AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1124050

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 31 sgRNAs with CRISPR-Local

Find 111 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TACAATTACTCGTGCTATTA+TGG 0.109957 7_3:-75081634 Msa1124050:CDS
CTGCAGGTCAAGGCTGATTT+TGG 0.138857 7_3:-75082001 Msa1124050:intron
TACTGGTGATGTTTCTAAAA+AGG 0.173626 7_3:-75082239 Msa1124050:five_prime_UTR
TCGGATTAACCAACACAATT+AGG 0.275265 7_3:-75082305 Msa1124050:five_prime_UTR
CAGTGTGCATATTGATTTAG+AGG 0.321280 7_3:-75081684 Msa1124050:CDS
TGAGTTGAGAAGGTTGAATA+AGG 0.323601 7_3:-75082506 Msa1124050:five_prime_UTR
CACTTGTAGGCTCTCTTCTA+TGG 0.338739 7_3:-75082458 Msa1124050:five_prime_UTR
ACAATTACTCGTGCTATTAT+GGG 0.418679 7_3:-75081633 Msa1124050:CDS
TTAACTTAAATCATACTGAT+AGG 0.430639 7_3:-75082130 Msa1124050:CDS
AACCAACACAATTAGGCTCT+TGG 0.438251 7_3:-75082298 Msa1124050:five_prime_UTR
GATAAGAGGAAGCGGTGAAG+GGG 0.453973 7_3:-75082573 None:intergenic
TTGTAATAGAAGATATGAAT+AGG 0.461497 7_3:-75082334 Msa1124050:five_prime_UTR
GAAGTAAATGTAAAGGAAGA+AGG 0.468064 7_3:-75081710 Msa1124050:CDS
AGCCTTGCTCTGCAAATACT+TGG 0.488191 7_3:+75081958 None:intergenic
AGATAAGAGGAAGCGGTGAA+GGG 0.491215 7_3:-75082574 None:intergenic
AGATATGAATAGGCTCTCTT+CGG 0.510356 7_3:-75082324 Msa1124050:five_prime_UTR
AGAAGAGGAACCTCACTTGT+AGG 0.517175 7_3:-75082471 Msa1124050:five_prime_UTR
GTCCAAGTATTTGCAGAGCA+AGG 0.527011 7_3:-75081960 Msa1124050:CDS
AGCCAAGAGCCTAATTGTGT+TGG 0.531992 7_3:+75082296 None:intergenic
TTACTGAGTTGGACTTAAAG+TGG 0.536061 7_3:-75082186 Msa1124050:five_prime_UTR
ATAAGAGGAAGCGGTGAAGG+GGG 0.538898 7_3:-75082572 None:intergenic
TTGAAGTTGTTGAGTTGAGA+AGG 0.559117 7_3:-75082516 Msa1124050:five_prime_UTR
GAGCAAAGAAGTAAATGTAA+AGG 0.561628 7_3:-75081717 Msa1124050:CDS
TGTATGCTATCTTACTGAGT+TGG 0.580470 7_3:-75082197 Msa1124050:five_prime_UTR
AGGAGCTGCATATGTAGAAG+AGG 0.591272 7_3:-75082486 Msa1124050:five_prime_UTR
ATGATTTAAGTTAATAACCA+TGG 0.599391 7_3:+75082139 None:intergenic
TCATACTGATAGGACAGTGA+TGG 0.631868 7_3:-75082120 Msa1124050:intron
TAGAAGAGAGCCTACAAGTG+AGG 0.633933 7_3:+75082461 None:intergenic
TAGTTGTGCCTGCCAAAACA+CGG 0.641537 7_3:+75082260 None:intergenic
AGCAGAACATGCAATGAGTG+CGG 0.674542 7_3:-75081750 Msa1124050:CDS
TAACTTGCTGAGAAATACCA+TGG 0.684621 7_3:-75082156 Msa1124050:exon

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTGTAATAGAAGATATGAAT+AGG - chr7_3:75081850-75081869 Msa1124050:intron 20.0%
!!! ATGATTTAAGTTAATAACCA+TGG + chr7_3:75082048-75082067 None:intergenic 20.0%
