AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0958270

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0958270 MtrunA17_Chr5g0393501 28.916 166 97 3 2 146 76 241 1.47e-18 79.0
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 41 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGAAGTTCCTATCTGGATA+TGG 0.289906 6_3:+72072911 Msa0958270:intron
GTACCTTTGAAGTTCCTATC+TGG 0.333773 6_3:+72072905 Msa0958270:intron
AGGAATTTGCCGAAAGTATC+AGG 0.335653 6_3:-72073057 None:intergenic
AATCGTGATGTTTCACTCTA+AGG 0.341127 6_3:-72073077 None:intergenic
TAGGAACTACCTGATACTTT+CGG 0.400617 6_3:+72073048 Msa0958270:intron
ATCTACTTCCACCAAGGTAC+TGG 0.428620 6_3:-72072798 None:intergenic
TCCGAACATCACATTTCGTA+TGG 0.444579 6_3:-72073163 None:intergenic
TTGTGCTGCCAATGGTATTG+AGG 0.463000 6_3:+72073203 Msa0958270:CDS
CGAAATGTGATGTTCGGAAA+AGG 0.465930 6_3:+72073168 Msa0958270:CDS
CCCATACGAAATGTGATGTT+CGG 0.471184 6_3:+72073162 Msa0958270:CDS
TGCCACACTCATGGAATGAT+AGG 0.480870 6_3:-72072869 None:intergenic
TCGTCGATCCATATCCAGAT+AGG 0.486078 6_3:-72072919 None:intergenic
GGCCGTTGTTGACAGATGGT+TGG 0.487397 6_3:+72072725 Msa0958270:CDS
GTCATGCGTTTATCAACGCT+TGG 0.494559 6_3:-72073286 None:intergenic
TGTGCTGCCAATGGTATTGA+GGG 0.501205 6_3:+72073204 Msa0958270:CDS
CCGAACATCACATTTCGTAT+GGG 0.503117 6_3:-72073162 None:intergenic
ATTATTGCTTTCCAGTACCT+TGG 0.503165 6_3:+72072787 Msa0958270:CDS
ACACGATGTTGCCACACTCA+TGG 0.518160 6_3:-72072878 None:intergenic
ACAGGAATGATATTGTCATA+AGG 0.528831 6_3:-72073117 None:intergenic
AGTCGGCCGTTGTTGACAGA+TGG 0.531450 6_3:+72072721 Msa0958270:CDS
TGATAGGGTGGATAATCAGC+TGG 0.541144 6_3:-72072853 None:intergenic
CGAACATCACATTTCGTATG+GGG 0.542386 6_3:-72073161 None:intergenic
TCTGTATATTTGAGTCTCAC+AGG 0.543494 6_3:-72073135 None:intergenic
ATTGCTTTCCAGTACCTTGG+TGG 0.549152 6_3:+72072790 Msa0958270:CDS
GTCTCCGCCCTCAATACCAT+TGG 0.581950 6_3:-72073211 None:intergenic
CACGATTACGTCATGTTGTG+CGG 0.590860 6_3:+72073093 Msa0958270:CDS
TGTTCAACAAATCAGTTAGT+CGG 0.609582 6_3:+72072704 Msa0958270:CDS
ATGTGATGTTCGGAAAAGGT+TGG 0.616153 6_3:+72073172 Msa0958270:CDS
TTTCAAGTGCAAGTGCGTCG+TGG 0.639560 6_3:+72073242 Msa0958270:CDS
GCCACACTCATGGAATGATA+GGG 0.654738 6_3:-72072868 None:intergenic
ACACTCATGGAATGATAGGG+TGG 0.656827 6_3:-72072865 None:intergenic
CTCCAACCATCTGTCAACAA+CGG 0.679074 6_3:-72072727 None:intergenic
TTTGAAATCTACTTCCACCA+AGG 0.681040 6_3:-72072804 None:intergenic
TGGATCGACGAAATCACCGA+AGG 0.700849 6_3:+72072931 Msa0958270:CDS
GCTGCCAATGGTATTGAGGG+CGG 0.739556 6_3:+72073207 Msa0958270:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ACAGTTTTTTTTTCTTTTTT+AGG + chr6_3:72073029-72073048 Msa0958270:intron 15.0%
!! AAAAAACAATAAACAACCTT+CGG - chr6_3:72072950-72072969 None:intergenic 20.0%
!! TTTTGATGCTATTCATTTAG+AGG + chr6_3:72072967-72072986 Msa0958270:intron 25.0%
TGTTCAACAAATCAGTTAGT+CGG + chr6_3:72072704-72072723 Msa0958270:CDS 30.0%
TGATTATTCTACGAGTTTAG+TGG + chr6_3:72072757-72072776 Msa0958270:intron 30.0%
ACAGGAATGATATTGTCATA+AGG - chr6_3:72073120-72073139 None:intergenic 30.0%
ATTATTGCTTTCCAGTACCT+TGG + chr6_3:72072787-72072806 Msa0958270:CDS 35.0%
! TTTGAAATCTACTTCCACCA+AGG - chr6_3:72072807-72072826 None:intergenic 35.0%
TATCCAGATAGGAACTTCAA+AGG - chr6_3:72072911-72072930 None:intergenic 35.0%
TTGAAGTTCCTATCTGGATA+TGG + chr6_3:72072911-72072930 Msa0958270:intron 35.0%
