AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0512900


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 23 sgRNAs with CRISPR-Local

Find 140 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACCTGAGTCAAATTTGATTT+TGG 0.143815 3_4:-62949476 None:intergenic
AATTTGTTTGGGATCTGATT+TGG 0.292556 3_4:+62950128 Msa0512900:CDS
AAGCATATCACTGCAGATAT+TGG 0.320627 3_4:-62949519 None:intergenic
GGATCTGATTTGGCTTCATC+TGG 0.324293 3_4:+62950138 Msa0512900:CDS
GTTGTTTGCGTGTATTGTTT+TGG 0.356104 3_4:-62949308 None:intergenic
TGCTCTCGAGTGCAAAGCTT+TGG 0.369375 3_4:-62949277 None:intergenic
ACTTCAATTCTGGAAACGTC+TGG 0.392283 3_4:+62950252 Msa0512900:CDS
CACACACATAGCAACAATCT+AGG 0.462178 3_4:+62949557 Msa0512900:CDS
GCCAAAATCAAATTTGACTC+AGG 0.511927 3_4:+62949475 Msa0512900:CDS
GTCTGGGAACTGTATTGCTT+AGG 0.535518 3_4:+62950269 Msa0512900:CDS
ATGGACAGAATTCCCGTCGT+TGG 0.536101 3_4:-62950224 None:intergenic
GATGCGTTCATGCCAACGAC+GGG 0.540957 3_4:+62950212 Msa0512900:CDS
TGCAGATATCGAAAAGTGAA+TGG 0.542015 3_4:+62949440 Msa0512900:intron
TGCTATGTGTGTGGAAAGAA+AGG 0.547994 3_4:-62949547 None:intergenic
CTTCAATTCTGGAAACGTCT+GGG 0.550347 3_4:+62950253 Msa0512900:CDS
AAAATGGACAAATGCTAACA+AGG 0.592765 3_4:-62950103 None:intergenic
ATAATGTAGAAAGAATTGTA+TGG 0.603694 3_4:+62950073 Msa0512900:intron
CTAGATTGTTGCTATGTGTG+TGG 0.632111 3_4:-62949556 None:intergenic
AGATGCGTTCATGCCAACGA+CGG 0.660867 3_4:+62950211 Msa0512900:CDS
TGGTTTGACATCAGTAAGAG+CGG 0.666613 3_4:+62950158 Msa0512900:CDS
ACAATACACGCAAACAACAG+AGG 0.686335 3_4:+62949313 Msa0512900:CDS
TTCACACTACTAGACGTCCA+CGG 0.691367 3_4:-62950189 None:intergenic
TAAGAGCGGAAGCGACACCG+TGG 0.723748 3_4:+62950172 Msa0512900:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTAAGTTTGATTTAAAATTG+GGG - chr3_4:62949377-62949396 None:intergenic 15.0%
!!! CTTAAGTTTGATTTAAAATT+GGG - chr3_4:62949378-62949397 None:intergenic 15.0%
!!! TTAAGTTTGATTTAAAATTG+GGG - chr3_4:62949377-62949396 None:intergenic 15.0%
!!! CTTAAGTTTGATTTAAAATT+GGG - chr3_4:62949378-62949397 None:intergenic 15.0%
!!! CCTTAAGTTTGATTTAAAAT+TGG - chr3_4:62949379-62949398 None:intergenic 20.0%
!!! CCAATTTTAAATCAAACTTA+AGG + chr3_4:62949376-62949395 Msa0512900:intron 20.0%
!! ATAATGTAGAAAGAATTGTA+TGG + chr3_4:62950073-62950092 Msa0512900:intron 20.0%
