AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0973810

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0973810 MtrunA17_Chr6g0452661 92.821 195 14 0 1 195 37 231 5.98e-135 377
Msa0973810 MtrunA17_Chr5g0439111 56.129 155 57 4 1 146 37 189 8.38e-38 130
Msa0973810 MtrunA17_Chr6g0452691 59.000 100 41 0 2 101 38 137 2.80e-36 125
Msa0973810 MtrunA17_Chr6g0452671 53.636 110 50 1 1 110 39 147 3.92e-32 115
Msa0973810 MtrunA17_Chr4g0055441 43.038 158 48 3 1 157 30 146 8.21e-31 110
Msa0973810 MtrunA17_Chr6g0449311 46.400 125 55 2 1 116 1 122 2.44e-26 98.6
Msa0973810 MtrunA17_Chr5g0402611 38.356 73 37 2 2 67 37 108 9.64e-11 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0973810 AT3G47870.1 48.529 68 34 1 1 68 64 130 3.28e-13 67.4
Msa0973810 AT3G26660.1 33.784 74 48 1 2 75 34 106 2.51e-12 61.6
Msa0973810 AT3G26620.1 33.784 74 48 1 2 75 34 106 3.55e-12 61.2

Find 36 sgRNAs with CRISPR-Local

Find 36 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGTGCAAATTTCCCAATTCA+TGG 0.256731 6_4:+6524908 Msa0973810:CDS
AAGAGTTAAAACAATTAAAA+TGG 0.318507 6_4:+6524981 Msa0973810:CDS
GAAGATACTAAACGAAATTA+AGG 0.321068 6_4:+6524832 Msa0973810:CDS
AAACTTGAATATAAATTCTA+TGG 0.323327 6_4:+6525207 Msa0973810:CDS
ACACCAAGACATCCATGAAT+TGG 0.323416 6_4:-6524920 None:intergenic
ATTGGACAATAATGAAGATT+TGG 0.353897 6_4:+6525291 Msa0973810:CDS
ATATTCAAGTTTGTATCAAT+TGG 0.365326 6_4:-6525196 None:intergenic
AAATTAGAACACTATTTGAT+TGG 0.377878 6_4:+6525329 Msa0973810:CDS
GGCGATGCTCATCGTTTGTT+TGG 0.378693 6_4:+6524794 Msa0973810:CDS
GGACAATGTCAAATTAGAAT+TGG 0.404194 6_4:+6525273 Msa0973810:CDS
TTCCCAATTCATGGATGTCT+TGG 0.407544 6_4:+6524917 Msa0973810:CDS
TTTAACAATTATAGTGATGT+TGG 0.420923 6_4:+6525085 Msa0973810:CDS
CACCAAGACATCCATGAATT+GGG 0.452237 6_4:-6524919 None:intergenic
AATTAGAACACTATTTGATT+GGG 0.461389 6_4:+6525330 Msa0973810:CDS
GGTGTTATTCATATGTATGC+AGG 0.474469 6_4:+6524938 Msa0973810:CDS
AACACTTGAAAACTAGTAGA+AGG 0.479558 6_4:-6525064 None:intergenic
GCCGATAAACCAAAGATGTT+CGG 0.490468 6_4:+6524773 None:intergenic
AATTTGACATTGTCCCCACC+AGG 0.497390 6_4:-6525265 None:intergenic
TTGAAAACTAGTAGAAGGTA+TGG 0.499253 6_4:-6525059 None:intergenic
ATATAAATTCTATGGATACA+AGG 0.500818 6_4:+6525215 Msa0973810:CDS
GGAGAATTATTAACATCATG+AGG 0.523658 6_4:-6525175 None:intergenic
TAGAACACTATTTGATTGGG+AGG 0.541236 6_4:+6525333 Msa0973810:CDS
TCACTAACATAAGAAGAAGA+TGG 0.561786 6_4:-6525145 None:intergenic
GAGAATTATTAACATCATGA+GGG 0.568165 6_4:-6525174 None:intergenic
TATAAATTCTATGGATACAA+GGG 0.572771 6_4:+6525216 Msa0973810:CDS
TTTGATTGGGAGGAAACAGA+AGG 0.589385 6_4:+6525343 Msa0973810:CDS
ATTATTAACATCATGAGGGG+TGG 0.592676 6_4:-6525170 None:intergenic
ATACTAAACGAAATTAAGGA+TGG 0.622219 6_4:+6524836 Msa0973810:CDS
AAAACTAGTAGAAGGTATGG+AGG 0.635254 6_4:-6525056 None:intergenic
GTGGTGATAGCAACCCTGGT+GGG 0.642025 6_4:+6525251 Msa0973810:CDS
AGAATTATTAACATCATGAG+GGG 0.645064 6_4:-6525173 None:intergenic
TTGAGTGGTGATAGCAACCC+TGG 0.645703 6_4:+6525247 Msa0973810:CDS
ATTTGACATTGTCCCCACCA+GGG 0.654875 6_4:-6525264 None:intergenic
ACAAGGGTTGCAAAATTGAG+TGG 0.655912 6_4:+6525232 Msa0973810:CDS
TGGTGATAGCAACCCTGGTG+GGG 0.705436 6_4:+6525252 Msa0973810:CDS
