AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0380013919.01


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 20 sgRNAs with CRISPR-Local

Find 106 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAAGAAAACATAGAGATTA+TGG 0.215607 3:-48390208 MsG0380013919.01.T01:CDS
TACGTAAATTATAAGTAAAA+AGG 0.320012 3:+48390131 None:intergenic
CCCTCATCGTCTAGTGGTTT+AGG 0.347484 3:-48391305 MsG0380013919.01.T01:CDS
CTCTCTTTCAAGGAGGCAAC+GGG 0.349769 3:-48391278 MsG0380013919.01.T01:CDS
AACGGGGATTCGACTTCCCC+TGG 0.367840 3:-48391261 MsG0380013919.01.T01:CDS
TTATTTCTAATAAATACTTC+GGG 0.385730 3:+48390235 None:intergenic
TTTAGGACATCTCTCTTTCA+AGG 0.418451 3:-48391288 MsG0380013919.01.T01:CDS
TTATCTCGATGATATAAAAT+CGG 0.425719 3:+48390313 None:intergenic
AATATCACGAATAACAATAT+CGG 0.432137 3:+48390339 None:intergenic
TTTATTTCTAATAAATACTT+CGG 0.454517 3:+48390234 None:intergenic
ACGGGGATTCGACTTCCCCT+GGG 0.464493 3:-48391260 MsG0380013919.01.T01:CDS
TCTCTCTTTCAAGGAGGCAA+CGG 0.550761 3:-48391279 MsG0380013919.01.T01:CDS
CGGGGATTCGACTTCCCCTG+GGG 0.598264 3:-48391259 MsG0380013919.01.T01:CDS
TCCTAAACCACTAGACGATG+AGG 0.634037 3:+48391304 None:intergenic
AGTATGCCCTCATCGTCTAG+TGG 0.655450 3:-48391311 MsG0380013919.01.T01:CDS
TCTTTCGTCAGTAAATTCAG+TGG 0.659250 3:+48390282 None:intergenic
CCTAAACCACTAGACGATGA+GGG 0.665401 3:+48391305 None:intergenic
AGGACATCTCTCTTTCAAGG+AGG 0.674472 3:-48391285 MsG0380013919.01.T01:CDS
GGGGATTCGACTTCCCCTGG+GGG 0.678595 3:-48391258 MsG0380013919.01.T01:CDS
TCTCTTTCAAGGAGGCAACG+GGG 0.717958 3:-48391277 MsG0380013919.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACATTATACTAAAAAAAAAA+AGG + Chr3:48390927-48390946 None:intergenic 10.0%
!!! ATTTTTTTTTTTATTTGGTA+TGG - Chr3:48390998-48391017 MsG0380013919.01.T01:intron 10.0%
!!! TGATATATTGATATTTTTAT+GGG + Chr3:48390632-48390651 None:intergenic 10.0%
!!! TTGATATATTGATATTTTTA+TGG + Chr3:48390633-48390652 None:intergenic 10.0%
!!! TTTATTTCTAATAAATACTT+CGG + Chr3:48391188-48391207 None:intergenic 10.0%
!!! TTTTTTTTAGTATAATGTAA+AGG - Chr3:48390929-48390948 MsG0380013919.01.T01:intron 10.0%
!! ACTTATAATTTACGTAAAAA+CGG - Chr3:48391295-48391314 MsG0380013919.01.T01:CDS 15.0%
!! AGAATTAAATAGTATAACAT+AGG + Chr3:48391036-48391055 None:intergenic 15.0%
!! TACGTAAATTATAAGTAAAA+AGG + Chr3:48391291-48391310 None:intergenic 15.0%
!!! AATCTAAAATAGAAAAACAA+AGG - Chr3:48390693-48390712 MsG0380013919.01.T01:intron 15.0%
!!! ATCTAAAATAGAAAAACAAA+GGG - Chr3:48390694-48390713 MsG0380013919.01.T01:intron 15.0%
!!! ATTTTAAAATCTAAAGTCTT+AGG - Chr3:48390489-48390508 MsG0380013919.01.T01:intron 15.0%
!!! TTATTTCTAATAAATACTTC+GGG + Chr3:48391187-48391206 None:intergenic 15.0%
!! AAAAAAATCTCATTTCTAAC+AGG - Chr3:48390897-48390916 MsG0380013919.01.T01:intron 20.0%
!! AAAAAATCTCATTTCTAACA+GGG - Chr3:48390898-48390917 MsG0380013919.01.T01:intron 20.0%
