AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene62306

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 25 sgRNAs with CRISPR-Local

Find 70 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTACTTCTCTCATCTTATA+AGG 0.247292 2.3:+21624469 MS.gene62306:CDS
ACTGTTGGTGCTGGTGTTGC+TGG 0.278594 2.3:+21624843 MS.gene62306:CDS
TGAAGGTGATTCTTGTGTTT+TGG 0.303850 2.3:+21624606 MS.gene62306:CDS
CGATGTAGGCGAAGTTAATT+CGG 0.329255 2.3:+21624791 MS.gene62306:intron
TATTGCTCTGGTTGTACTCT+TGG 0.344765 2.3:+21624866 MS.gene62306:CDS
GGGTTCAATTTCATTGATGA+TGG 0.393070 2.3:-21624290 None:intergenic
CTCATCAACATATCGGCATC+AGG 0.407565 2.3:+21625308 MS.gene62306:CDS
ATTGCTCTGGTTGTACTCTT+GGG 0.449876 2.3:+21624867 MS.gene62306:CDS
TGGTGTTGCTGGTATTGCTC+TGG 0.454038 2.3:+21624854 MS.gene62306:CDS
AATGTTATCACTGTTGGTGC+TGG 0.466483 2.3:+21624834 MS.gene62306:CDS
CATTTCCCTCATCAACATAT+CGG 0.470848 2.3:+21625301 MS.gene62306:CDS
TCAAGAGCAAGAACTGGAAC+AGG 0.482132 2.3:-21624432 None:intergenic
CCAGTTCTTGCTCTTGACAT+CGG 0.484096 2.3:+21624438 MS.gene62306:CDS
GCAGTTATCAACATCTTCGT+TGG 0.491361 2.3:+21625264 MS.gene62306:intron
CTCTGGTTGTACTCTTGGGA+AGG 0.498339 2.3:+21624871 MS.gene62306:CDS
CCGATGTCAAGAGCAAGAAC+TGG 0.503027 2.3:-21624438 None:intergenic
TGAACAAACATGATGAAAAG+AGG 0.506916 2.3:-21624498 None:intergenic
GGTTCAATTTCATTGATGAT+GGG 0.521972 2.3:-21624289 None:intergenic
ATATCGGCATCAGGGCAACT+TGG 0.528755 2.3:+21625317 MS.gene62306:CDS
ATATTTAGGGGATAGAATGA+AGG 0.532536 2.3:+21624589 MS.gene62306:intron
GATGCTAATGTTATCACTGT+TGG 0.589755 2.3:+21624828 MS.gene62306:CDS
TCATCAACATATCGGCATCA+GGG 0.604907 2.3:+21625309 MS.gene62306:CDS
AACTGGAACAGGAACAACAA+AGG 0.628523 2.3:-21624421 None:intergenic
CTGATGCCGATATGTTGATG+AGG 0.666580 2.3:-21625307 None:intergenic
TGATGCCGATATGTTGATGA+GGG 0.679239 2.3:-21625306 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATAGATTGATTTTATATTT+GGG + chr2.3:21625227-21625246 MS.gene62306:intron 10.0%
!! TACTGGATTTATTATATTTA+GGG + chr2.3:21624576-21624595 MS.gene62306:intron 15.0%
!! TTACTGGATTTATTATATTT+AGG + chr2.3:21624575-21624594 MS.gene62306:intron 15.0%
!!! AAGTTTTGATTTGATTTATT+TGG + chr2.3:21624951-21624970 MS.gene62306:intron 15.0%
!!! CTATAGATTGATTTTATATT+TGG + chr2.3:21625226-21625245 MS.gene62306:intron 15.0%
!! ACTGGATTTATTATATTTAG+GGG + chr2.3:21624577-21624596 MS.gene62306:intron 20.0%
!! TTACATATAAACAAAACACA+CGG - chr2.3:21625136-21625155 None:intergenic 20.0%