!! TTAACTTAAATCATACTGAT+AGG - chr7_3:75082054-75082073 Msa1124050:intron 20.0%
!! TTGTAATAGAAGATATGAAT+AGG - chr7_3:75081850-75081869 Msa1124050:intron 20.0%
!!! ATGATTTAAGTTAATAACCA+TGG + chr7_3:75082048-75082067 None:intergenic 20.0%
!! TTAACTTAAATCATACTGAT+AGG - chr7_3:75082054-75082073 Msa1124050:intron 20.0%
!! TGACATAATTTCTTTTCTCA+TGG - chr7_3:75081818-75081837 Msa1124050:CDS 25.0%
!! GACATAATTTCTTTTCTCAT+GGG - chr7_3:75081819-75081838 Msa1124050:CDS 25.0%
!! CTTTGAATGGTAATTCATTT+TGG + chr7_3:75082123-75082142 None:intergenic 25.0%
! CAAAATGAATTACCATTCAA+AGG - chr7_3:75082121-75082140 Msa1124050:CDS 25.0%
! ATTTCTAACTTAATGGTACT+TGG + chr7_3:75082253-75082272 None:intergenic 25.0%
! GTTAAAGAAAATTAGAAGAC+TGG + chr7_3:75082346-75082365 None:intergenic 25.0%
!!! TGTTTTGAAGTCAATGAAAT+TGG - chr7_3:75082411-75082430 Msa1124050:five_prime_UTR 25.0%
!! TTTTTCTTTGTTGCAAAACA+TGG + chr7_3:75082528-75082547 None:intergenic 25.0%
!! TGACATAATTTCTTTTCTCA+TGG - chr7_3:75081818-75081837 Msa1124050:CDS 25.0%
!! GACATAATTTCTTTTCTCAT+GGG - chr7_3:75081819-75081838 Msa1124050:CDS 25.0%
!! CTTTGAATGGTAATTCATTT+TGG + chr7_3:75082123-75082142 None:intergenic 25.0%
! CAAAATGAATTACCATTCAA+AGG - chr7_3:75082121-75082140 Msa1124050:CDS 25.0%
! ATTTCTAACTTAATGGTACT+TGG + chr7_3:75082253-75082272 None:intergenic 25.0%
! GTTAAAGAAAATTAGAAGAC+TGG + chr7_3:75082346-75082365 None:intergenic 25.0%
!!! TGTTTTGAAGTCAATGAAAT+TGG - chr7_3:75082411-75082430 Msa1124050:five_prime_UTR 25.0%
!! TTTTTCTTTGTTGCAAAACA+TGG + chr7_3:75082528-75082547 None:intergenic 25.0%
! TACTGGTGATGTTTCTAAAA+AGG - chr7_3:75081945-75081964 Msa1124050:intron 30.0%
! ACTGGTGATGTTTCTAAAAA+GGG - chr7_3:75081946-75081965 Msa1124050:intron 30.0%
! AGTACTTGATAACCTTTGAA+TGG + chr7_3:75082136-75082155 None:intergenic 30.0%
GTACCATTAAGTTAGAAATG+CGG - chr7_3:75082254-75082273 Msa1124050:five_prime_UTR 30.0%
TACCATTAAGTTAGAAATGC+GGG - chr7_3:75082255-75082274 Msa1124050:five_prime_UTR 30.0%
TAAAAAGTAAACAAGCAGCA+AGG + chr7_3:75082295-75082314 None:intergenic 30.0%
!!! TTGCTGCTTGTTTACTTTTT+AGG - chr7_3:75082294-75082313 Msa1124050:five_prime_UTR 30.0%
GAGCAAAGAAGTAAATGTAA+AGG - chr7_3:75082467-75082486 Msa1124050:five_prime_UTR 30.0%
GAAGTAAATGTAAAGGAAGA+AGG - chr7_3:75082474-75082493 Msa1124050:five_prime_UTR 30.0%
! TACAATTACTCGTGCTATTA+TGG - chr7_3:75082550-75082569 Msa1124050:five_prime_UTR 30.0%
! ACAATTACTCGTGCTATTAT+GGG - chr7_3:75082551-75082570 Msa1124050:five_prime_UTR 30.0%