!! AATATCACGAATAACAATAT+CGG + Chr3:48391083-48391102 None:intergenic 20.0%
!! ATTGAAAAATCAATGAATCA+AGG + Chr3:48390550-48390569 None:intergenic 20.0%
!! TGTGGAAAAAATATGTAATA+TGG + Chr3:48390440-48390459 None:intergenic 20.0%
!! TTATCTCGATGATATAAAAT+CGG + Chr3:48391109-48391128 None:intergenic 20.0%
!! TTTAGTATAATGTAAAGGTT+CGG - Chr3:48390934-48390953 MsG0380013919.01.T01:intron 20.0%
!!! ACATATTTTTTCCACAAATT+CGG - Chr3:48390444-48390463 MsG0380013919.01.T01:intron 20.0%
!!! CGAAATCAATTGATATTTTT+TGG + Chr3:48390852-48390871 None:intergenic 20.0%
!!! GAAAGATTTTTCATTTCTAT+GGG - Chr3:48391154-48391173 MsG0380013919.01.T01:intron 20.0%
! ATGAAATGATATAACCCATT+TGG - Chr3:48390347-48390366 MsG0380013919.01.T01:intron 25.0%
! ATTATAAGTAAAAAGGCAGT+AGG + Chr3:48391284-48391303 None:intergenic 25.0%
! GAAAGAAAACATAGAGATTA+TGG - Chr3:48391211-48391230 MsG0380013919.01.T01:intron 25.0%
! TTTCAATCAAGTTAGCAATA+AGG - Chr3:48390563-48390582 MsG0380013919.01.T01:intron 25.0%
!! AAAATCTAAAGTCTTAGGAA+AGG - Chr3:48390494-48390513 MsG0380013919.01.T01:intron 25.0%
!! AATTGATTTCGTATGTGAAA+GGG - Chr3:48390861-48390880 MsG0380013919.01.T01:intron 25.0%
!! CGAAAGATTTTTCATTTCTA+TGG - Chr3:48391153-48391172 MsG0380013919.01.T01:intron 25.0%
!! GAGATTTTATTCTTCTGTAT+GGG + Chr3:48390399-48390418 None:intergenic 25.0%
!!! AAATGGGTTATATCATTTCA+TGG + Chr3:48390348-48390367 None:intergenic 25.0%
!!! GATTTTGAAAAATTCCTATC+GGG - Chr3:48390466-48390485 MsG0380013919.01.T01:intron 25.0%
!!! GGATTTTGAAAAATTCCTAT+CGG - Chr3:48390465-48390484 MsG0380013919.01.T01:intron 25.0%
!!! TTAGATTTTAAAATCCCGAT+AGG + Chr3:48390483-48390502 None:intergenic 25.0%
!!! TTTTTCAAAATCCGAATTTG+TGG + Chr3:48390458-48390477 None:intergenic 25.0%
!!! TTTTTTGGATTTGTATCCAT+CGG + Chr3:48390837-48390856 None:intergenic 25.0%
ACTACAAAAGGAAATTGATC+AGG - Chr3:48390190-48390209 MsG0380013919.01.T01:CDS 30.0%
ATCAAGTTAGCAATAAGGAA+CGG - Chr3:48390568-48390587 MsG0380013919.01.T01:intron 30.0%
CTACAAAAGGAAATTGATCA+GGG - Chr3:48390191-48390210 MsG0380013919.01.T01:CDS 30.0%
! AGACTAAAATTGATTCTTCC+TGG - Chr3:48390225-48390244 MsG0380013919.01.T01:CDS 30.0%
! ATTTTCAGAGAACACCAAAT+GGG + Chr3:48390364-48390383 None:intergenic 30.0%
! CAATTGATTTCGTATGTGAA+AGG - Chr3:48390860-48390879 MsG0380013919.01.T01:intron 30.0%
! CGAGATTTTATTCTTCTGTA+TGG + Chr3:48390400-48390419 None:intergenic 30.0%
! GACTAAAATTGATTCTTCCT+GGG - Chr3:48390226-48390245 MsG0380013919.01.T01:CDS 30.0%
! TTTTTGGATTTGTATCCATC+GGG + Chr3:48390836-48390855 None:intergenic 30.0%
TCTTTCGTCAGTAAATTCAG+TGG + Chr3:48391140-48391159 None:intergenic 35.0%
TGGGTTATATCATTTCATGG+TGG + Chr3:48390345-48390364 None:intergenic 35.0%
! GATTTTCAGAGAACACCAAA+TGG + Chr3:48390365-48390384 None:intergenic 35.0%
! GTTCTCTGAAAATCACCAAT+GGG - Chr3:48390371-48390390 MsG0380013919.01.T01:intron 35.0%