! AAAATAATTCTGATGAGATG+AGG - chr2.3:21624557-21624576 None:intergenic 25.0%
! AAGTGAGAATAATAAAGACA+AGG - chr2.3:21625376-21625395 None:intergenic 25.0%
! AATGAAACAAACAGGAAAAT+AGG - chr2.3:21625112-21625131 None:intergenic 25.0%
! GTTAATTCGGAAAAATTCAA+CGG + chr2.3:21624804-21624823 MS.gene62306:CDS 25.0%
! TTGTAATTTAGTCAAACCAT+TGG + chr2.3:21624896-21624915 MS.gene62306:intron 25.0%
!! AAAATCTGGAACTTAACTAA+CGG - chr2.3:21624315-21624334 None:intergenic 25.0%
!! CTTAAGAAGTGTAATTATGA+AGG + chr2.3:21624742-21624761 MS.gene62306:intron 25.0%
!! GTCTTTATTATTCTCACTTT+TGG + chr2.3:21625377-21625396 MS.gene62306:intron 25.0%
!!! TCTCATCAGAATTATTTTAC+TGG + chr2.3:21624559-21624578 MS.gene62306:intron 25.0%
AAGTTCGTTCAATCACAAAT+GGG + chr2.3:21624520-21624539 MS.gene62306:intron 30.0%
ATATTTAGGGGATAGAATGA+AGG + chr2.3:21624589-21624608 MS.gene62306:intron 30.0%
GTTACTTCTCTCATCTTATA+AGG + chr2.3:21624469-21624488 MS.gene62306:CDS 30.0%
TGAACAAACATGATGAAAAG+AGG - chr2.3:21624501-21624520 None:intergenic 30.0%
! AAATCAACAAAATCTGGAAC+AGG - chr2.3:21624372-21624391 None:intergenic 30.0%
! AAATCTGGAACTTAACTAAC+GGG - chr2.3:21624314-21624333 None:intergenic 30.0%
! ACTTCTTAAGCATCTTTTCA+AGG - chr2.3:21624732-21624751 None:intergenic 30.0%
! GGTTCAATTTCATTGATGAT+GGG - chr2.3:21624292-21624311 None:intergenic 30.0%
! GTTAAGTTCCAGATTTTCAA+TGG + chr2.3:21624318-21624337 MS.gene62306:intron 30.0%
ACAAGCAGCAAATTCAATCA+AGG - chr2.3:21625065-21625084 None:intergenic 35.0%
ACGCGAAAATCAACAAAATC+TGG - chr2.3:21624378-21624397 None:intergenic 35.0%
AGGAATGTGAAAGACAAAAG+TGG - chr2.3:21625356-21625375 None:intergenic 35.0%
ATTGTGACGATTATCGATGT+AGG + chr2.3:21624777-21624796 MS.gene62306:intron 35.0%
CAAGTTCGTTCAATCACAAA+TGG + chr2.3:21624519-21624538 MS.gene62306:intron 35.0%
CATTTCCCTCATCAACATAT+CGG + chr2.3:21625301-21625320 MS.gene62306:CDS 35.0%
GATGCTAATGTTATCACTGT+TGG + chr2.3:21624828-21624847 MS.gene62306:CDS 35.0%
GGGTTCAATTTCATTGATGA+TGG - chr2.3:21624293-21624312 None:intergenic 35.0%
! AATCTGGAACTTAACTAACG+GGG - chr2.3:21624313-21624332 None:intergenic 35.0%
! GAAGGTGATTCTTGTGTTTT+GGG + chr2.3:21624607-21624626 MS.gene62306:CDS 35.0%
! TGAAGGTGATTCTTGTGTTT+TGG + chr2.3:21624606-21624625 MS.gene62306:CDS 35.0%
!! TCTCACTTTTGGTTAAATGC+AGG + chr2.3:21625388-21625407 MS.gene62306:intron 35.0%
AACTGGAACAGGAACAACAA+AGG - chr2.3:21624424-21624443 None:intergenic 40.0%
AATGTTATCACTGTTGGTGC+TGG + chr2.3:21624834-21624853 MS.gene62306:CDS 40.0%
