AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1223860


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1223860 MtrunA17_Chr4g0075751 92.857 140 9 1 1 139 1 140 5.87e-41 133
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 33 sgRNAs with CRISPR-Local

Find 110 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCCACTGCTACTACTTCTT+CGG 0.329034 8_1:-88483965 None:intergenic
TTCTTCAACTGTTGCTGCTA+TGG 0.377581 8_1:-88484214 None:intergenic
TTACCTCAACAGTGGCCATT+TGG 0.390008 8_1:-88483351 None:intergenic
TGTGTACTCTCAGCTTCAAC+TGG 0.435451 8_1:-88484006 None:intergenic
TGCTACTACTTCTTCGGTGG+TGG 0.459750 8_1:-88483959 None:intergenic
ACTACTTCTTCGGTGGTGGC+TGG 0.461076 8_1:-88483955 None:intergenic
CACAAGTAACTGAGGAAGCC+AGG 0.463325 8_1:+88484025 Msa1223860:CDS
CGGGTTCTCTACCTCTGCCC+TGG 0.474403 8_1:-88484043 None:intergenic
ATTCATCTTTCCATTCCAAA+TGG 0.477645 8_1:+88483336 Msa1223860:exon
CGGTGTTGTTTCCTCGACCT+TGG 0.487832 8_1:-88483908 None:intergenic
AGAAACTACTGAAACAGAAT+CGG 0.495909 8_1:+88484116 Msa1223860:CDS
GAAGTAGTAGCAGTGGAGAA+AGG 0.498978 8_1:+88483970 Msa1223860:CDS
CAGGGCAGAGGTAGAGAACC+CGG 0.499260 8_1:+88484044 Msa1223860:CDS
GGTGGTGGCTGGTTCTGAAG+TGG 0.534204 8_1:-88483944 None:intergenic
AGAGGAAGTATCAGCTGAAG+AGG 0.536609 8_1:+88484089 Msa1223860:CDS
ATTCCAAATGGCCACTGTTG+AGG 0.536707 8_1:+88483348 Msa1223860:exon
AACTGAGGAAGCCAGGGCAG+AGG 0.537053 8_1:+88484032 Msa1223860:CDS
TCAACAGTGGCCATTTGGAA+TGG 0.543349 8_1:-88483346 None:intergenic
GTGGTGGCTGGTTCTGAAGT+GGG 0.546159 8_1:-88483943 None:intergenic
CACCGAAGAAGTAGTAGCAG+TGG 0.549057 8_1:+88483963 Msa1223860:CDS
GAAGTGGGAACCTCGGAGGC+CGG 0.549296 8_1:-88483928 None:intergenic
AGAAGAAGTATCAACTGAAG+AGG 0.562005 8_1:+88484161 Msa1223860:CDS
CACTGCTACTACTTCTTCGG+TGG 0.564441 8_1:-88483962 None:intergenic
TGGTTCTGAAGTGGGAACCT+CGG 0.596316 8_1:-88483935 None:intergenic
AGTTGAGGTAACCAAGGTCG+AGG 0.604857 8_1:+88483897 Msa1223860:CDS
GACAGAAAATGAAACAGTTG+AGG 0.607247 8_1:+88483882 Msa1223860:CDS
ACAAGTAACTGAGGAAGCCA+GGG 0.632141 8_1:+88484026 Msa1223860:CDS
TGAGAGTACACAAGTAACTG+AGG 0.633074 8_1:+88484017 Msa1223860:CDS
TGAAACAGTTGAGGTAACCA+AGG 0.643241 8_1:+88483891 Msa1223860:CDS
TTCTGAAGTGGGAACCTCGG+AGG 0.645606 8_1:-88483932 None:intergenic
GGAAACAACACCGGCCTCCG+AGG 0.649162 8_1:+88483918 Msa1223860:CDS
TCTTTGAATTACCTCAACAG+TGG 0.681859 8_1:-88483359 None:intergenic