AGTGGTGATAGCAACCCTGG+TGG 0.759892 6_4:+6525250 Msa0973810:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAGAGTTAAAACAATTAAAA+TGG + chr6_4:6524981-6525000 Msa0973810:CDS 15.0%
!! AAACTTGAATATAAATTCTA+TGG + chr6_4:6525207-6525226 Msa0973810:CDS 15.0%
!!! AAACATTTTGTTGTTGTAAA+TGG - chr6_4:6525033-6525052 None:intergenic 20.0%
!! TTTAACAATTATAGTGATGT+TGG + chr6_4:6525085-6525104 Msa0973810:CDS 20.0%
!!! ATATTCAAGTTTGTATCAAT+TGG - chr6_4:6525199-6525218 None:intergenic 20.0%
!! ATATAAATTCTATGGATACA+AGG + chr6_4:6525215-6525234 Msa0973810:CDS 20.0%
!! TATAAATTCTATGGATACAA+GGG + chr6_4:6525216-6525235 Msa0973810:CDS 20.0%
!! AAATTAGAACACTATTTGAT+TGG + chr6_4:6525329-6525348 Msa0973810:CDS 20.0%
!! AATTAGAACACTATTTGATT+GGG + chr6_4:6525330-6525349 Msa0973810:CDS 20.0%
! GAAGATACTAAACGAAATTA+AGG + chr6_4:6524832-6524851 Msa0973810:CDS 25.0%
! ATACTAAACGAAATTAAGGA+TGG + chr6_4:6524836-6524855 Msa0973810:CDS 25.0%
! AGAATTATTAACATCATGAG+GGG - chr6_4:6525176-6525195 None:intergenic 25.0%
! GAGAATTATTAACATCATGA+GGG - chr6_4:6525177-6525196 None:intergenic 25.0%
! ATTGGACAATAATGAAGATT+TGG + chr6_4:6525291-6525310 Msa0973810:CDS 25.0%
TTGAAAACTAGTAGAAGGTA+TGG - chr6_4:6525062-6525081 None:intergenic 30.0%
AACACTTGAAAACTAGTAGA+AGG - chr6_4:6525067-6525086 None:intergenic 30.0%
TCACTAACATAAGAAGAAGA+TGG - chr6_4:6525148-6525167 None:intergenic 30.0%
GGAGAATTATTAACATCATG+AGG - chr6_4:6525178-6525197 None:intergenic 30.0%
GGACAATGTCAAATTAGAAT+TGG + chr6_4:6525273-6525292 Msa0973810:CDS 30.0%
!! GGTGTTATTCATATGTATGC+AGG + chr6_4:6524938-6524957 Msa0973810:CDS 35.0%
! AAAACTAGTAGAAGGTATGG+AGG - chr6_4:6525059-6525078 None:intergenic 35.0%
ATTATTAACATCATGAGGGG+TGG - chr6_4:6525173-6525192 None:intergenic 35.0%
TAGAACACTATTTGATTGGG+AGG + chr6_4:6525333-6525352 Msa0973810:CDS 35.0%
CGTGCAAATTTCCCAATTCA+TGG + chr6_4:6524908-6524927 Msa0973810:CDS 40.0%
TTCCCAATTCATGGATGTCT+TGG + chr6_4:6524917-6524936 Msa0973810:CDS 40.0%
CACCAAGACATCCATGAATT+GGG - chr6_4:6524922-6524941 None:intergenic 40.0%
ACACCAAGACATCCATGAAT+TGG - chr6_4:6524923-6524942 None:intergenic 40.0%
ACAAGGGTTGCAAAATTGAG+TGG + chr6_4:6525232-6525251 Msa0973810:CDS 40.0%
TTTGATTGGGAGGAAACAGA+AGG + chr6_4:6525343-6525362 Msa0973810:CDS 40.0%
ATTTGACATTGTCCCCACCA+GGG - chr6_4:6525267-6525286 None:intergenic 45.0%
AATTTGACATTGTCCCCACC+AGG - chr6_4:6525268-6525287 None:intergenic 45.0%
GGCGATGCTCATCGTTTGTT+TGG + chr6_4:6524794-6524813 Msa0973810:CDS 50.0%
TTGAGTGGTGATAGCAACCC+TGG + chr6_4:6525247-6525266 Msa0973810:CDS 50.0%
AGTGGTGATAGCAACCCTGG+TGG + chr6_4:6525250-6525269 Msa0973810:CDS 55.0%
GTGGTGATAGCAACCCTGGT+GGG + chr6_4:6525251-6525270 Msa0973810:CDS 55.0%
TGGTGATAGCAACCCTGGTG+GGG + chr6_4:6525252-6525271 Msa0973810:CDS 55.0%
Chromosome Type Strat End Strand Name
chr6_4 gene 6524788 6525375 6524788 ID=Msa0973810;Name=Msa0973810
chr6_4 mRNA 6524788 6525375 6524788 ID=Msa0973810-mRNA-1;Parent=Msa0973810;Name=Msa0973810-mRNA-1;_AED=0.29;_eAED=0.29;_QI=0|-1|0|1|-1|1|1|0|195
chr6_4 exon 6524788 6525375 6524788 ID=Msa0973810-mRNA-1:exon:2635;Parent=Msa0973810-mRNA-1
chr6_4 CDS 6524788 6525375 6524788 ID=Msa0973810-mRNA-1:cds;Parent=Msa0973810-mRNA-1
Gene Sequence