! TACTGGTGATGTTTCTAAAA+AGG - chr7_3:75081945-75081964 Msa1124050:intron 30.0%
! ACTGGTGATGTTTCTAAAAA+GGG - chr7_3:75081946-75081965 Msa1124050:intron 30.0%
! AGTACTTGATAACCTTTGAA+TGG + chr7_3:75082136-75082155 None:intergenic 30.0%
GTACCATTAAGTTAGAAATG+CGG - chr7_3:75082254-75082273 Msa1124050:five_prime_UTR 30.0%
TACCATTAAGTTAGAAATGC+GGG - chr7_3:75082255-75082274 Msa1124050:five_prime_UTR 30.0%
TAAAAAGTAAACAAGCAGCA+AGG + chr7_3:75082295-75082314 None:intergenic 30.0%
!!! TTGCTGCTTGTTTACTTTTT+AGG - chr7_3:75082294-75082313 Msa1124050:five_prime_UTR 30.0%
GAGCAAAGAAGTAAATGTAA+AGG - chr7_3:75082467-75082486 Msa1124050:five_prime_UTR 30.0%
GAAGTAAATGTAAAGGAAGA+AGG - chr7_3:75082474-75082493 Msa1124050:five_prime_UTR 30.0%
! TACAATTACTCGTGCTATTA+TGG - chr7_3:75082550-75082569 Msa1124050:five_prime_UTR 30.0%
! ACAATTACTCGTGCTATTAT+GGG - chr7_3:75082551-75082570 Msa1124050:five_prime_UTR 30.0%
!! TTGAAGTTGTTGAGTTGAGA+AGG - chr7_3:75081668-75081687 Msa1124050:CDS 35.0%
! TGAGTTGAGAAGGTTGAATA+AGG - chr7_3:75081678-75081697 Msa1124050:CDS 35.0%
AGATATGAATAGGCTCTCTT+CGG - chr7_3:75081860-75081879 Msa1124050:intron 35.0%
TCGGATTAACCAACACAATT+AGG - chr7_3:75081879-75081898 Msa1124050:intron 35.0%
!! TTTTGATTGATGCCGTGTTT+TGG - chr7_3:75081912-75081931 Msa1124050:intron 35.0%
! ATGTTTCTAAAAAGGGTCGA+TGG - chr7_3:75081953-75081972 Msa1124050:CDS 35.0%
TGTATGCTATCTTACTGAGT+TGG - chr7_3:75081987-75082006 Msa1124050:CDS 35.0%
! TTACTGAGTTGGACTTAAAG+TGG - chr7_3:75081998-75082017 Msa1124050:CDS 35.0%
!! TAACTTGCTGAGAAATACCA+TGG - chr7_3:75082028-75082047 Msa1124050:intron 35.0%
TTTGGACAGAGTAAACTTCA+AGG + chr7_3:75082105-75082124 None:intergenic 35.0%
AACCCGCATTTCTAACTTAA+TGG + chr7_3:75082260-75082279 None:intergenic 35.0%
!! CAGTGTGCATATTGATTTAG+AGG - chr7_3:75082500-75082519 Msa1124050:five_prime_UTR 35.0%
!! TTGAAGTTGTTGAGTTGAGA+AGG - chr7_3:75081668-75081687 Msa1124050:CDS 35.0%
! TGAGTTGAGAAGGTTGAATA+AGG - chr7_3:75081678-75081697 Msa1124050:CDS 35.0%
AGATATGAATAGGCTCTCTT+CGG - chr7_3:75081860-75081879 Msa1124050:intron 35.0%
TCGGATTAACCAACACAATT+AGG - chr7_3:75081879-75081898 Msa1124050:intron 35.0%
!! TTTTGATTGATGCCGTGTTT+TGG - chr7_3:75081912-75081931 Msa1124050:intron 35.0%
! ATGTTTCTAAAAAGGGTCGA+TGG - chr7_3:75081953-75081972 Msa1124050:CDS 35.0%
TGTATGCTATCTTACTGAGT+TGG - chr7_3:75081987-75082006 Msa1124050:CDS 35.0%
! TTACTGAGTTGGACTTAAAG+TGG - chr7_3:75081998-75082017 Msa1124050:CDS 35.0%
!! TAACTTGCTGAGAAATACCA+TGG - chr7_3:75082028-75082047 Msa1124050:intron 35.0%