CAAGGTCGAGGAAACAACAC+CGG 0.700669 8_1:+88483909 Msa1223860:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATTGATTATTGATCTTTTT+TGG - chr8_1:88483627-88483646 None:intergenic 15.0%
!!! AATTGATTATTGATCTTTTT+TGG - chr8_1:88483627-88483646 None:intergenic 15.0%
!! AAACAAAAATATTAGTCCAA+TGG + chr8_1:88483547-88483566 Msa1223860:intron 20.0%
!!! ATTTGTTGTTTATAATCCAT+TGG - chr8_1:88483566-88483585 None:intergenic 20.0%
!! TGGATTATGAAAAATAAACA+CGG - chr8_1:88483607-88483626 None:intergenic 20.0%
!! AAACAAAAATATTAGTCCAA+TGG + chr8_1:88483547-88483566 Msa1223860:intron 20.0%
!!! ATTTGTTGTTTATAATCCAT+TGG - chr8_1:88483566-88483585 None:intergenic 20.0%
!! TGGATTATGAAAAATAAACA+CGG - chr8_1:88483607-88483626 None:intergenic 20.0%
!!! AATATTTTTGTTTGATCCAC+TGG - chr8_1:88483540-88483559 None:intergenic 25.0%
! GATTATGAAAAATAAACACG+GGG - chr8_1:88483605-88483624 None:intergenic 25.0%
! GGATTATGAAAAATAAACAC+GGG - chr8_1:88483606-88483625 None:intergenic 25.0%
!!! AATATTTTTGTTTGATCCAC+TGG - chr8_1:88483540-88483559 None:intergenic 25.0%
! GATTATGAAAAATAAACACG+GGG - chr8_1:88483605-88483624 None:intergenic 25.0%
! GGATTATGAAAAATAAACAC+GGG - chr8_1:88483606-88483625 None:intergenic 25.0%
ATTCATCTTTCCATTCCAAA+TGG + chr8_1:88483336-88483355 Msa1223860:exon 30.0%
ATATGACCAAGTAACTCATA+GGG - chr8_1:88483780-88483799 None:intergenic 30.0%
TATATGACCAAGTAACTCAT+AGG - chr8_1:88483781-88483800 None:intergenic 30.0%
TAACAAAACATGTTGAGCAT+TGG + chr8_1:88483805-88483824 Msa1223860:intron 30.0%
AGAAACTACTGAAACAGAAT+CGG + chr8_1:88484116-88484135 Msa1223860:CDS 30.0%
ATTCATCTTTCCATTCCAAA+TGG + chr8_1:88483336-88483355 Msa1223860:exon 30.0%
ATATGACCAAGTAACTCATA+GGG - chr8_1:88483780-88483799 None:intergenic 30.0%
TATATGACCAAGTAACTCAT+AGG - chr8_1:88483781-88483800 None:intergenic 30.0%
TAACAAAACATGTTGAGCAT+TGG + chr8_1:88483805-88483824 Msa1223860:intron 30.0%
AGAAACTACTGAAACAGAAT+CGG + chr8_1:88484116-88484135 Msa1223860:CDS 30.0%
TCTTTGAATTACCTCAACAG+TGG - chr8_1:88483362-88483381 None:intergenic 35.0%
! GCATTGGTGGTTAATGAAAA+TGG + chr8_1:88483821-88483840 Msa1223860:intron 35.0%
TTAATGAAAATGGATCCTGC+AGG + chr8_1:88483831-88483850 Msa1223860:intron 35.0%
! TCATTTTCTGTCACAGTTGT+TGG - chr8_1:88483874-88483893 None:intergenic 35.0%
GACAGAAAATGAAACAGTTG+AGG + chr8_1:88483882-88483901 Msa1223860:CDS 35.0%
!! TCTTTCACTTCGACTTTTTC+AGG - chr8_1:88484072-88484091 None:intergenic 35.0%
TGAAAAAGTCGAAGTGAAAG+AGG + chr8_1:88484071-88484090 Msa1223860:CDS 35.0%
