AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1157890

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 35 sgRNAs with CRISPR-Local

Find 104 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATAGTTCGGTCAAGTTTAA+TGG 0.182925 7_4:-46946152 None:intergenic
CCTCTTGAATTTCATCATAT+TGG 0.290781 7_4:-46946029 None:intergenic
GGGCTTGTAATGATAAAATT+AGG 0.310965 7_4:+46945694 Msa1157890:three_prime_UTR
CATTAAACTTGACCGAACTA+TGG 0.312029 7_4:+46946153 Msa1157890:three_prime_UTR
AAGCAACTGGATGTAGAAAA+TGG 0.318856 7_4:+46945387 Msa1157890:CDS
TTTCAGCTATTTCTTGAAGT+TGG 0.320279 7_4:-46945494 None:intergenic
TTCAGCTATTTCTTGAAGTT+GGG 0.333923 7_4:-46945493 None:intergenic
TGAATTTGAAGTGGACGATT+TGG 0.364457 7_4:+46946065 Msa1157890:three_prime_UTR
CAACTCATTCAAGTTTGTCT+TGG 0.392517 7_4:-46946098 None:intergenic
ACTTCAAGAAATAGCTGAAA+AGG 0.439447 7_4:+46945497 Msa1157890:CDS
CAAGACAAACTTGAATGAGT+TGG 0.474939 7_4:+46946099 Msa1157890:three_prime_UTR
CGTAGATATTGTTGATTCAA+AGG 0.501732 7_4:-46945830 None:intergenic
AGGAAGTAGAGGAAAGCAAC+TGG 0.506296 7_4:+46945374 Msa1157890:CDS
CTTTGAATCAACAATATCTA+CGG 0.516508 7_4:+46945831 Msa1157890:three_prime_UTR
GAAGTGGACGATTTGGATGA+CGG 0.516696 7_4:+46946072 Msa1157890:three_prime_UTR
TTGTAATGATAAAATTAGGA+AGG 0.521315 7_4:+46945698 Msa1157890:three_prime_UTR
GAATTTCTTGAGGACAACAT+AGG 0.552325 7_4:+46945958 Msa1157890:three_prime_UTR
CAAAACAAATTTCCTACTTG+CGG 0.563047 7_4:+46945729 Msa1157890:three_prime_UTR
ATGGGAAAGGAGCGTGTGGA+AGG 0.570245 7_4:+46945552 Msa1157890:CDS
TATAAATGTTGAATTTCAAG+AGG 0.571453 7_4:+46946002 Msa1157890:three_prime_UTR
GAAAGGAGCGTGTGGAAGGT+CGG 0.572671 7_4:+46945556 Msa1157890:CDS
GAAACTCGAAAAGGAAGTAG+AGG 0.574679 7_4:+46945363 Msa1157890:CDS
CACATATGATGAATTTCTTG+AGG 0.586111 7_4:+46945948 Msa1157890:three_prime_UTR
CCAATATGATGAAATTCAAG+AGG 0.593615 7_4:+46946029 Msa1157890:three_prime_UTR
TGTAATGATAAAATTAGGAA+GGG 0.605914 7_4:+46945699 Msa1157890:three_prime_UTR
TCAAGAAATAGCTGAAAAGG+AGG 0.608931 7_4:+46945500 Msa1157890:CDS
CATAGGTGATGAATTTCAGA+AGG 0.611702 7_4:+46945975 Msa1157890:three_prime_UTR
CTCAAAACAGCACCGCAAGT+AGG 0.626879 7_4:-46945741 None:intergenic
CATAGATGAGGAATTTCAAG+AGG 0.630357 7_4:+46945921 Msa1157890:three_prime_UTR
CATCGGTGATGAATTTGAAG+TGG 0.646556 7_4:+46946056 Msa1157890:three_prime_UTR
GGGTTGCATAACTTGACACA+AGG 0.650513 7_4:+46945654 Msa1157890:three_prime_UTR
TGAGAAAGATGACATAGATG+AGG 0.652596 7_4:+46945909 Msa1157890:three_prime_UTR