AGAGATGAACTTGGATCCAA+TGG - chr2.3:21624915-21624934 None:intergenic 40.0%
ATTGCTCTGGTTGTACTCTT+GGG + chr2.3:21624867-21624886 MS.gene62306:CDS 40.0%
CAAGAATTTGCCATCCAACA+TGG + chr2.3:21624698-21624717 MS.gene62306:intron 40.0%
CACACGGAAATGAAACAAAC+AGG - chr2.3:21625120-21625139 None:intergenic 40.0%
CATGCAACAAGAGATGAACT+TGG - chr2.3:21624924-21624943 None:intergenic 40.0%
CGATGTAGGCGAAGTTAATT+CGG + chr2.3:21624791-21624810 MS.gene62306:intron 40.0%
GAACAGGACCATTGAAAATC+TGG - chr2.3:21624329-21624348 None:intergenic 40.0%
GCAGTTATCAACATCTTCGT+TGG + chr2.3:21625264-21625283 MS.gene62306:intron 40.0%
GTTGGATGGCAAATTCTTGT+TGG - chr2.3:21624697-21624716 None:intergenic 40.0%
TATTGCTCTGGTTGTACTCT+TGG + chr2.3:21624866-21624885 MS.gene62306:CDS 40.0%
TCAAGGATCTTAAGCCATGT+TGG - chr2.3:21624715-21624734 None:intergenic 40.0%
TCATCAACATATCGGCATCA+GGG + chr2.3:21625309-21625328 MS.gene62306:CDS 40.0%
TTGGGAGGTAGGAGTAAAAA+TGG + chr2.3:21624625-21624644 MS.gene62306:intron 40.0%
! AATCTGGAACAGGAACAACA+CGG - chr2.3:21624362-21624381 None:intergenic 40.0%
! TGATGCCGATATGTTGATGA+GGG - chr2.3:21625309-21625328 None:intergenic 40.0%
!!! ATTCTTGTGTTTTGGGAGGT+AGG + chr2.3:21624614-21624633 MS.gene62306:intron 40.0%
ACAAAGGCGATGAGAAAAGC+TGG - chr2.3:21624408-21624427 None:intergenic 45.0%
CCAGTTCTTGCTCTTGACAT+CGG + chr2.3:21624438-21624457 MS.gene62306:CDS 45.0%
CTCATCAACATATCGGCATC+AGG + chr2.3:21625308-21625327 MS.gene62306:CDS 45.0%
CTGATGCCGATATGTTGATG+AGG - chr2.3:21625310-21625329 None:intergenic 45.0%
GGATCTTAAGCCATGTTGGA+TGG - chr2.3:21624711-21624730 None:intergenic 45.0%
TCAAGAGCAAGAACTGGAAC+AGG - chr2.3:21624435-21624454 None:intergenic 45.0%
!! GGTGATTCTTGTGTTTTGGG+AGG + chr2.3:21624610-21624629 MS.gene62306:CDS 45.0%
ACACGGTGGAAAACTGGAAC+AGG - chr2.3:21624345-21624364 None:intergenic 50.0%
ATATCGGCATCAGGGCAACT+TGG + chr2.3:21625317-21625336 MS.gene62306:CDS 50.0%
CCGATGTCAAGAGCAAGAAC+TGG - chr2.3:21624441-21624460 None:intergenic 50.0%
CTCTGGTTGTACTCTTGGGA+AGG + chr2.3:21624871-21624890 MS.gene62306:CDS 50.0%
GGAACAACACGGTGGAAAAC+TGG - chr2.3:21624351-21624370 None:intergenic 50.0%
!! TGGTGTTGCTGGTATTGCTC+TGG + chr2.3:21624854-21624873 MS.gene62306:CDS 50.0%
CTGGAACAGGAACAACACGG+TGG - chr2.3:21624359-21624378 None:intergenic 55.0%
!! ACTGTTGGTGCTGGTGTTGC+TGG + chr2.3:21624843-21624862 MS.gene62306:CDS 55.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 21624277 21625423 21624277 ID=MS.gene62306