!! TCTTTTGCTTCGACTTTTTC+AGG - chr8_1:88484144-88484163 None:intergenic 35.0%
!! AGAAGAAGTATCAACTGAAG+AGG + chr8_1:88484161-88484180 Msa1223860:CDS 35.0%
TCTTTGAATTACCTCAACAG+TGG - chr8_1:88483362-88483381 None:intergenic 35.0%
! GCATTGGTGGTTAATGAAAA+TGG + chr8_1:88483821-88483840 Msa1223860:intron 35.0%
TTAATGAAAATGGATCCTGC+AGG + chr8_1:88483831-88483850 Msa1223860:intron 35.0%
! TCATTTTCTGTCACAGTTGT+TGG - chr8_1:88483874-88483893 None:intergenic 35.0%
GACAGAAAATGAAACAGTTG+AGG + chr8_1:88483882-88483901 Msa1223860:CDS 35.0%
!! TCTTTCACTTCGACTTTTTC+AGG - chr8_1:88484072-88484091 None:intergenic 35.0%
TGAAAAAGTCGAAGTGAAAG+AGG + chr8_1:88484071-88484090 Msa1223860:CDS 35.0%
!! TCTTTTGCTTCGACTTTTTC+AGG - chr8_1:88484144-88484163 None:intergenic 35.0%
!! AGAAGAAGTATCAACTGAAG+AGG + chr8_1:88484161-88484180 Msa1223860:CDS 35.0%
! ATTCACACAGCATTTTCCAG+TGG + chr8_1:88483521-88483540 Msa1223860:intron 40.0%
CATGTTCCCTATGAGTTACT+TGG + chr8_1:88483771-88483790 Msa1223860:intron 40.0%
!! CAAAACATGTTGAGCATTGG+TGG + chr8_1:88483808-88483827 Msa1223860:intron 40.0%
TGAAACAGTTGAGGTAACCA+AGG + chr8_1:88483891-88483910 Msa1223860:CDS 40.0%
! TGAGAGTACACAAGTAACTG+AGG + chr8_1:88484017-88484036 Msa1223860:CDS 40.0%
!!! ACTTCGACTTTTTCAGGTTC+CGG - chr8_1:88484066-88484085 None:intergenic 40.0%
TTCTTCAACTGTTGCTGCTA+TGG - chr8_1:88484217-88484236 None:intergenic 40.0%
! ATTCACACAGCATTTTCCAG+TGG + chr8_1:88483521-88483540 Msa1223860:intron 40.0%
CATGTTCCCTATGAGTTACT+TGG + chr8_1:88483771-88483790 Msa1223860:intron 40.0%
!! CAAAACATGTTGAGCATTGG+TGG + chr8_1:88483808-88483827 Msa1223860:intron 40.0%
TGAAACAGTTGAGGTAACCA+AGG + chr8_1:88483891-88483910 Msa1223860:CDS 40.0%
! TGAGAGTACACAAGTAACTG+AGG + chr8_1:88484017-88484036 Msa1223860:CDS 40.0%
!!! ACTTCGACTTTTTCAGGTTC+CGG - chr8_1:88484066-88484085 None:intergenic 40.0%
TTCTTCAACTGTTGCTGCTA+TGG - chr8_1:88484217-88484236 None:intergenic 40.0%
TCAACAGTGGCCATTTGGAA+TGG - chr8_1:88483349-88483368 None:intergenic 45.0%
ATTCCAAATGGCCACTGTTG+AGG + chr8_1:88483348-88483367 Msa1223860:exon 45.0%
TTACCTCAACAGTGGCCATT+TGG - chr8_1:88483354-88483373 None:intergenic 45.0%
CTCCACTGCTACTACTTCTT+CGG - chr8_1:88483968-88483987 None:intergenic 45.0%
GAAGTAGTAGCAGTGGAGAA+AGG + chr8_1:88483970-88483989 Msa1223860:CDS 45.0%
TGTGTACTCTCAGCTTCAAC+TGG - chr8_1:88484009-88484028 None:intergenic 45.0%
ACAAGTAACTGAGGAAGCCA+GGG + chr8_1:88484026-88484045 Msa1223860:CDS 45.0%
