + Chr4:44082036-44082055 MsG0480020584.01.T01:CDS 25.0%
!! CTTTTGTGAAATATTCTCTA+TGG - Chr4:44081092-44081111 None:intergenic 25.0%
!!! TTTTTGAAAGATGATTTGGA+TGG + Chr4:44081533-44081552 MsG0480020584.01.T01:intron 25.0%
CTTACATATGCGTATTATTG+CGG - Chr4:44081928-44081947 None:intergenic 30.0%
TAAAAGACGACGAATTGAAT+TGG - Chr4:44081658-44081677 None:intergenic 30.0%
TGCGATAACAAGATAATCAT+AGG - Chr4:44081187-44081206 None:intergenic 30.0%
TTCAGATTCAGTTATGTTGA+TGG - Chr4:44081136-44081155 None:intergenic 30.0%
ATTGCTTACCTCCTTTGTAT+GGG - Chr4:44081257-44081276 None:intergenic 35.0%
CAGAATCTATCCCAAAAACA+AGG + Chr4:44081217-44081236 MsG0480020584.01.T01:CDS 35.0%
CGCAATAATACGCATATGTA+AGG + Chr4:44081926-44081945 MsG0480020584.01.T01:intron 35.0%
CTCTCAAGTATTCATCAACT+TGG - Chr4:44081571-44081590 None:intergenic 35.0%
CTGAAACTATTGATAGAAGG+AGG + Chr4:44082039-44082058 MsG0480020584.01.T01:CDS 35.0%
GATAATCATAGGTGATCTGA+CGG - Chr4:44081176-44081195 None:intergenic 35.0%
GATGAATACTTGAGAGTGAA+GGG + Chr4:44081575-44081594 MsG0480020584.01.T01:intron 35.0%
TGATGAATACTTGAGAGTGA+AGG + Chr4:44081574-44081593 MsG0480020584.01.T01:intron 35.0%
TGATGGCACTTGATATAACA+AGG - Chr4:44081119-44081138 None:intergenic 35.0%
! AAAGATGATTTGGATGGTCA+TGG + Chr4:44081539-44081558 MsG0480020584.01.T01:intron 35.0%
! AAGATGATTTGGATGGTCAT+GGG + Chr4:44081540-44081559 MsG0480020584.01.T01:intron 35.0%
! CGTCGTCTTTTATTATCTCT+AGG + Chr4:44081666-44081685 MsG0480020584.01.T01:intron 35.0%
! CGTTTTCGCTATTGACATTA+TGG + Chr4:44081607-44081626 MsG0480020584.01.T01:intron 35.0%
! GATTATCTTGTTATCGCAAC+TGG + Chr4:44081189-44081208 MsG0480020584.01.T01:CDS 35.0%
!! ACGACGAATTGAATTGGTTT+TGG - Chr4:44081652-44081671 None:intergenic 35.0%
!!! AACTGTTATTTTCCGCTATC+TGG - Chr4:44081900-44081919 None:intergenic 35.0%
!!! ACTGTTATTTTCCGCTATCT+GGG - Chr4:44081899-44081918 None:intergenic 35.0%
!!! AGTCTTTCAGTCCTTGTTTT+TGG - Chr4:44081231-44081250 None:intergenic 35.0%
!!! GTCTTTCAGTCCTTGTTTTT+GGG - Chr4:44081230-44081249 None:intergenic 35.0%
AATACTTGAGAGTGAAGGGA+AGG + Chr4:44081579-44081598 MsG0480020584.01.T01:intron 40.0%
CATGCAGTGTTGTCAAATAG+TGG + Chr4:44081709-44081728 MsG0480020584.01.T01:intron 40.0%
CATTGCTTACCTCCTTTGTA+TGG - Chr4:44081258-44081277 None:intergenic 40.0%
CTATTGTCAATCCCAGATAG+CGG + Chr4:44081885-44081904 MsG0480020584.01.T01:intron 40.0%
GAAAGACTTGACCCATACAA+AGG + Chr4:44081243-44081262 MsG0480020584.01.T01:CDS 40.0%
GATACGCTATTTAGCACAGA+TGG + Chr4:44081770-44081789 MsG0480020584.01.T01:intron 40.0%
GTCAAATAGTGGCATAGTAG+CGG + Chr4:44081720-44081739 MsG0480020584.01.T01:intron 40.0%
GTTGTTTGGTTGCGATTGAA+CGG + Chr4:44081366-44081385 MsG0480020584.01.T01:intron 40.0%
TGGGATTGACAATAGGTGAT+TGG - Chr4:44081880-44081899 None:intergenic 40.0%
! AAACAAGGAGTGTATGCACA+AGG + Chr4:44081991-44082010 MsG0480020584.01.T01:CDS 40.0%
! GATTGGTCAATCTCAGATAG+CGG - Chr4:44081863-44081882 None:intergenic 40.0%