!!! CCTTAAGTTTGATTTAAAAT+TGG - chr3_4:62949379-62949398 None:intergenic 20.0%
!!! CCAATTTTAAATCAAACTTA+AGG + chr3_4:62949376-62949395 Msa0512900:intron 20.0%
!! ATAATGTAGAAAGAATTGTA+TGG + chr3_4:62950073-62950092 Msa0512900:intron 20.0%
!!! TGTCCATTTTTCAATTTGTT+TGG + chr3_4:62950116-62950135 Msa0512900:CDS 25.0%
!!! GTCCATTTTTCAATTTGTTT+GGG + chr3_4:62950117-62950136 Msa0512900:CDS 25.0%
! ATCCCAAACAAATTGAAAAA+TGG - chr3_4:62950122-62950141 None:intergenic 25.0%
!!! TGTCCATTTTTCAATTTGTT+TGG + chr3_4:62950116-62950135 Msa0512900:CDS 25.0%
!!! GTCCATTTTTCAATTTGTTT+GGG + chr3_4:62950117-62950136 Msa0512900:CDS 25.0%
! ATCCCAAACAAATTGAAAAA+TGG - chr3_4:62950122-62950141 None:intergenic 25.0%
AATAAAACTGATCATACCCT+CGG + chr3_4:62949342-62949361 Msa0512900:intron 30.0%
!!! AAATTTGATTTTGGCTTAGG+AGG - chr3_4:62949470-62949489 None:intergenic 30.0%
!!! GTCAAATTTGATTTTGGCTT+AGG - chr3_4:62949473-62949492 None:intergenic 30.0%
!! ACCTGAGTCAAATTTGATTT+TGG - chr3_4:62949479-62949498 None:intergenic 30.0%
TTGTTGGAAACTATCTGTAA+TGG - chr3_4:62949948-62949967 None:intergenic 30.0%
TCCAACAAAAAACTTCTGTT+TGG + chr3_4:62949960-62949979 Msa0512900:intron 30.0%
!!! ACCAAACAGAAGTTTTTTGT+TGG - chr3_4:62949964-62949983 None:intergenic 30.0%
TGATGTTTATTGTTCCTACA+AGG - chr3_4:62950040-62950059 None:intergenic 30.0%
AAAATGGACAAATGCTAACA+AGG - chr3_4:62950106-62950125 None:intergenic 30.0%
! AATTTGTTTGGGATCTGATT+TGG + chr3_4:62950128-62950147 Msa0512900:CDS 30.0%
TCCATCAAAAACTTCAATTC+TGG + chr3_4:62950242-62950261 Msa0512900:CDS 30.0%
! TCCAGAATTGAAGTTTTTGA+TGG - chr3_4:62950246-62950265 None:intergenic 30.0%
AATAAAACTGATCATACCCT+CGG + chr3_4:62949342-62949361 Msa0512900:intron 30.0%
!!! AAATTTGATTTTGGCTTAGG+AGG - chr3_4:62949470-62949489 None:intergenic 30.0%
!!! GTCAAATTTGATTTTGGCTT+AGG - chr3_4:62949473-62949492 None:intergenic 30.0%
!! ACCTGAGTCAAATTTGATTT+TGG - chr3_4:62949479-62949498 None:intergenic 30.0%
TTGTTGGAAACTATCTGTAA+TGG - chr3_4:62949948-62949967 None:intergenic 30.0%
TCCAACAAAAAACTTCTGTT+TGG + chr3_4:62949960-62949979 Msa0512900:intron 30.0%
!!! ACCAAACAGAAGTTTTTTGT+TGG - chr3_4:62949964-62949983 None:intergenic 30.0%
TGATGTTTATTGTTCCTACA+AGG - chr3_4:62950040-62950059 None:intergenic 30.0%
AAAATGGACAAATGCTAACA+AGG - chr3_4:62950106-62950125 None:intergenic 30.0%