TTTGGACAGAGTAAACTTCA+AGG + chr7_3:75082105-75082124 None:intergenic 35.0%
AACCCGCATTTCTAACTTAA+TGG + chr7_3:75082260-75082279 None:intergenic 35.0%
!! CAGTGTGCATATTGATTTAG+AGG - chr7_3:75082500-75082519 Msa1124050:five_prime_UTR 35.0%
AACCAACACAATTAGGCTCT+TGG - chr7_3:75081886-75081905 Msa1124050:intron 40.0%
TCATACTGATAGGACAGTGA+TGG - chr7_3:75082064-75082083 Msa1124050:intron 40.0%
CAGTAGAGGATAGGCAAATT+GGG + chr7_3:75082166-75082185 None:intergenic 40.0%
AACCAACACAATTAGGCTCT+TGG - chr7_3:75081886-75081905 Msa1124050:intron 40.0%
TCATACTGATAGGACAGTGA+TGG - chr7_3:75082064-75082083 Msa1124050:intron 40.0%
CAGTAGAGGATAGGCAAATT+GGG + chr7_3:75082166-75082185 None:intergenic 40.0%
AGGAGCTGCATATGTAGAAG+AGG - chr7_3:75081698-75081717 Msa1124050:CDS 45.0%
AGAAGAGGAACCTCACTTGT+AGG - chr7_3:75081713-75081732 Msa1124050:CDS 45.0%
TAGAAGAGAGCCTACAAGTG+AGG + chr7_3:75081726-75081745 None:intergenic 45.0%
CACTTGTAGGCTCTCTTCTA+TGG - chr7_3:75081726-75081745 Msa1124050:CDS 45.0%
AGCCAAGAGCCTAATTGTGT+TGG + chr7_3:75081891-75081910 None:intergenic 45.0%
TAGTTGTGCCTGCCAAAACA+CGG + chr7_3:75081927-75081946 None:intergenic 45.0%
GCAGTAGAGGATAGGCAAAT+TGG + chr7_3:75082167-75082186 None:intergenic 45.0%
ATTTGCCTATCCTCTACTGC+AGG - chr7_3:75082167-75082186 Msa1124050:five_prime_UTR 45.0%
!! TGCAGGTCAAGGCTGATTTT+GGG - chr7_3:75082184-75082203 Msa1124050:five_prime_UTR 45.0%
GTCCAAGTATTTGCAGAGCA+AGG - chr7_3:75082224-75082243 Msa1124050:five_prime_UTR 45.0%
AGCCTTGCTCTGCAAATACT+TGG + chr7_3:75082229-75082248 None:intergenic 45.0%
AGCAGAACATGCAATGAGTG+CGG - chr7_3:75082434-75082453 Msa1124050:five_prime_UTR 45.0%
! CGTGCTATTATGGGTAGAGT+AGG - chr7_3:75082560-75082579 Msa1124050:five_prime_UTR 45.0%
AGGAGCTGCATATGTAGAAG+AGG - chr7_3:75081698-75081717 Msa1124050:CDS 45.0%
AGAAGAGGAACCTCACTTGT+AGG - chr7_3:75081713-75081732 Msa1124050:CDS 45.0%
TAGAAGAGAGCCTACAAGTG+AGG + chr7_3:75081726-75081745 None:intergenic 45.0%
CACTTGTAGGCTCTCTTCTA+TGG - chr7_3:75081726-75081745 Msa1124050:CDS 45.0%
AGCCAAGAGCCTAATTGTGT+TGG + chr7_3:75081891-75081910 None:intergenic 45.0%
TAGTTGTGCCTGCCAAAACA+CGG + chr7_3:75081927-75081946 None:intergenic 45.0%
GCAGTAGAGGATAGGCAAAT+TGG + chr7_3:75082167-75082186 None:intergenic 45.0%
ATTTGCCTATCCTCTACTGC+AGG - chr7_3:75082167-75082186 Msa1124050:five_prime_UTR 45.0%
!! TGCAGGTCAAGGCTGATTTT+GGG - chr7_3:75082184-75082203 Msa1124050:five_prime_UTR 45.0%
GTCCAAGTATTTGCAGAGCA+AGG - chr7_3:75082224-75082243 Msa1124050:five_prime_UTR 45.0%
AGCCTTGCTCTGCAAATACT+TGG + chr7_3:75082229-75082248 None:intergenic 45.0%