GAAATTCAAGAGGATGACAT+CGG 0.668632 7_4:+46946039 Msa1157890:three_prime_UTR
ACAAACTTGAATGAGTTGGA+TGG 0.694834 7_4:+46946103 Msa1157890:three_prime_UTR
TGTTATGGGAAAGGAGCGTG+TGG 0.707391 7_4:+46945548 Msa1157890:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATGTAAAAATTTAAAGTTA+CGG + chr7_4:46945421-46945440 Msa1157890:intron 10.0%
!!! TTTTATTATATTACAACTTT+TGG + chr7_4:46946271-46946290 Msa1157890:three_prime_UTR 10.0%
!!! TTTATTATATTACAACTTTT+GGG + chr7_4:46946272-46946291 Msa1157890:three_prime_UTR 10.0%
!!! TATGTAAAAATTTAAAGTTA+CGG + chr7_4:46945421-46945440 Msa1157890:intron 10.0%
!!! TTTTATTATATTACAACTTT+TGG + chr7_4:46946271-46946290 Msa1157890:three_prime_UTR 10.0%
!!! TTTATTATATTACAACTTTT+GGG + chr7_4:46946272-46946291 Msa1157890:three_prime_UTR 10.0%
!!! TTATTATATTACAACTTTTG+GGG + chr7_4:46946273-46946292 Msa1157890:three_prime_UTR 15.0%
!!! TTATTATATTACAACTTTTG+GGG + chr7_4:46946273-46946292 Msa1157890:three_prime_UTR 15.0%
!! TTGTAATGATAAAATTAGGA+AGG + chr7_4:46945698-46945717 Msa1157890:three_prime_UTR 20.0%
!! TGTAATGATAAAATTAGGAA+GGG + chr7_4:46945699-46945718 Msa1157890:three_prime_UTR 20.0%
!!! TTTTATTTTCATATGCAACA+AGG + chr7_4:46945871-46945890 Msa1157890:three_prime_UTR 20.0%
!! TATAAATGTTGAATTTCAAG+AGG + chr7_4:46946002-46946021 Msa1157890:three_prime_UTR 20.0%
!! TTGTAATGATAAAATTAGGA+AGG + chr7_4:46945698-46945717 Msa1157890:three_prime_UTR 20.0%
!! TGTAATGATAAAATTAGGAA+GGG + chr7_4:46945699-46945718 Msa1157890:three_prime_UTR 20.0%
!!! TTTTATTTTCATATGCAACA+AGG + chr7_4:46945871-46945890 Msa1157890:three_prime_UTR 20.0%
!! TATAAATGTTGAATTTCAAG+AGG + chr7_4:46946002-46946021 Msa1157890:three_prime_UTR 20.0%
!!! ATGTTTTTTGAAACTCGAAA+AGG + chr7_4:46945354-46945373 Msa1157890:CDS 25.0%
!!! TGCATTTTTTGTTTGTTTCT+GGG + chr7_4:46945634-46945653 Msa1157890:three_prime_UTR 25.0%
! AAGGTGAAGAAACTTAAAAA+TGG + chr7_4:46945673-46945692 Msa1157890:three_prime_UTR 25.0%
! AGGTGAAGAAACTTAAAAAT+GGG + chr7_4:46945674-46945693 Msa1157890:three_prime_UTR 25.0%
! CTTTGAATCAACAATATCTA+CGG + chr7_4:46945831-46945850 Msa1157890:three_prime_UTR 25.0%
! AAAAAGACAAAACCATAGTT+CGG - chr7_4:46946168-46946187 None:intergenic 25.0%
!!! ATGTTTTTTGAAACTCGAAA+AGG + chr7_4:46945354-46945373 Msa1157890:CDS 25.0%
!!! TGCATTTTTTGTTTGTTTCT+GGG + chr7_4:46945634-46945653 Msa1157890:three_prime_UTR 25.0%
! AAGGTGAAGAAACTTAAAAA+TGG + chr7_4:46945673-46945692 Msa1157890:three_prime_UTR 25.0%
! AGGTGAAGAAACTTAAAAAT+GGG + chr7_4:46945674-46945693 Msa1157890:three_prime_UTR 25.0%