! AATTTGTTTGGGATCTGATT+TGG + chr3_4:62950128-62950147 Msa0512900:CDS 30.0%
TCCATCAAAAACTTCAATTC+TGG + chr3_4:62950242-62950261 Msa0512900:CDS 30.0%
! TCCAGAATTGAAGTTTTTGA+TGG - chr3_4:62950246-62950265 None:intergenic 30.0%
! GTTGTTTGCGTGTATTGTTT+TGG - chr3_4:62949641-62949660 None:intergenic 35.0%
GTTGTTGTGTGTGTAAAGAA+AGG + chr3_4:62949401-62949420 Msa0512900:intron 35.0%
TGCAGATATCGAAAAGTGAA+TGG + chr3_4:62949440-62949459 Msa0512900:intron 35.0%
GCCAAAATCAAATTTGACTC+AGG + chr3_4:62949475-62949494 Msa0512900:CDS 35.0%
AAGCATATCACTGCAGATAT+TGG - chr3_4:62949522-62949541 None:intergenic 35.0%
! CTAGGTTCGATTTAGAATTG+AGG + chr3_4:62949575-62949594 Msa0512900:intron 35.0%
! AATTGAGGTTAGTTACTCTG+AGG + chr3_4:62949590-62949609 Msa0512900:intron 35.0%
! ATTGAGGTTAGTTACTCTGA+GGG + chr3_4:62949591-62949610 Msa0512900:intron 35.0%
! GTTGTTTGCGTGTATTGTTT+TGG + chr3_4:62949641-62949660 Msa0512900:intron 35.0%
CTTGTAATCATTCCATGAGT+CGG + chr3_4:62949795-62949814 Msa0512900:intron 35.0%
TTGTAATCATTCCATGAGTC+GGG + chr3_4:62949796-62949815 Msa0512900:intron 35.0%
TCTGTAATGGCAAATGAAAG+AGG - chr3_4:62949935-62949954 None:intergenic 35.0%
CATGTTGTCCCAAATTTCTT+TGG + chr3_4:62950011-62950030 Msa0512900:intron 35.0%
CAAGGTTGCCAAAGAAATTT+GGG - chr3_4:62950022-62950041 None:intergenic 35.0%
ACAAGGTTGCCAAAGAAATT+TGG - chr3_4:62950023-62950042 None:intergenic 35.0%
AATTTCTTTGGCAACCTTGT+AGG + chr3_4:62950023-62950042 Msa0512900:intron 35.0%
! GTTGTTTGCGTGTATTGTTT+TGG - chr3_4:62949641-62949660 None:intergenic 35.0%
GTTGTTGTGTGTGTAAAGAA+AGG + chr3_4:62949401-62949420 Msa0512900:intron 35.0%
TGCAGATATCGAAAAGTGAA+TGG + chr3_4:62949440-62949459 Msa0512900:intron 35.0%
GCCAAAATCAAATTTGACTC+AGG + chr3_4:62949475-62949494 Msa0512900:CDS 35.0%
AAGCATATCACTGCAGATAT+TGG - chr3_4:62949522-62949541 None:intergenic 35.0%
! CTAGGTTCGATTTAGAATTG+AGG + chr3_4:62949575-62949594 Msa0512900:intron 35.0%
! AATTGAGGTTAGTTACTCTG+AGG + chr3_4:62949590-62949609 Msa0512900:intron 35.0%
! ATTGAGGTTAGTTACTCTGA+GGG + chr3_4:62949591-62949610 Msa0512900:intron 35.0%
! GTTGTTTGCGTGTATTGTTT+TGG + chr3_4:62949641-62949660 Msa0512900:intron 35.0%
CTTGTAATCATTCCATGAGT+CGG + chr3_4:62949795-62949814 Msa0512900:intron 35.0%
TTGTAATCATTCCATGAGTC+GGG + chr3_4:62949796-62949815 Msa0512900:intron 35.0%