AGCAGAACATGCAATGAGTG+CGG - chr7_3:75082434-75082453 Msa1124050:five_prime_UTR 45.0%
!!! GATTGATGCCGTGTTTTGGC+AGG - chr7_3:75081916-75081935 Msa1124050:intron 50.0%
!! GTTTTGGCAGGCACAACTAC+TGG - chr7_3:75081928-75081947 Msa1124050:intron 50.0%
CTTGACCTGCAGTAGAGGAT+AGG + chr7_3:75082175-75082194 None:intergenic 50.0%
CTATCCTCTACTGCAGGTCA+AGG - chr7_3:75082173-75082192 Msa1124050:five_prime_UTR 50.0%
!! CTGCAGGTCAAGGCTGATTT+TGG - chr7_3:75082183-75082202 Msa1124050:five_prime_UTR 50.0%
!!! GATTGATGCCGTGTTTTGGC+AGG - chr7_3:75081916-75081935 Msa1124050:intron 50.0%
!! GTTTTGGCAGGCACAACTAC+TGG - chr7_3:75081928-75081947 Msa1124050:intron 50.0%
CTTGACCTGCAGTAGAGGAT+AGG + chr7_3:75082175-75082194 None:intergenic 50.0%
CTATCCTCTACTGCAGGTCA+AGG - chr7_3:75082173-75082192 Msa1124050:five_prime_UTR 50.0%
!! CTGCAGGTCAAGGCTGATTT+TGG - chr7_3:75082183-75082202 Msa1124050:five_prime_UTR 50.0%
TCAGCCTTGACCTGCAGTAG+AGG + chr7_3:75082180-75082199 None:intergenic 55.0%
TCAGCCTTGACCTGCAGTAG+AGG + chr7_3:75082180-75082199 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr7_3 gene 75081625 75082581 75081625 ID=Msa1124050;Name=Msa1124050
chr7_3 mRNA 75081625 75082581 75081625 ID=Msa1124050-mRNA-1;Parent=Msa1124050;Name=Msa1124050-mRNA-1;_AED=0.38;_eAED=0.38;_QI=422|0.5|0.33|1|0.5|0.66|3|0|112
chr7_3 exon 75081625 75081859 75081625 ID=Msa1124050-mRNA-1:exon:20150;Parent=Msa1124050-mRNA-1
chr7_3 exon 75081953 75082017 75081953 ID=Msa1124050-mRNA-1:exon:20149;Parent=Msa1124050-mRNA-1
chr7_3 exon 75082121 75082581 75082121 ID=Msa1124050-mRNA-1:exon:20148;Parent=Msa1124050-mRNA-1
chr7_3 five_prime_UTR 75082160 75082581 75082160 ID=Msa1124050-mRNA-1:five_prime_utr;Parent=Msa1124050-mRNA-1
chr7_3 CDS 75082121 75082159 75082121 ID=Msa1124050-mRNA-1:cds;Parent=Msa1124050-mRNA-1
chr7_3 CDS 75081953 75082017 75081953 ID=Msa1124050-mRNA-1:cds;Parent=Msa1124050-mRNA-1
chr7_3 CDS 75081625 75081859 75081625 ID=Msa1124050-mRNA-1:cds;Parent=Msa1124050-mRNA-1
Gene Sequence

>Msa1124050

ATGGTTATTAACTTAAATCATACTGATAGGACAGTGATGGTCAAGGCTGATTTTGGGTCTGTTATTGATGCTTTGTCCAAGTATTTGCAGAGCAAGGCTGCCAATCTTCTAATTTTCTTTAACTTTGTTGATTCTAATGACATTCTGTTCATTATTGCTGTTTTCTTTTGTTTTGAAGTCAATGAAATTGGAGCAGAACATGCAATGAGTGCGGACAATGTCACGAGCAAAGAAGTAAATGTAAAGGAAGAAGGTTTCAGTGTGCATATTGATTTAGAGGAACCATGTTTTGCAACAAAGAAAAAAGTACAATTACTCGTGCTATTATGGGTAGAGTAG
Protein sequence

>Msa1124050

MVINLNHTDRTVMVKADFGSVIDALSKYLQSKAANLLIFFNFVDSNDILFIIAVFFCFEVNEIGAEHAMSADNVTSKEVNVKEEGFSVHIDLEEPCFATKKKVQLLVLLWVE*