!!! CTTCGACTTTTTCAGGTTCC+GGG - chr8_1:88484065-88484084 None:intergenic 45.0%
!! AGAGGAAGTATCAGCTGAAG+AGG + chr8_1:88484089-88484108 Msa1223860:CDS 45.0%
TCAACAGTGGCCATTTGGAA+TGG - chr8_1:88483349-88483368 None:intergenic 45.0%
ATTCCAAATGGCCACTGTTG+AGG + chr8_1:88483348-88483367 Msa1223860:exon 45.0%
TTACCTCAACAGTGGCCATT+TGG - chr8_1:88483354-88483373 None:intergenic 45.0%
CTCCACTGCTACTACTTCTT+CGG - chr8_1:88483968-88483987 None:intergenic 45.0%
GAAGTAGTAGCAGTGGAGAA+AGG + chr8_1:88483970-88483989 Msa1223860:CDS 45.0%
TGTGTACTCTCAGCTTCAAC+TGG - chr8_1:88484009-88484028 None:intergenic 45.0%
ACAAGTAACTGAGGAAGCCA+GGG + chr8_1:88484026-88484045 Msa1223860:CDS 45.0%
!!! CTTCGACTTTTTCAGGTTCC+GGG - chr8_1:88484065-88484084 None:intergenic 45.0%
!! AGAGGAAGTATCAGCTGAAG+AGG + chr8_1:88484089-88484108 Msa1223860:CDS 45.0%
! CTTGCTGTGTTTCAACCTGC+AGG - chr8_1:88483849-88483868 None:intergenic 50.0%
AGTTGAGGTAACCAAGGTCG+AGG + chr8_1:88483897-88483916 Msa1223860:CDS 50.0%
CAAGGTCGAGGAAACAACAC+CGG + chr8_1:88483909-88483928 Msa1223860:CDS 50.0%
!! TGGTTCTGAAGTGGGAACCT+CGG - chr8_1:88483938-88483957 None:intergenic 50.0%
TGCTACTACTTCTTCGGTGG+TGG - chr8_1:88483962-88483981 None:intergenic 50.0%
CACTGCTACTACTTCTTCGG+TGG - chr8_1:88483965-88483984 None:intergenic 50.0%
CACCGAAGAAGTAGTAGCAG+TGG + chr8_1:88483963-88483982 Msa1223860:CDS 50.0%
CACAAGTAACTGAGGAAGCC+AGG + chr8_1:88484025-88484044 Msa1223860:CDS 50.0%
! CTTGCTGTGTTTCAACCTGC+AGG - chr8_1:88483849-88483868 None:intergenic 50.0%
AGTTGAGGTAACCAAGGTCG+AGG + chr8_1:88483897-88483916 Msa1223860:CDS 50.0%
CAAGGTCGAGGAAACAACAC+CGG + chr8_1:88483909-88483928 Msa1223860:CDS 50.0%
!! TGGTTCTGAAGTGGGAACCT+CGG - chr8_1:88483938-88483957 None:intergenic 50.0%
TGCTACTACTTCTTCGGTGG+TGG - chr8_1:88483962-88483981 None:intergenic 50.0%
CACTGCTACTACTTCTTCGG+TGG - chr8_1:88483965-88483984 None:intergenic 50.0%
CACCGAAGAAGTAGTAGCAG+TGG + chr8_1:88483963-88483982 Msa1223860:CDS 50.0%
CACAAGTAACTGAGGAAGCC+AGG + chr8_1:88484025-88484044 Msa1223860:CDS 50.0%
!! CGGTGTTGTTTCCTCGACCT+TGG - chr8_1:88483911-88483930 None:intergenic 55.0%
!! TTCTGAAGTGGGAACCTCGG+AGG - chr8_1:88483935-88483954 None:intergenic 55.0%
!! GTGGTGGCTGGTTCTGAAGT+GGG - chr8_1:88483946-88483965 None:intergenic 55.0%
! ACTACTTCTTCGGTGGTGGC+TGG - chr8_1:88483958-88483977 None:intergenic 55.0%
!! CGGTGTTGTTTCCTCGACCT+TGG - chr8_1:88483911-88483930 None:intergenic 55.0%