AGACTTGACCCATACAAAGG+AGG + Chr4:44081246-44081265 MsG0480020584.01.T01:CDS 45.0%
CACAGATGGTTTCCAGATAG+TGG + Chr4:44081784-44081803 MsG0480020584.01.T01:intron 45.0%
CTGTGCTAAATAGCGTATCG+TGG - Chr4:44081769-44081788 None:intergenic 45.0%
! ATGATTTGGATGGTCATGGG+AGG + Chr4:44081543-44081562 MsG0480020584.01.T01:intron 45.0%
! ATGCTGACTGCGTCAATGAA+TGG - Chr4:44081339-44081358 None:intergenic 45.0%
! CGCTATCTGGGATTGACAAT+AGG - Chr4:44081887-44081906 None:intergenic 45.0%
! TCTGAAGTCTTCACTGCTGA+TGG + Chr4:44081150-44081169 MsG0480020584.01.T01:CDS 45.0%
!! TCAGCATGTTGGTGGTTGTT+TGG + Chr4:44081352-44081371 MsG0480020584.01.T01:intron 45.0%
ACGCTGCTTAAGCCACTATC+TGG - Chr4:44081799-44081818 None:intergenic 50.0%
ACTGTCCTTTCTGCGAAGGA+TGG - Chr4:44081063-44081082 None:intergenic 50.0%
AGCAAGCACAATAGTGGTCG+TGG - Chr4:44081470-44081489 None:intergenic 50.0%
AGTTTCACCTAGCCATGCTG+TGG - Chr4:44081514-44081533 None:intergenic 50.0%
CATTGACGCAGTCAGCATGT+TGG + Chr4:44081341-44081360 MsG0480020584.01.T01:intron 50.0%
GATCACTGTCCTTTCTGCGA+AGG - Chr4:44081067-44081086 None:intergenic 50.0%
GCAAGCACAATAGTGGTCGT+GGG - Chr4:44081469-44081488 None:intergenic 50.0%
GGCAAGTTTGAGAGCAATGG+TGG + Chr4:44081035-44081054 MsG0480020584.01.T01:CDS 50.0%
TCGCACAGCAAGCACAATAG+TGG - Chr4:44081476-44081495 None:intergenic 50.0%
TGTGACCACTTTCCACAGCA+TGG + Chr4:44081499-44081518 MsG0480020584.01.T01:intron 50.0%
CCACTTTCCACAGCATGGCT+AGG + Chr4:44081504-44081523 MsG0480020584.01.T01:intron 55.0%
CCTAGCCATGCTGTGGAAAG+TGG - Chr4:44081507-44081526 None:intergenic 55.0%
TGACGCAGTCAGCATGTTGG+TGG + Chr4:44081344-44081363 MsG0480020584.01.T01:intron 55.0%
TGGAGCCATCCTTCGCAGAA+AGG + Chr4:44081055-44081074 MsG0480020584.01.T01:CDS 55.0%
Chromosome Type Strat End Strand Name
Chr4 gene 44081033 44082080 44081033 ID=MsG0480020584.01;Name=MsG0480020584.01
Chr4 mRNA 44081033 44082080 44081033 ID=MsG0480020584.01.T01;Parent=MsG0480020584.01;Name=MsG0480020584.01.T01;_AED=0.22;_eAED=0.22;_QI=0|0|0|1|1|1|2|0|109
Chr4 exon 44081033 44081267 44081033 ID=MsG0480020584.01.T01:exon:11958;Parent=MsG0480020584.01.T01
Chr4 exon 44081986 44082080 44081986 ID=MsG0480020584.01.T01:exon:11959;Parent=MsG0480020584.01.T01
Chr4 CDS 44081033 44081267 44081033 ID=MsG0480020584.01.T01:cds;Parent=MsG0480020584.01.T01
Chr4 CDS 44081986 44082080 44081986 ID=MsG0480020584.01.T01:cds;Parent=MsG0480020584.01.T01
Gene Sequence

>MsG0480020584.01.T01

ATGGCAAGTTTGAGAGCAATGGTGGAGCCATCCTTCGCAGAAAGGACAGTGATCAACCATAGAGAATATTTCACAAAAGGTGACCTTGTTATATCAAGTGCCATCAACATAACTGAATCTGAAGTCTTCACTGCTGATGGCCGTCAGATCACCTATGATTATCTTGTTATCGCAACTGGTCACACAGAATCTATCCCAAAAACAAGGACTGAAAGACTTGACCCATACAAAGGAGGAAATAAACAAGGAGTGTATGCACAAGGTCATGCTCAATTAGTTGCCAAGAATCTGAAACTATTGATAGAAGGAGGAGCGAAAGAACGTAAATAG
Protein sequence

>MsG0480020584.01.T01

MASLRAMVEPSFAERTVINHREYFTKGDLVISSAINITESEVFTADGRQITYDYLVIATGHTESIPKTRTERLDPYKGGNKQGVYAQGHAQLVAKNLKLLIEGGAKERK*