AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0013620


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0013620 MtrunA17_Chr6g0476171 73.333 105 27 1 19 123 138 241 2.34e-50 161
Msa0013620 MtrunA17_Chr1g0163111 39.759 83 46 3 41 122 144 223 4.81e-14 67.0
Msa0013620 MtrunA17_Chr1g0163131 45.205 73 38 1 51 123 232 302 8.59e-14 67.4
Msa0013620 MtrunA17_Chr1g0163151 38.889 90 47 3 35 122 133 216 1.82e-13 65.5
Msa0013620 MtrunA17_Chr1g0163201 41.379 87 43 3 38 122 307 387 1.85e-12 63.9
Msa0013620 MtrunA17_Chr1g0163091 73.529 34 9 0 125 158 41 74 2.56e-11 58.5
Msa0013620 MtrunA17_Chr1g0163181 36.364 88 52 2 35 122 341 424 7.40e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 30 sgRNAs with CRISPR-Local

Find 120 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGGAATATGTGAGCAATTT+TGG 0.126491 1_1:-21047011 Msa0013620:CDS
CTCGCCAACCCTTATTCTTT+TGG 0.238182 1_1:+21045941 None:intergenic
TTGAAGGGACCAAAAGAATA+AGG 0.244081 1_1:-21045950 Msa0013620:CDS
TTGAATTTGTCATGTAAATT+CGG 0.311912 1_1:+21046842 None:intergenic
TGTAATGAGCATCTCGACTA+TGG 0.311981 1_1:-21046609 Msa0013620:CDS
AAAAGACATGATATATTTAG+TGG 0.333899 1_1:-21046684 Msa0013620:CDS
GACGATGCCAGAAGAAGATA+TGG 0.392753 1_1:-21047030 None:intergenic
TGATATATTTAGTGGAAATT+CGG 0.394530 1_1:-21046676 Msa0013620:CDS
ACATATTCCATATCTTCTTC+TGG 0.395565 1_1:+21047023 None:intergenic
TGAAGGGACCAAAAGAATAA+GGG 0.442926 1_1:-21045949 Msa0013620:CDS
GAATTTACATGACAAATTCA+AGG 0.456040 1_1:-21046840 Msa0013620:CDS
GAGCTTGGAAGGTGAATATG+AGG 0.471494 1_1:-21045914 Msa0013620:CDS
GAATACTCGAACGAGTTTGA+AGG 0.498358 1_1:-21045966 Msa0013620:CDS
AGAGGAAGAAACATGGTTTG+TGG 0.504030 1_1:-21046640 Msa0013620:CDS
AGAGATTGCAAAGTAAAGAC+TGG 0.518373 1_1:-21046555 Msa0013620:CDS
TGTGCAAAATCATGTGTTCA+AGG 0.521657 1_1:-21046505 Msa0013620:intron
TATTCTTTCGTAAACAGAGT+TGG 0.531443 1_1:+21045984 None:intergenic
GACTATGGGTGGTTCACTGA+AGG 0.552574 1_1:-21046594 Msa0013620:CDS
ATGGGTGGTTCACTGAAGGC+TGG 0.558556 1_1:-21046590 Msa0013620:CDS
TTCGGTGGAGTTGAAAGTAG+AGG 0.559890 1_1:-21046658 Msa0013620:CDS
TATATTTAGTGGAAATTCGG+TGG 0.560367 1_1:-21046673 Msa0013620:CDS
GTAATGAGCATCTCGACTAT+GGG 0.561899 1_1:-21046608 Msa0013620:CDS
TGGCGAGGATAGAGCTTGGA+AGG 0.576297 1_1:-21045925 Msa0013620:CDS
AATACTCGAACGAGTTTGAA+GGG 0.590562 1_1:-21045965 Msa0013620:CDS