! TGTTCTCTGAAAATCACCAA+TGG - Chr3:48390370-48390389 MsG0380013919.01.T01:intron 35.0%
! TTTAGGACATCTCTCTTTCA+AGG - Chr3:48390131-48390150 MsG0380013919.01.T01:CDS 35.0%
!! ATGCTATACAACTTTTTCCC+TGG - Chr3:48390742-48390761 MsG0380013919.01.T01:intron 35.0%
!! TGCTATACAACTTTTTCCCT+GGG - Chr3:48390743-48390762 MsG0380013919.01.T01:intron 35.0%
!!! ATGGTGGATCAGCAATTTTT+GGG + Chr3:48390329-48390348 None:intergenic 35.0%
ACCAATTGAACTACAATCCC+AGG + Chr3:48390763-48390782 None:intergenic 40.0%
CCAATTGAACTACAATCCCA+GGG + Chr3:48390762-48390781 None:intergenic 40.0%
CCTCTTTCAGTTACAGTACA+GGG - Chr3:48390665-48390684 MsG0380013919.01.T01:intron 40.0%
CTCTTTCAGTTACAGTACAG+GGG - Chr3:48390666-48390685 MsG0380013919.01.T01:intron 40.0%
GTTCGGACGAAGAAAGAAAA+AGG - Chr3:48390951-48390970 MsG0380013919.01.T01:intron 40.0%
!!! CATGGTGGATCAGCAATTTT+TGG + Chr3:48390330-48390349 None:intergenic 40.0%
AGGACATCTCTCTTTCAAGG+AGG - Chr3:48390134-48390153 MsG0380013919.01.T01:CDS 45.0%
CCCTGGGATTGTAGTTCAAT+TGG - Chr3:48390759-48390778 MsG0380013919.01.T01:intron 45.0%
CCCTGTACTGTAACTGAAAG+AGG + Chr3:48390668-48390687 None:intergenic 45.0%
CCTAAACCACTAGACGATGA+GGG + Chr3:48390117-48390136 None:intergenic 45.0%
CGTTGGAAATATGTCTACGC+TGG - Chr3:48390287-48390306 MsG0380013919.01.T01:CDS 45.0%
GCACTTTAGCGAAATCGACA+CGG + Chr3:48390606-48390625 None:intergenic 45.0%
GCCTCTTTCAGTTACAGTAC+AGG - Chr3:48390664-48390683 MsG0380013919.01.T01:intron 45.0%
TCCTAAACCACTAGACGATG+AGG + Chr3:48390118-48390137 None:intergenic 45.0%
TCTCTCTTTCAAGGAGGCAA+CGG - Chr3:48390140-48390159 MsG0380013919.01.T01:CDS 45.0%
TTTGTATCCATCGGGACTGA+CGG + Chr3:48390828-48390847 None:intergenic 45.0%
!!! AAGTAATTTTTTTTTTTATT+TGG - Chr3:48390993-48391012 MsG0380013919.01.T01:intron 5.0%
CCCTCATCGTCTAGTGGTTT+AGG - Chr3:48390114-48390133 MsG0380013919.01.T01:CDS 50.0%
CTCTCTTTCAAGGAGGCAAC+GGG - Chr3:48390141-48390160 MsG0380013919.01.T01:CDS 50.0%
TCTCTTTCAAGGAGGCAACG+GGG - Chr3:48390142-48390161 MsG0380013919.01.T01:CDS 50.0%
TCTTCTGTATGGGAGCCCAT+TGG + Chr3:48390389-48390408 None:intergenic 50.0%
TTGTATCCATCGGGACTGAC+GGG + Chr3:48390827-48390846 None:intergenic 50.0%
TTTGTAGTACCCTACCCCCA+GGG + Chr3:48390178-48390197 None:intergenic 50.0%
! TGGGGGTAGGGTACTACAAA+AGG - Chr3:48390178-48390197 MsG0380013919.01.T01:CDS 50.0%
! TTTTGTAGTACCCTACCCCC+AGG + Chr3:48390179-48390198 None:intergenic 50.0%
!! ACGCTGGTTCAAATCCAGCT+CGG - Chr3:48390303-48390322 MsG0380013919.01.T01:CDS 50.0%
!! GGGACGGACTGTAAATTCGT+TGG - Chr3:48390270-48390289 MsG0380013919.01.T01:CDS 50.0%
TCGATGCCCGAGCGGTTAAT+GGG - Chr3:48390249-48390268 MsG0380013919.01.T01:CDS 55.0%
TTGTAGTACCCTACCCCCAG+GGG + Chr3:48390177-48390196 None:intergenic 55.0%
!! CAGCAATTTTTGGGCCGAGC+TGG + Chr3:48390320-48390339 None:intergenic 55.0%