TAGGAACTACCTGATACTTT+CGG + chr6_3:72073048-72073067 Msa0958270:intron 35.0%
AATCGTGATGTTTCACTCTA+AGG - chr6_3:72073080-72073099 None:intergenic 35.0%
TCTGTATATTTGAGTCTCAC+AGG - chr6_3:72073138-72073157 None:intergenic 35.0%
!! GTACCTTTGAAGTTCCTATC+TGG + chr6_3:72072905-72072924 Msa0958270:intron 40.0%
!! AGGAATTTGCCGAAAGTATC+AGG - chr6_3:72073060-72073079 None:intergenic 40.0%
CGAACATCACATTTCGTATG+GGG - chr6_3:72073164-72073183 None:intergenic 40.0%
CCGAACATCACATTTCGTAT+GGG - chr6_3:72073165-72073184 None:intergenic 40.0%
CCCATACGAAATGTGATGTT+CGG + chr6_3:72073162-72073181 Msa0958270:CDS 40.0%
TCCGAACATCACATTTCGTA+TGG - chr6_3:72073166-72073185 None:intergenic 40.0%
CGAAATGTGATGTTCGGAAA+AGG + chr6_3:72073168-72073187 Msa0958270:CDS 40.0%
ATGTGATGTTCGGAAAAGGT+TGG + chr6_3:72073172-72073191 Msa0958270:CDS 40.0%
CTCCAACCATCTGTCAACAA+CGG - chr6_3:72072730-72072749 None:intergenic 45.0%
ATTGCTTTCCAGTACCTTGG+TGG + chr6_3:72072790-72072809 Msa0958270:CDS 45.0%
ATCTACTTCCACCAAGGTAC+TGG - chr6_3:72072801-72072820 None:intergenic 45.0%
TGATAGGGTGGATAATCAGC+TGG - chr6_3:72072856-72072875 None:intergenic 45.0%
ACACTCATGGAATGATAGGG+TGG - chr6_3:72072868-72072887 None:intergenic 45.0%
ACCCTATCATTCCATGAGTG+TGG + chr6_3:72072867-72072886 Msa0958270:intron 45.0%
GCCACACTCATGGAATGATA+GGG - chr6_3:72072871-72072890 None:intergenic 45.0%
TGCCACACTCATGGAATGAT+AGG - chr6_3:72072872-72072891 None:intergenic 45.0%
TCGTCGATCCATATCCAGAT+AGG - chr6_3:72072922-72072941 None:intergenic 45.0%
CACGATTACGTCATGTTGTG+CGG + chr6_3:72073093-72073112 Msa0958270:CDS 45.0%
! ACGAGTTTTTGTGCTGCCAA+TGG + chr6_3:72073195-72073214 Msa0958270:CDS 45.0%
TTGTGCTGCCAATGGTATTG+AGG + chr6_3:72073203-72073222 Msa0958270:CDS 45.0%
! TGTGCTGCCAATGGTATTGA+GGG + chr6_3:72073204-72073223 Msa0958270:CDS 45.0%
ACACGATGTTGCCACACTCA+TGG - chr6_3:72072881-72072900 None:intergenic 50.0%
TGGATCGACGAAATCACCGA+AGG + chr6_3:72072931-72072950 Msa0958270:CDS 50.0%
! TTTCAAGTGCAAGTGCGTCG+TGG + chr6_3:72073242-72073261 Msa0958270:CDS 50.0%
AGTCGGCCGTTGTTGACAGA+TGG + chr6_3:72072721-72072740 Msa0958270:CDS 55.0%
GGCCGTTGTTGACAGATGGT+TGG + chr6_3:72072725-72072744 Msa0958270:CDS 55.0%
! GCTGCCAATGGTATTGAGGG+CGG + chr6_3:72073207-72073226 Msa0958270:CDS 55.0%
GTCTCCGCCCTCAATACCAT+TGG - chr6_3:72073214-72073233 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr6_3 gene 72072703 72073296 72072703 ID=Msa0958270;Name=Msa0958270
chr6_3 mRNA 72072703 72073296 72072703 ID=Msa0958270-mRNA-1;Parent=Msa0958270;Name=Msa0958270-mRNA-1;_AED=0.25;_eAED=0.25;_QI=0|0.33|0|1|0.33|0.5|4|0|147
chr6_3 exon 72072703 72072755 72072703 ID=Msa0958270-mRNA-1:exon:13059;Parent=Msa0958270-mRNA-1
chr6_3 exon 72072777 72072885 72072777 ID=Msa0958270-mRNA-1:exon:13060;Parent=Msa0958270-mRNA-1
chr6_3 exon 72072917 72072952 72072917 ID=Msa0958270-mRNA-1:exon:13061;Parent=Msa0958270-mRNA-1
chr6_3 exon 72073051 72073296 72073051 ID=Msa0958270-mRNA-1:exon:13062;Parent=Msa0958270-mRNA-1
chr6_3 CDS 72072703 72072755 72072703 ID=Msa0958270-mRNA-1:cds;Parent=Msa0958270-mRNA-1
chr6_3 CDS 72072777 72072885 72072777 ID=Msa0958270-mRNA-1:cds;Parent=Msa0958270-mRNA-1
chr6_3 CDS 72072917 72072952 72072917 ID=Msa0958270-mRNA-1:cds;Parent=Msa0958270-mRNA-1
chr6_3 CDS 72073051 72073296 72073051 ID=Msa0958270-mRNA-1:cds;Parent=Msa0958270-mRNA-1
Gene Sequence