!! TTCTGAAGTGGGAACCTCGG+AGG - chr8_1:88483935-88483954 None:intergenic 55.0%
!! GTGGTGGCTGGTTCTGAAGT+GGG - chr8_1:88483946-88483965 None:intergenic 55.0%
! ACTACTTCTTCGGTGGTGGC+TGG - chr8_1:88483958-88483977 None:intergenic 55.0%
!! GGTGGTGGCTGGTTCTGAAG+TGG - chr8_1:88483947-88483966 None:intergenic 60.0%
AACTGAGGAAGCCAGGGCAG+AGG + chr8_1:88484032-88484051 Msa1223860:CDS 60.0%
CAGGGCAGAGGTAGAGAACC+CGG + chr8_1:88484044-88484063 Msa1223860:CDS 60.0%
!! GGTGGTGGCTGGTTCTGAAG+TGG - chr8_1:88483947-88483966 None:intergenic 60.0%
AACTGAGGAAGCCAGGGCAG+AGG + chr8_1:88484032-88484051 Msa1223860:CDS 60.0%
CAGGGCAGAGGTAGAGAACC+CGG + chr8_1:88484044-88484063 Msa1223860:CDS 60.0%
GGAAACAACACCGGCCTCCG+AGG + chr8_1:88483918-88483937 Msa1223860:CDS 65.0%
GAAGTGGGAACCTCGGAGGC+CGG - chr8_1:88483931-88483950 None:intergenic 65.0%
CGGGTTCTCTACCTCTGCCC+TGG - chr8_1:88484046-88484065 None:intergenic 65.0%
GGAAACAACACCGGCCTCCG+AGG + chr8_1:88483918-88483937 Msa1223860:CDS 65.0%
GAAGTGGGAACCTCGGAGGC+CGG - chr8_1:88483931-88483950 None:intergenic 65.0%
CGGGTTCTCTACCTCTGCCC+TGG - chr8_1:88484046-88484065 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 88483268 88484257 88483268 ID=Msa1223860;Name=Msa1223860
chr8_1 mRNA 88483268 88484257 88483268 ID=Msa1223860-mRNA-1;Parent=Msa1223860;Name=Msa1223860-mRNA-1;_AED=0.01;_eAED=0.01;_QI=87|1|0.5|1|1|1|2|0|139
chr8_1 exon 88483268 88483369 88483268 ID=Msa1223860-mRNA-1:exon:32083;Parent=Msa1223860-mRNA-1
chr8_1 exon 88483853 88484257 88483853 ID=Msa1223860-mRNA-1:exon:32084;Parent=Msa1223860-mRNA-1
chr8_1 five_prime_UTR 88483268 88483354 88483268 ID=Msa1223860-mRNA-1:five_prime_utr;Parent=Msa1223860-mRNA-1
chr8_1 CDS 88483355 88483369 88483355 ID=Msa1223860-mRNA-1:cds;Parent=Msa1223860-mRNA-1
chr8_1 CDS 88483853 88484257 88483853 ID=Msa1223860-mRNA-1:cds;Parent=Msa1223860-mRNA-1
Gene Sequence

>Msa1223860

ATGGCCACTGTTGAGGTTGAAACACAGCAAGCACCAACAACTGTGACAGAAAATGAAACAGTTGAGGTAACCAAGGTCGAGGAAACAACACCGGCCTCCGAGGTTCCCACTTCAGAACCAGCCACCACCGAAGAAGTAGTAGCAGTGGAGAAAGGAGAAACTGAAGTTCCAGTTGAAGCTGAGAGTACACAAGTAACTGAGGAAGCCAGGGCAGAGGTAGAGAACCCGGAACCTGAAAAAGTCGAAGTGAAAGAGGAAGTATCAGCTGAAGAGGCTAAAGAAACTACTGAAACAGAATCGGCACCTGAAAAAGTCGAAGCAAAAGAAGAAGTATCAACTGAAGAGGCTAAAGAAACTACTGAAACAGAATCAGCAGCCATAGCAGCAACAGTTGAAGAAGTAACCACCACAGAAGCATAA

Protein sequence

>Msa1223860

MATVEVETQQAPTTVTENETVEVTKVEETTPASEVPTSEPATTEEVVAVEKGETEVPVEAESTQVTEEARAEVENPEPEKVEVKEEVSAEEAKETTETESAPEKVEAKEEVSTEEAKETTETESAAIAATVEEVTTTEA*