TCTGTAATGGCAAATGAAAG+AGG - chr3_4:62949935-62949954 None:intergenic 35.0%
CATGTTGTCCCAAATTTCTT+TGG + chr3_4:62950011-62950030 Msa0512900:intron 35.0%
CAAGGTTGCCAAAGAAATTT+GGG - chr3_4:62950022-62950041 None:intergenic 35.0%
ACAAGGTTGCCAAAGAAATT+TGG - chr3_4:62950023-62950042 None:intergenic 35.0%
AATTTCTTTGGCAACCTTGT+AGG + chr3_4:62950023-62950042 Msa0512900:intron 35.0%
ACAATACACGCAAACAACAG+AGG + chr3_4:62949313-62949332 Msa0512900:CDS 40.0%
!!! TTGATTTTGGCTTAGGAGGT+TGG - chr3_4:62949466-62949485 None:intergenic 40.0%
TGCTATGTGTGTGGAAAGAA+AGG - chr3_4:62949550-62949569 None:intergenic 40.0%
CTAGATTGTTGCTATGTGTG+TGG - chr3_4:62949559-62949578 None:intergenic 40.0%
CACACACATAGCAACAATCT+AGG + chr3_4:62949557-62949576 Msa0512900:CDS 40.0%
ACAATACACGCAAACAACAG+AGG - chr3_4:62949313-62949332 None:intergenic 40.0%
GACACCAGTAGAAAAGAATG+CGG - chr3_4:62949709-62949728 None:intergenic 40.0%
ACTCCTTGAAGAATTGAAGG+CGG - chr3_4:62949875-62949894 None:intergenic 40.0%
CCAACTCCTTGAAGAATTGA+AGG - chr3_4:62949878-62949897 None:intergenic 40.0%
CCTTCAATTCTTCAAGGAGT+TGG + chr3_4:62949875-62949894 Msa0512900:intron 40.0%
AGGACAAGGAAATCAAAGTG+CGG - chr3_4:62949915-62949934 None:intergenic 40.0%
ATGGCAAATGAAAGAGGACA+AGG - chr3_4:62949929-62949948 None:intergenic 40.0%
TGGTTTGACATCAGTAAGAG+CGG + chr3_4:62950158-62950177 Msa0512900:CDS 40.0%
! ACTTCAATTCTGGAAACGTC+TGG + chr3_4:62950252-62950271 Msa0512900:CDS 40.0%
! CTTCAATTCTGGAAACGTCT+GGG + chr3_4:62950253-62950272 Msa0512900:CDS 40.0%
ACAATACACGCAAACAACAG+AGG + chr3_4:62949313-62949332 Msa0512900:CDS 40.0%
!!! TTGATTTTGGCTTAGGAGGT+TGG - chr3_4:62949466-62949485 None:intergenic 40.0%
TGCTATGTGTGTGGAAAGAA+AGG - chr3_4:62949550-62949569 None:intergenic 40.0%
CTAGATTGTTGCTATGTGTG+TGG - chr3_4:62949559-62949578 None:intergenic 40.0%
CACACACATAGCAACAATCT+AGG + chr3_4:62949557-62949576 Msa0512900:CDS 40.0%
ACAATACACGCAAACAACAG+AGG - chr3_4:62949313-62949332 None:intergenic 40.0%
GACACCAGTAGAAAAGAATG+CGG - chr3_4:62949709-62949728 None:intergenic 40.0%
ACTCCTTGAAGAATTGAAGG+CGG - chr3_4:62949875-62949894 None:intergenic 40.0%
CCAACTCCTTGAAGAATTGA+AGG - chr3_4:62949878-62949897 None:intergenic 40.0%
CCTTCAATTCTTCAAGGAGT+TGG + chr3_4:62949875-62949894 Msa0512900:intron 40.0%
AGGACAAGGAAATCAAAGTG+CGG - chr3_4:62949915-62949934 None:intergenic 40.0%