>Msa0958270

ATGTTCAACAAATCAGTTAGTCGGCCGTTGTTGACAGATGGTTGGAGTGCATTTGGAAGTAAGATTATTGCTTTCCAGTACCTTGGTGGAAGTAGATTTCAAATCTTTGTTTTTGCTCATAACGTTACTCCAGCTGATTATCCACCCTATCATTCCATGAGTTTCCTATCTGGATATGGATCGACGAAATCACCGAAGGAACTACCTGATACTTTCGGCAAATTCCTTAGAGTGAAACATCACGATTACGTCATGTTGTGCGGACCTTATGACAATATCATTCCTGTGAGACTCAAATATACAGATGACCCCATACGAAATGTGATGTTCGGAAAAGGTTGGACGAGTTTTTGTGCTGCCAATGGTATTGAGGGCGGAGACGTGTTGATTTTCAAGTGCAAGTGCGTCGTGGACAAAAAATATGTTATCGTATCCAAGCGTTGA
Protein sequence

>Msa0958270

MFNKSVSRPLLTDGWSAFGSKIIAFQYLGGSRFQIFVFAHNVTPADYPPYHSMSFLSGYGSTKSPKELPDTFGKFLRVKHHDYVMLCGPYDNIIPVRLKYTDDPIRNVMFGKGWTSFCAANGIEGGDVLIFKCKCVVDKKYVIVSKR*