! CTTTGAATCAACAATATCTA+CGG + chr7_4:46945831-46945850 Msa1157890:three_prime_UTR 25.0%
! AAAAAGACAAAACCATAGTT+CGG - chr7_4:46946168-46946187 None:intergenic 25.0%
!! TTCAGCTATTTCTTGAAGTT+GGG - chr7_4:46945496-46945515 None:intergenic 30.0%
!! TTTCAGCTATTTCTTGAAGT+TGG - chr7_4:46945497-46945516 None:intergenic 30.0%
ACTTCAAGAAATAGCTGAAA+AGG + chr7_4:46945497-46945516 Msa1157890:CDS 30.0%
!!! GAAGCTTTTAAAGCTGTTAT+GGG + chr7_4:46945534-46945553 Msa1157890:CDS 30.0%
!!! TTTTAAAGCTGTTATGGGAA+AGG + chr7_4:46945539-46945558 Msa1157890:CDS 30.0%
!!! CTGCATTTTTTGTTTGTTTC+TGG + chr7_4:46945633-46945652 Msa1157890:three_prime_UTR 30.0%
GGGCTTGTAATGATAAAATT+AGG + chr7_4:46945694-46945713 Msa1157890:three_prime_UTR 30.0%
CAAAACAAATTTCCTACTTG+CGG + chr7_4:46945729-46945748 Msa1157890:three_prime_UTR 30.0%
!! CGTAGATATTGTTGATTCAA+AGG - chr7_4:46945833-46945852 None:intergenic 30.0%
CACATATGATGAATTTCTTG+AGG + chr7_4:46945948-46945967 Msa1157890:three_prime_UTR 30.0%
CCTCTTGAATTTCATCATAT+TGG - chr7_4:46946032-46946051 None:intergenic 30.0%
CCAATATGATGAAATTCAAG+AGG + chr7_4:46946029-46946048 Msa1157890:three_prime_UTR 30.0%
!!! AGTTGGATGGTGTTTTATTT+TGG + chr7_4:46946116-46946135 Msa1157890:three_prime_UTR 30.0%
!! TTCAGCTATTTCTTGAAGTT+GGG - chr7_4:46945496-46945515 None:intergenic 30.0%
!! TTTCAGCTATTTCTTGAAGT+TGG - chr7_4:46945497-46945516 None:intergenic 30.0%
ACTTCAAGAAATAGCTGAAA+AGG + chr7_4:46945497-46945516 Msa1157890:CDS 30.0%
!!! GAAGCTTTTAAAGCTGTTAT+GGG + chr7_4:46945534-46945553 Msa1157890:CDS 30.0%
!!! TTTTAAAGCTGTTATGGGAA+AGG + chr7_4:46945539-46945558 Msa1157890:CDS 30.0%
!!! CTGCATTTTTTGTTTGTTTC+TGG + chr7_4:46945633-46945652 Msa1157890:three_prime_UTR 30.0%
GGGCTTGTAATGATAAAATT+AGG + chr7_4:46945694-46945713 Msa1157890:three_prime_UTR 30.0%
CAAAACAAATTTCCTACTTG+CGG + chr7_4:46945729-46945748 Msa1157890:three_prime_UTR 30.0%
!! CGTAGATATTGTTGATTCAA+AGG - chr7_4:46945833-46945852 None:intergenic 30.0%
CACATATGATGAATTTCTTG+AGG + chr7_4:46945948-46945967 Msa1157890:three_prime_UTR 30.0%
CCTCTTGAATTTCATCATAT+TGG - chr7_4:46946032-46946051 None:intergenic 30.0%
CCAATATGATGAAATTCAAG+AGG + chr7_4:46946029-46946048 Msa1157890:three_prime_UTR 30.0%
!!! AGTTGGATGGTGTTTTATTT+TGG + chr7_4:46946116-46946135 Msa1157890:three_prime_UTR 30.0%
AAGCAACTGGATGTAGAAAA+TGG + chr7_4:46945387-46945406 Msa1157890:CDS 35.0%
TCAAGAAATAGCTGAAAAGG+AGG + chr7_4:46945500-46945519 Msa1157890:CDS 35.0%