chr2.3 mRNA 21624277 21625423 21624277 ID=MS.gene62306.t1;Parent=MS.gene62306
chr2.3 exon 21624277 21624313 21624277 ID=MS.gene62306.t1.exon1;Parent=MS.gene62306.t1
chr2.3 CDS 21624277 21624313 21624277 ID=cds.MS.gene62306.t1;Parent=MS.gene62306.t1
chr2.3 exon 21624409 21624521 21624409 ID=MS.gene62306.t1.exon2;Parent=MS.gene62306.t1
chr2.3 CDS 21624409 21624521 21624409 ID=cds.MS.gene62306.t1;Parent=MS.gene62306.t1
chr2.3 exon 21624604 21624631 21624604 ID=MS.gene62306.t1.exon3;Parent=MS.gene62306.t1
chr2.3 CDS 21624604 21624631 21624604 ID=cds.MS.gene62306.t1;Parent=MS.gene62306.t1
chr2.3 exon 21624799 21624892 21624799 ID=MS.gene62306.t1.exon4;Parent=MS.gene62306.t1
chr2.3 CDS 21624799 21624892 21624799 ID=cds.MS.gene62306.t1;Parent=MS.gene62306.t1
chr2.3 exon 21625268 21625338 21625268 ID=MS.gene62306.t1.exon5;Parent=MS.gene62306.t1
chr2.3 CDS 21625268 21625338 21625268 ID=cds.MS.gene62306.t1;Parent=MS.gene62306.t1
chr2.3 exon 21625410 21625423 21625410 ID=MS.gene62306.t1.exon6;Parent=MS.gene62306.t1
chr2.3 CDS 21625410 21625423 21625410 ID=cds.MS.gene62306.t1;Parent=MS.gene62306.t1
Gene Sequence

>MS.gene62306

ATGAAATTAAAACCCATCATCAATGAAATTGAACCCCGTTAGTTAAGTTCCAGATTTTCAATGGTCCTGTTCCAGTTTTCCACCGTGTTGTTCCTGTTCCAGATTTTGTTGATTTTCGCGTTTGTGTACCAGCTTTTCTCATCGCCTTTGTTGTTCCTGTTCCAGTTCTTGCTCTTGACATCGGATTCAACTGTTACTTCTCTCATCTTATAAGGTTTGTTCCTCTTTTCATCATGTTTGTTCAAGTTCGTTCAATCACAAATGGGTCACTTTTGTTCCTCATCTCATCAGAATTATTTTACTGGATTTATTATATTTAGGGGATAGAATGAAGGTGATTCTTGTGTTTTGGGAGGTAGGAGTAAAAATGGTTATTAAGTTAGAAGTCAGTAGTTAACTGTAAGTATATGAGATTAACCAACAAGAATTTGCCATCCAACATGGCTTAAGATCCTTGAAAAGATGCTTAAGAAGTGTAATTATGAAGGTTTGTTTCTTAAATTGTGACGATTATCGATGTAGGCGAAGTTAATTCGGAAAAATTCAACGGTGATGCTAATGTTATCACTGTTGGTGCTGGTGTTGCTGGTATTGCTCTGGTTGTACTCTTGGGAAGGTATTGTAATTTAGTCAAACCATTGGATCCAAGTTCATCTCTTGTTGCATGTGTTTAGAAGTTTTGATTTGATTTATTTGGTGATTGAACTAGATAAATTTTGAATTAATAAGTGTTAGTTAGTTGCTGCTTGTGAATTCAGTTTCAATTGATTTGTGTTTTTAACAATCCTTGATTGAATTTGCTGCTTGTAATTTGATTTGATTAGCTTGCTGACCTATTTTCCTGTTTGTTTCATTTCCGTGTGTTTTGTTTATATGTAAAATTTGAGTTTTTTTTTTAGATCTCTGCTAGTTAATTTTCTGTTAACACTCAAAATTATTTGATTGTTTTCTATAGATTGATTTTATATTTGGGTAATTGTAATTTATGCAGTTATCAACATCTTCGTTGGCATTTGTTTATCTGCATTTCCCTCATCAACATATCGGCATCAGGGCAACTTGGTAACACATTTTCGCCACTTTTGTCTTTCACATTCCTTGTCTTTATTATTCTCACTTTTGGTTAAATGCAGGTGAACAAGCTTAA
Protein sequence

>MS.gene62306.t1

MKLKPIINEIEPPFLIAFVVPVPVLALDIGFNCYFSHLIRFVPLFIMFVQNEGDSCVLGGEVNSEKFNGDANVITVGAGVAGIALVVLLGSYQHLRWHLFICISLINISASGQLGEQA