>Msa0973810

ATGTTCGGCGATGCTCATCGTTTGTTTGGTGTTTCAAACATACAGAAGATACTAAACGAAATTAAGGATGGTGATCAAAGAGATGAAGCAATGAAATCAATTGTTATTGAGTCGAAAATTCGTGCAAATTTCCCAATTCATGGATGTCTTGGTGTTATTCATATGTATGCAGGTATGATAAATGACTCTTCTAAAGAGTTAAAACAATTAAAATGGCTATTAGCTTATTGTAAGCAAAACAACCATTTACAACAACAAAATGTTTATTCCTCCATACCTTCTACTAGTTTTCAAGTGTTTAACAATTATAGTGATGTTGGTAATTATTATCACAATAGTGAAAATAATATGATGATACCATCTTCTTCTTATGTTAGTGAAACCACCCCTCATGATGTTAATAATTCTCCAATTGATACAAACTTGAATATAAATTCTATGGATACAAGGGTTGCAAAATTGAGTGGTGATAGCAACCCTGGTGGGGACAATGTCAAATTAGAATTGGACAATAATGAAGATTTGGACGACTTTGATATACAAATTAGAACACTATTTGATTGGGAGGAAACAGAAGGATTTTTATAA
Protein sequence

>Msa0973810

MFGDAHRLFGVSNIQKILNEIKDGDQRDEAMKSIVIESKIRANFPIHGCLGVIHMYAGMINDSSKELKQLKWLLAYCKQNNHLQQQNVYSSIPSTSFQVFNNYSDVGNYYHNSENNMMIPSSSYVSETTPHDVNNSPIDTNLNINSMDTRVAKLSGDSNPGGDNVKLELDNNEDLDDFDIQIRTLFDWEETEGFL*