!!! CGAAGCTTTTAAAGCTGTTA+TGG + chr7_4:46945533-46945552 Msa1157890:CDS 35.0%
!!! CTTTGGTTTTTATTTGTGCG+AGG + chr7_4:46945780-46945799 Msa1157890:three_prime_UTR 35.0%
TGAGAAAGATGACATAGATG+AGG + chr7_4:46945909-46945928 Msa1157890:three_prime_UTR 35.0%
CATAGATGAGGAATTTCAAG+AGG + chr7_4:46945921-46945940 Msa1157890:three_prime_UTR 35.0%
GAATTTCTTGAGGACAACAT+AGG + chr7_4:46945958-46945977 Msa1157890:three_prime_UTR 35.0%
CATAGGTGATGAATTTCAGA+AGG + chr7_4:46945975-46945994 Msa1157890:three_prime_UTR 35.0%
GAAATTCAAGAGGATGACAT+CGG + chr7_4:46946039-46946058 Msa1157890:three_prime_UTR 35.0%
! TGAATTTGAAGTGGACGATT+TGG + chr7_4:46946065-46946084 Msa1157890:three_prime_UTR 35.0%
! CAACTCATTCAAGTTTGTCT+TGG - chr7_4:46946101-46946120 None:intergenic 35.0%
CAAGACAAACTTGAATGAGT+TGG + chr7_4:46946099-46946118 Msa1157890:three_prime_UTR 35.0%
! ACAAACTTGAATGAGTTGGA+TGG + chr7_4:46946103-46946122 Msa1157890:three_prime_UTR 35.0%
CATAGTTCGGTCAAGTTTAA+TGG - chr7_4:46946155-46946174 None:intergenic 35.0%
CATTAAACTTGACCGAACTA+TGG + chr7_4:46946153-46946172 Msa1157890:three_prime_UTR 35.0%
AAGCAACTGGATGTAGAAAA+TGG + chr7_4:46945387-46945406 Msa1157890:CDS 35.0%
TCAAGAAATAGCTGAAAAGG+AGG + chr7_4:46945500-46945519 Msa1157890:CDS 35.0%
!!! CGAAGCTTTTAAAGCTGTTA+TGG + chr7_4:46945533-46945552 Msa1157890:CDS 35.0%
!!! CTTTGGTTTTTATTTGTGCG+AGG + chr7_4:46945780-46945799 Msa1157890:three_prime_UTR 35.0%
TGAGAAAGATGACATAGATG+AGG + chr7_4:46945909-46945928 Msa1157890:three_prime_UTR 35.0%
CATAGATGAGGAATTTCAAG+AGG + chr7_4:46945921-46945940 Msa1157890:three_prime_UTR 35.0%
GAATTTCTTGAGGACAACAT+AGG + chr7_4:46945958-46945977 Msa1157890:three_prime_UTR 35.0%
CATAGGTGATGAATTTCAGA+AGG + chr7_4:46945975-46945994 Msa1157890:three_prime_UTR 35.0%
GAAATTCAAGAGGATGACAT+CGG + chr7_4:46946039-46946058 Msa1157890:three_prime_UTR 35.0%
! TGAATTTGAAGTGGACGATT+TGG + chr7_4:46946065-46946084 Msa1157890:three_prime_UTR 35.0%
! CAACTCATTCAAGTTTGTCT+TGG - chr7_4:46946101-46946120 None:intergenic 35.0%
CAAGACAAACTTGAATGAGT+TGG + chr7_4:46946099-46946118 Msa1157890:three_prime_UTR 35.0%
! ACAAACTTGAATGAGTTGGA+TGG + chr7_4:46946103-46946122 Msa1157890:three_prime_UTR 35.0%
CATAGTTCGGTCAAGTTTAA+TGG - chr7_4:46946155-46946174 None:intergenic 35.0%
CATTAAACTTGACCGAACTA+TGG + chr7_4:46946153-46946172 Msa1157890:three_prime_UTR 35.0%
GAAACTCGAAAAGGAAGTAG+AGG + chr7_4:46945363-46945382 Msa1157890:CDS 40.0%
!! GCGTGTTTTACTTGTTGCTT+TGG + chr7_4:46945763-46945782 Msa1157890:three_prime_UTR 40.0%