ATGGCAAATGAAAGAGGACA+AGG - chr3_4:62949929-62949948 None:intergenic 40.0%
TGGTTTGACATCAGTAAGAG+CGG + chr3_4:62950158-62950177 Msa0512900:CDS 40.0%
! ACTTCAATTCTGGAAACGTC+TGG + chr3_4:62950252-62950271 Msa0512900:CDS 40.0%
! CTTCAATTCTGGAAACGTCT+GGG + chr3_4:62950253-62950272 Msa0512900:CDS 40.0%
!! ATTGGGGTTAGTTACTCCGA+GGG - chr3_4:62949361-62949380 None:intergenic 45.0%
!! AATTGGGGTTAGTTACTCCG+AGG - chr3_4:62949362-62949381 None:intergenic 45.0%
TTCTCTCGACTCCAAAGCTT+TGG + chr3_4:62949672-62949691 Msa0512900:intron 45.0%
! AGCTCCGCATTCTTTTCTAC+TGG + chr3_4:62949702-62949721 Msa0512900:intron 45.0%
TTGAAAAGTTGCCCGACTCA+TGG - chr3_4:62949810-62949829 None:intergenic 45.0%
TCTCCGCCTTCAATTCTTCA+AGG + chr3_4:62949869-62949888 Msa0512900:intron 45.0%
GAATGTCAAGTACACTGCTG+AGG - chr3_4:62949992-62950011 None:intergenic 45.0%
!! GGATCTGATTTGGCTTCATC+TGG + chr3_4:62950138-62950157 Msa0512900:CDS 45.0%
TTCACACTACTAGACGTCCA+CGG - chr3_4:62950192-62950211 None:intergenic 45.0%
!! ATTGGGGTTAGTTACTCCGA+GGG - chr3_4:62949361-62949380 None:intergenic 45.0%
!! AATTGGGGTTAGTTACTCCG+AGG - chr3_4:62949362-62949381 None:intergenic 45.0%
TTCTCTCGACTCCAAAGCTT+TGG + chr3_4:62949672-62949691 Msa0512900:intron 45.0%
! AGCTCCGCATTCTTTTCTAC+TGG + chr3_4:62949702-62949721 Msa0512900:intron 45.0%
TTGAAAAGTTGCCCGACTCA+TGG - chr3_4:62949810-62949829 None:intergenic 45.0%
TCTCCGCCTTCAATTCTTCA+AGG + chr3_4:62949869-62949888 Msa0512900:intron 45.0%
GAATGTCAAGTACACTGCTG+AGG - chr3_4:62949992-62950011 None:intergenic 45.0%
!! GGATCTGATTTGGCTTCATC+TGG + chr3_4:62950138-62950157 Msa0512900:CDS 45.0%
TTCACACTACTAGACGTCCA+CGG - chr3_4:62950192-62950211 None:intergenic 45.0%
TGCTCTCGAGTGCAAAGCTT+TGG - chr3_4:62949280-62949299 None:intergenic 50.0%
! GTCGGGCAACTTTTCAACCA+AGG + chr3_4:62949813-62949832 Msa0512900:intron 50.0%
GCGGAGAACATCATACTTCC+AGG - chr3_4:62949856-62949875 None:intergenic 50.0%
AGATGCGTTCATGCCAACGA+CGG + chr3_4:62950211-62950230 Msa0512900:CDS 50.0%
ATGGACAGAATTCCCGTCGT+TGG - chr3_4:62950227-62950246 None:intergenic 50.0%
TGCTCTCGAGTGCAAAGCTT+TGG - chr3_4:62949280-62949299 None:intergenic 50.0%
! GTCGGGCAACTTTTCAACCA+AGG + chr3_4:62949813-62949832 Msa0512900:intron 50.0%
GCGGAGAACATCATACTTCC+AGG - chr3_4:62949856-62949875 None:intergenic 50.0%