AACGGGGATTCGACTTCCCC+TGG - Chr3:48390158-48390177 MsG0380013919.01.T01:CDS 60.0%
ACGGGGATTCGACTTCCCCT+GGG - Chr3:48390159-48390178 MsG0380013919.01.T01:CDS 60.0%
ATTCGACTTCCCCTGGGGGT+AGG - Chr3:48390165-48390184 MsG0380013919.01.T01:CDS 60.0%
CGATGCCCGAGCGGTTAATG+GGG - Chr3:48390250-48390269 MsG0380013919.01.T01:CDS 60.0%
GTCCGTCCCCATTAACCGCT+CGG + Chr3:48390259-48390278 None:intergenic 60.0%
GTCGATGCCCGAGCGGTTAA+TGG - Chr3:48390248-48390267 MsG0380013919.01.T01:CDS 60.0%
TCCGTCCCCATTAACCGCTC+GGG + Chr3:48390258-48390277 None:intergenic 60.0%
TTCGACTTCCCCTGGGGGTA+GGG - Chr3:48390166-48390185 MsG0380013919.01.T01:CDS 60.0%
CAGCTTCCGCCTTGACAGGG+CGG + Chr3:48390793-48390812 None:intergenic 65.0%
CCCTGTCAAGGCGGAAGCTG+CGG - Chr3:48390793-48390812 MsG0380013919.01.T01:intron 65.0%
CCGCAGCTTCCGCCTTGACA+GGG + Chr3:48390796-48390815 None:intergenic 65.0%
CCTGTCAAGGCGGAAGCTGC+GGG - Chr3:48390794-48390813 MsG0380013919.01.T01:intron 65.0%
CGGGGATTCGACTTCCCCTG+GGG - Chr3:48390160-48390179 MsG0380013919.01.T01:CDS 65.0%
GCCCGAGCGGTTAATGGGGA+CGG - Chr3:48390254-48390273 MsG0380013919.01.T01:CDS 65.0%
GGGGATTCGACTTCCCCTGG+GGG - Chr3:48390161-48390180 MsG0380013919.01.T01:CDS 65.0%
TCGAGTCCCGTCAGTCCCGA+TGG - Chr3:48390818-48390837 MsG0380013919.01.T01:intron 65.0%
TTCCTGGGTCGATGCCCGAG+CGG - Chr3:48390241-48390260 MsG0380013919.01.T01:CDS 65.0%
!! AGAGCACCGCCCTGTCAAGG+CGG - Chr3:48390784-48390803 MsG0380013919.01.T01:intron 65.0%
!! GTCAGAGCACCGCCCTGTCA+AGG - Chr3:48390781-48390800 MsG0380013919.01.T01:intron 65.0%
CCCGCAGCTTCCGCCTTGAC+AGG + Chr3:48390797-48390816 None:intergenic 70.0%
!! AACCGCTCGGGCATCGACCC+AGG + Chr3:48390246-48390265 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
Chr3 gene 48390111 48391330 48390111 ID=MsG0380013919.01;Name=MsG0380013919.01
Chr3 mRNA 48390111 48391330 48390111 ID=MsG0380013919.01.T01;Parent=MsG0380013919.01;Name=MsG0380013919.01.T01;_AED=0.50;_eAED=1.00;_QI=0|0|0|1|0|0|2|0|109
Chr3 exon 48391254 48391330 48391254 ID=MsG0380013919.01.T01:exon:9378;Parent=MsG0380013919.01.T01
Chr3 exon 48390111 48390363 48390111 ID=MsG0380013919.01.T01:exon:9377;Parent=MsG0380013919.01.T01
Chr3 CDS 48391254 48391330 48391254 ID=MsG0380013919.01.T01:cds;Parent=MsG0380013919.01.T01
Chr3 CDS 48390111 48390363 48390111 ID=MsG0380013919.01.T01:cds;Parent=MsG0380013919.01.T01
Gene Sequence

>MsG0380013919.01.T01

ATGCCCTCATCGTCTAGTGGTTTAGGACATCTCTCTTTCAAGGAGGCAACGGGGATTCGACTTCCCCTGGGGGTAGGCTCCGATATTGTTATTCGTGATATTGATCCGATTTTATATCATCGAGATAAAATTTATACCACTGAATTTACTGACGAAAGATTTTTCATTTCTATGGGATTAAATCCCGAAGTATTTATTAGAAATAAAAGAGAAAGAAAACATAGAGATTATGGAAGTCAATATTCTCGCATTTATAGCTACTGCACTCTTCATTCTAGTTCCTACTGCCTTTTTACTTATAATTTACGTAAAAACGGTAAGTCAAAGTGA

Protein sequence

>MsG0380013919.01.T01

MPSSSSGLGHLSFKEATGIRLPLGVGSDIVIRDIDPILYHRDKIYTTEFTDERFFISMGLNPEVFIRNKRERKHRDYGSQYSRIYSYCTLHSSSYCLFTYNLRKNGKSK*