TGAAAGTAGAGGAAGAAACA+TGG 0.594057 1_1:-21046647 Msa0013620:CDS
CAAAAGAATAAGGGTTGGCG+AGG 0.624941 1_1:-21045940 Msa0013620:CDS
GGGTTGGCGAGGATAGAGCT+TGG 0.634141 1_1:-21045929 Msa0013620:CDS
GGGACCAAAAGAATAAGGGT+TGG 0.648022 1_1:-21045945 Msa0013620:CDS
ATGAGCATCTCGACTATGGG+TGG 0.649686 1_1:-21046605 Msa0013620:CDS
GGAAGAAACATGGTTTGTGG+AGG 0.653505 1_1:-21046637 Msa0013620:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTATTAGAGATATTAATTAA+AGG + chr1_1:21046904-21046923 None:intergenic 10.0%
!! TTATTAGAGATATTAATTAA+AGG + chr1_1:21046904-21046923 None:intergenic 10.0%
!! TTGAATTTGTCATGTAAATT+CGG + chr1_1:21046092-21046111 None:intergenic 20.0%
!! AAAAGACATGATATATTTAG+TGG - chr1_1:21046247-21046266 Msa0013620:intron 20.0%
!! TGATATATTTAGTGGAAATT+CGG - chr1_1:21046255-21046274 Msa0013620:intron 20.0%
!!! AAAGAAAGCATCTTAAAAAA+AGG + chr1_1:21046802-21046821 None:intergenic 20.0%
!! TTGAATTTGTCATGTAAATT+CGG + chr1_1:21046092-21046111 None:intergenic 20.0%
!! AAAAGACATGATATATTTAG+TGG - chr1_1:21046247-21046266 Msa0013620:intron 20.0%
!! TGATATATTTAGTGGAAATT+CGG - chr1_1:21046255-21046274 Msa0013620:intron 20.0%
!!! AAAGAAAGCATCTTAAAAAA+AGG + chr1_1:21046802-21046821 None:intergenic 20.0%
! AGAACAAAGAAAACAGTTTA+AGG + chr1_1:21046046-21046065 None:intergenic 25.0%
! GAATTTACATGACAAATTCA+AGG - chr1_1:21046091-21046110 Msa0013620:intron 25.0%
!! TTTTGTAACATCATTAGACA+AGG - chr1_1:21046115-21046134 Msa0013620:intron 25.0%
! TTTGTTCTTATATATGCAGT+TGG - chr1_1:21046201-21046220 Msa0013620:intron 25.0%
! AGAACAAAGAAAACAGTTTA+AGG + chr1_1:21046046-21046065 None:intergenic 25.0%
! GAATTTACATGACAAATTCA+AGG - chr1_1:21046091-21046110 Msa0013620:intron 25.0%
!! TTTTGTAACATCATTAGACA+AGG - chr1_1:21046115-21046134 Msa0013620:intron 25.0%
! TTTGTTCTTATATATGCAGT+TGG - chr1_1:21046201-21046220 Msa0013620:intron 25.0%
ACATATTCCATATCTTCTTC+TGG + chr1_1:21045911-21045930 None:intergenic 30.0%
! ATGGAATATGTGAGCAATTT+TGG - chr1_1:21045920-21045939 Msa0013620:CDS 30.0%
TATATTTAGTGGAAATTCGG+TGG - chr1_1:21046258-21046277 Msa0013620:intron 30.0%
!! AAACTTGCTTGTCACTTTAA+GGG - chr1_1:21046464-21046483 Msa0013620:intron 30.0%
TATTCTCTAATTGTGAGACT+TGG - chr1_1:21046506-21046525 Msa0013620:CDS 30.0%
ACTTGGTTTATCAAGAAAAC+AGG - chr1_1:21046523-21046542 Msa0013620:CDS 30.0%