CATCGGTGATGAATTTGAAG+TGG + chr7_4:46946056-46946075 Msa1157890:three_prime_UTR 40.0%
GAAACTCGAAAAGGAAGTAG+AGG + chr7_4:46945363-46945382 Msa1157890:CDS 40.0%
!! GCGTGTTTTACTTGTTGCTT+TGG + chr7_4:46945763-46945782 Msa1157890:three_prime_UTR 40.0%
CATCGGTGATGAATTTGAAG+TGG + chr7_4:46946056-46946075 Msa1157890:three_prime_UTR 40.0%
AGGAAGTAGAGGAAAGCAAC+TGG + chr7_4:46945374-46945393 Msa1157890:CDS 45.0%
GGGTTGCATAACTTGACACA+AGG + chr7_4:46945654-46945673 Msa1157890:three_prime_UTR 45.0%
! GAAGTGGACGATTTGGATGA+CGG + chr7_4:46946072-46946091 Msa1157890:three_prime_UTR 45.0%
AGGAAGTAGAGGAAAGCAAC+TGG + chr7_4:46945374-46945393 Msa1157890:CDS 45.0%
GGGTTGCATAACTTGACACA+AGG + chr7_4:46945654-46945673 Msa1157890:three_prime_UTR 45.0%
! GAAGTGGACGATTTGGATGA+CGG + chr7_4:46946072-46946091 Msa1157890:three_prime_UTR 45.0%
! TGTTATGGGAAAGGAGCGTG+TGG + chr7_4:46945548-46945567 Msa1157890:CDS 50.0%
CTCAAAACAGCACCGCAAGT+AGG - chr7_4:46945744-46945763 None:intergenic 50.0%
! TGTTATGGGAAAGGAGCGTG+TGG + chr7_4:46945548-46945567 Msa1157890:CDS 50.0%
CTCAAAACAGCACCGCAAGT+AGG - chr7_4:46945744-46945763 None:intergenic 50.0%
! ATGGGAAAGGAGCGTGTGGA+AGG + chr7_4:46945552-46945571 Msa1157890:CDS 55.0%
! GAAAGGAGCGTGTGGAAGGT+CGG + chr7_4:46945556-46945575 Msa1157890:CDS 55.0%
! ATGGGAAAGGAGCGTGTGGA+AGG + chr7_4:46945552-46945571 Msa1157890:CDS 55.0%
! GAAAGGAGCGTGTGGAAGGT+CGG + chr7_4:46945556-46945575 Msa1157890:CDS 55.0%
Chromosome Type Strat End Strand Name
chr7_4 gene 46945354 46946341 46945354 ID=Msa1157890;Name=Msa1157890
chr7_4 mRNA 46945354 46946341 46945354 ID=Msa1157890-mRNA-1;Parent=Msa1157890;Name=Msa1157890-mRNA-1;_AED=0.30;_eAED=0.30;_QI=0|0|0.5|1|1|1|2|718|63
chr7_4 exon 46945354 46945413 46945354 ID=Msa1157890-mRNA-1:exon:12438;Parent=Msa1157890-mRNA-1
chr7_4 exon 46945492 46946341 46945492 ID=Msa1157890-mRNA-1:exon:12439;Parent=Msa1157890-mRNA-1
chr7_4 CDS 46945354 46945413 46945354 ID=Msa1157890-mRNA-1:cds;Parent=Msa1157890-mRNA-1
chr7_4 CDS 46945492 46945623 46945492 ID=Msa1157890-mRNA-1:cds;Parent=Msa1157890-mRNA-1
chr7_4 three_prime_UTR 46945624 46946341 46945624 ID=Msa1157890-mRNA-1:three_prime_utr;Parent=Msa1157890-mRNA-1
Gene Sequence

>Msa1157890

ATGTTTTTTGAAACTCGAAAAGGAAGTAGAGGAAAGCAACTGGATGTAGAAAATGGAAAATCCCAACTTCAAGAAATAGCTGAAAAGGAGGAAAGTGATATCGAAGCTTTTAAAGCTGTTATGGGAAAGGAGCGTGTGGAAGGTCGGATTTTGATTGTGTTGCAAAATTGTGATGTTTGTGTGAACTTGTGA
Protein sequence

>Msa1157890

MFFETRKGSRGKQLDVENGKSQLQEIAEKEESDIEAFKAVMGKERVEGRILIVLQNCDVCVNL*