AGATGCGTTCATGCCAACGA+CGG + chr3_4:62950211-62950230 Msa0512900:CDS 50.0%
ATGGACAGAATTCCCGTCGT+TGG - chr3_4:62950227-62950246 None:intergenic 50.0%
AGCTGCACGAGCCAAAGCTT+TGG - chr3_4:62949266-62949285 None:intergenic 55.0%
CGTGTTTGTCGCTGATGCCT+TGG - chr3_4:62949833-62949852 None:intergenic 55.0%
GATGCGTTCATGCCAACGAC+GGG + chr3_4:62950212-62950231 Msa0512900:CDS 55.0%
AGCTGCACGAGCCAAAGCTT+TGG - chr3_4:62949266-62949285 None:intergenic 55.0%
CGTGTTTGTCGCTGATGCCT+TGG - chr3_4:62949833-62949852 None:intergenic 55.0%
GATGCGTTCATGCCAACGAC+GGG + chr3_4:62950212-62950231 Msa0512900:CDS 55.0%
GCATCAGCGACAAACACGCC+TGG + chr3_4:62949835-62949854 Msa0512900:intron 60.0%
TAAGAGCGGAAGCGACACCG+TGG + chr3_4:62950172-62950191 Msa0512900:CDS 60.0%
GCATCAGCGACAAACACGCC+TGG + chr3_4:62949835-62949854 Msa0512900:intron 60.0%
TAAGAGCGGAAGCGACACCG+TGG + chr3_4:62950172-62950191 Msa0512900:CDS 60.0%
Chromosome Type Strat End Strand Name
chr3_4 gene 62949255 62950290 62949255 ID=Msa0512900;Name=Msa0512900
chr3_4 mRNA 62949255 62950290 62949255 ID=Msa0512900-mRNA-1;Parent=Msa0512900;Name=Msa0512900-mRNA-1;_AED=0.44;_eAED=1.00;_QI=0|0|0|1|1|1|3|0|140
chr3_4 exon 62949255 62949334 62949255 ID=Msa0512900-mRNA-1:exon:15666;Parent=Msa0512900-mRNA-1
chr3_4 exon 62949445 62949578 62949445 ID=Msa0512900-mRNA-1:exon:15667;Parent=Msa0512900-mRNA-1
chr3_4 exon 62950082 62950290 62950082 ID=Msa0512900-mRNA-1:exon:15668;Parent=Msa0512900-mRNA-1
chr3_4 CDS 62949255 62949334 62949255 ID=Msa0512900-mRNA-1:cds;Parent=Msa0512900-mRNA-1
chr3_4 CDS 62949445 62949578 62949445 ID=Msa0512900-mRNA-1:cds;Parent=Msa0512900-mRNA-1
chr3_4 CDS 62950082 62950290 62950082 ID=Msa0512900-mRNA-1:cds;Parent=Msa0512900-mRNA-1
Gene Sequence

>Msa0512900

ATGGAATGCAGAGCTGCACGAGCCAAAGCTTTGCACTCGAGAGCAAATCTAATCCAAAACAATACACGCAAACAACAGAGATATCGAAAAGTGAATGGCCAACCTCCTAAGCCAAAATCAAATTTGACTCAGGTTCGAATGTTCGATTCACTTTCCAATATCTGCAGTGATATGCTTTATGACCTTTCTTTCCACACACATAGCAACAATCTAGAAAGAATTGTATGGCGACAAACCTTGTTAGCATTTGTCCATTTTTCAATTTGTTTGGGATCTGATTTGGCTTCATCTGGTTTGACATCAGTAAGAGCGGAAGCGACACCGTGGACGTCTAGTAGTGTGAAGATGCGTTCATGCCAACGACGGGAATTCTGTCCATCAAAAACTTCAATTCTGGAAACGTCTGGGAACTGTATTGCTTAG

Protein sequence

>Msa0512900

MECRAARAKALHSRANLIQNNTRKQQRYRKVNGQPPKPKSNLTQVRMFDSLSNICSDMLYDLSFHTHSNNLERIVWRQTLLAFVHFSICLGSDLASSGLTSVRAEATPWTSSSVKMRSCQRREFCPSKTSILETSGNCIA*