AAGAAAACAGGAAATTCAGA+AGG - chr1_1:21046535-21046554 Msa0013620:CDS 30.0%
ACTTTGATTAAAGATGATCG+AGG + chr1_1:21046622-21046641 None:intergenic 30.0%
TGCTTTACTGTTTAATGTTG+TGG + chr1_1:21046652-21046671 None:intergenic 30.0%
! TTTTTGCACTGAATCATCTT+AGG + chr1_1:21046677-21046696 None:intergenic 30.0%
!!! CTTTTTTTTGTTGTCTAGCT+AGG - chr1_1:21046775-21046794 Msa0013620:intron 30.0%
TATTCTTTCGTAAACAGAGT+TGG + chr1_1:21046950-21046969 None:intergenic 30.0%
ACATATTCCATATCTTCTTC+TGG + chr1_1:21045911-21045930 None:intergenic 30.0%
! ATGGAATATGTGAGCAATTT+TGG - chr1_1:21045920-21045939 Msa0013620:CDS 30.0%
TATATTTAGTGGAAATTCGG+TGG - chr1_1:21046258-21046277 Msa0013620:intron 30.0%
!! AAACTTGCTTGTCACTTTAA+GGG - chr1_1:21046464-21046483 Msa0013620:intron 30.0%
TATTCTCTAATTGTGAGACT+TGG - chr1_1:21046506-21046525 Msa0013620:CDS 30.0%
ACTTGGTTTATCAAGAAAAC+AGG - chr1_1:21046523-21046542 Msa0013620:CDS 30.0%
AAGAAAACAGGAAATTCAGA+AGG - chr1_1:21046535-21046554 Msa0013620:CDS 30.0%
ACTTTGATTAAAGATGATCG+AGG + chr1_1:21046622-21046641 None:intergenic 30.0%
TGCTTTACTGTTTAATGTTG+TGG + chr1_1:21046652-21046671 None:intergenic 30.0%
! TTTTTGCACTGAATCATCTT+AGG + chr1_1:21046677-21046696 None:intergenic 30.0%
!!! CTTTTTTTTGTTGTCTAGCT+AGG - chr1_1:21046775-21046794 Msa0013620:intron 30.0%
TATTCTTTCGTAAACAGAGT+TGG + chr1_1:21046950-21046969 None:intergenic 30.0%
! TGTCTTTTTAACAGCTCACT+TGG + chr1_1:21046235-21046254 None:intergenic 35.0%
TGAAAGTAGAGGAAGAAACA+TGG - chr1_1:21046284-21046303 Msa0013620:intron 35.0%
AGAGATTGCAAAGTAAAGAC+TGG - chr1_1:21046376-21046395 Msa0013620:intron 35.0%
TGTGCAAAATCATGTGTTCA+AGG - chr1_1:21046426-21046445 Msa0013620:intron 35.0%
!! GAAACTTGCTTGTCACTTTA+AGG - chr1_1:21046463-21046482 Msa0013620:intron 35.0%
!! AACTTGCTTGTCACTTTAAG+GGG - chr1_1:21046465-21046484 Msa0013620:intron 35.0%
AAAACAGGAAATTCAGAAGG+CGG - chr1_1:21046538-21046557 Msa0013620:CDS 35.0%
GTATGCACTGTTTCAATTCA+TGG + chr1_1:21046928-21046947 None:intergenic 35.0%
AATACTCGAACGAGTTTGAA+GGG - chr1_1:21046966-21046985 Msa0013620:intron 35.0%
TTGAAGGGACCAAAAGAATA+AGG - chr1_1:21046981-21047000 Msa0013620:CDS 35.0%
TGAAGGGACCAAAAGAATAA+GGG - chr1_1:21046982-21047001 Msa0013620:CDS 35.0%
! TGTCTTTTTAACAGCTCACT+TGG + chr1_1:21046235-21046254 None:intergenic 35.0%
TGAAAGTAGAGGAAGAAACA+TGG - chr1_1:21046284-21046303 Msa0013620:intron 35.0%
AGAGATTGCAAAGTAAAGAC+TGG - chr1_1:21046376-21046395 Msa0013620:intron 35.0%
TGTGCAAAATCATGTGTTCA+AGG - chr1_1:21046426-21046445 Msa0013620:intron 35.0%
!! GAAACTTGCTTGTCACTTTA+AGG - chr1_1:21046463-21046482 Msa0013620:intron 35.0%
!! AACTTGCTTGTCACTTTAAG+GGG - chr1_1:21046465-21046484 Msa0013620:intron 35.0%
AAAACAGGAAATTCAGAAGG+CGG - chr1_1:21046538-21046557 Msa0013620:CDS 35.0%
GTATGCACTGTTTCAATTCA+TGG + chr1_1:21046928-21046947 None:intergenic 35.0%
AATACTCGAACGAGTTTGAA+GGG - chr1_1:21046966-21046985 Msa0013620:intron 35.0%
TTGAAGGGACCAAAAGAATA+AGG - chr1_1:21046981-21047000 Msa0013620:CDS 35.0%
TGAAGGGACCAAAAGAATAA+GGG - chr1_1:21046982-21047001 Msa0013620:CDS 35.0%
AACAGAAGCCCAAAAACACA+TGG - chr1_1:21045956-21045975 Msa0013620:CDS 40.0%
! TCCTGAGACCATGTGTTTTT+GGG + chr1_1:21045967-21045986 None:intergenic 40.0%
AGAGGAAGAAACATGGTTTG+TGG - chr1_1:21046291-21046310 Msa0013620:intron 40.0%
TGTAATGAGCATCTCGACTA+TGG - chr1_1:21046322-21046341 Msa0013620:intron 40.0%
GTAATGAGCATCTCGACTAT+GGG - chr1_1:21046323-21046342 Msa0013620:intron 40.0%
TCTTGATGAACCTTGAGGAT+TGG + chr1_1:21046590-21046609 None:intergenic 40.0%
CAATGTCTTGATGAACCTTG+AGG + chr1_1:21046595-21046614 None:intergenic 40.0%
TAGTGTTGCACTAGCTACTA+TGG - chr1_1:21046741-21046760 Msa0013620:intron 40.0%
TTGCACTAGCTACTATGGAA+TGG - chr1_1:21046746-21046765 Msa0013620:intron 40.0%
GAATACTCGAACGAGTTTGA+AGG - chr1_1:21046965-21046984 Msa0013620:intron 40.0%
AACAGAAGCCCAAAAACACA+TGG - chr1_1:21045956-21045975 Msa0013620:CDS 40.0%
! TCCTGAGACCATGTGTTTTT+GGG + chr1_1:21045967-21045986 None:intergenic 40.0%
AGAGGAAGAAACATGGTTTG+TGG - chr1_1:21046291-21046310 Msa0013620:intron 40.0%
TGTAATGAGCATCTCGACTA+TGG - chr1_1:21046322-21046341 Msa0013620:intron 40.0%
GTAATGAGCATCTCGACTAT+GGG - chr1_1:21046323-21046342 Msa0013620:intron 40.0%
TCTTGATGAACCTTGAGGAT+TGG + chr1_1:21046590-21046609 None:intergenic 40.0%
CAATGTCTTGATGAACCTTG+AGG + chr1_1:21046595-21046614 None:intergenic 40.0%
TAGTGTTGCACTAGCTACTA+TGG - chr1_1:21046741-21046760 Msa0013620:intron 40.0%
TTGCACTAGCTACTATGGAA+TGG - chr1_1:21046746-21046765 Msa0013620:intron 40.0%
GAATACTCGAACGAGTTTGA+AGG - chr1_1:21046965-21046984 Msa0013620:intron 40.0%
! CTCCTGAGACCATGTGTTTT+TGG + chr1_1:21045968-21045987 None:intergenic 45.0%
TTCGGTGGAGTTGAAAGTAG+AGG - chr1_1:21046273-21046292 Msa0013620:intron 45.0%
! GGAAGAAACATGGTTTGTGG+AGG - chr1_1:21046294-21046313 Msa0013620:intron 45.0%
! GAAGCATCCATCATACCTGT+TGG + chr1_1:21046565-21046584 None:intergenic 45.0%
TGATGAACCTTGAGGATTGG+AGG + chr1_1:21046587-21046606 None:intergenic 45.0%
GGGACCAAAAGAATAAGGGT+TGG - chr1_1:21046986-21047005 Msa0013620:CDS 45.0%
! CTCGCCAACCCTTATTCTTT+TGG + chr1_1:21046993-21047012 None:intergenic 45.0%
! CAAAAGAATAAGGGTTGGCG+AGG - chr1_1:21046991-21047010 Msa0013620:CDS 45.0%
GAGCTTGGAAGGTGAATATG+AGG - chr1_1:21047017-21047036 Msa0013620:CDS 45.0%
! CTCCTGAGACCATGTGTTTT+TGG + chr1_1:21045968-21045987 None:intergenic 45.0%
TTCGGTGGAGTTGAAAGTAG+AGG - chr1_1:21046273-21046292 Msa0013620:intron 45.0%
! GGAAGAAACATGGTTTGTGG+AGG - chr1_1:21046294-21046313 Msa0013620:intron 45.0%
! GAAGCATCCATCATACCTGT+TGG + chr1_1:21046565-21046584 None:intergenic 45.0%
TGATGAACCTTGAGGATTGG+AGG + chr1_1:21046587-21046606 None:intergenic 45.0%
GGGACCAAAAGAATAAGGGT+TGG - chr1_1:21046986-21047005 Msa0013620:CDS 45.0%
! CTCGCCAACCCTTATTCTTT+TGG + chr1_1:21046993-21047012 None:intergenic 45.0%
! CAAAAGAATAAGGGTTGGCG+AGG - chr1_1:21046991-21047010 Msa0013620:CDS 45.0%
GAGCTTGGAAGGTGAATATG+AGG - chr1_1:21047017-21047036 Msa0013620:CDS 45.0%
GCCCAAAAACACATGGTCTC+AGG - chr1_1:21045963-21045982 Msa0013620:CDS 50.0%
ATGAGCATCTCGACTATGGG+TGG - chr1_1:21046326-21046345 Msa0013620:intron 50.0%
GACTATGGGTGGTTCACTGA+AGG - chr1_1:21046337-21046356 Msa0013620:intron 50.0%
AATTCAGAAGGCGGTCCAAC+AGG - chr1_1:21046547-21046566 Msa0013620:CDS 50.0%
GATGCTTCCTCCAATCCTCA+AGG - chr1_1:21046577-21046596 Msa0013620:CDS 50.0%
GCCCAAAAACACATGGTCTC+AGG - chr1_1:21045963-21045982 Msa0013620:CDS 50.0%
ATGAGCATCTCGACTATGGG+TGG - chr1_1:21046326-21046345 Msa0013620:intron 50.0%
GACTATGGGTGGTTCACTGA+AGG - chr1_1:21046337-21046356 Msa0013620:intron 50.0%
AATTCAGAAGGCGGTCCAAC+AGG - chr1_1:21046547-21046566 Msa0013620:CDS 50.0%
GATGCTTCCTCCAATCCTCA+AGG - chr1_1:21046577-21046596 Msa0013620:CDS 50.0%
ATGGGTGGTTCACTGAAGGC+TGG - chr1_1:21046341-21046360 Msa0013620:intron 55.0%
AGGCGGTCCAACAGGTATGA+TGG - chr1_1:21046555-21046574 Msa0013620:CDS 55.0%
TGGCGAGGATAGAGCTTGGA+AGG - chr1_1:21047006-21047025 Msa0013620:CDS 55.0%
ATGGGTGGTTCACTGAAGGC+TGG - chr1_1:21046341-21046360 Msa0013620:intron 55.0%
AGGCGGTCCAACAGGTATGA+TGG - chr1_1:21046555-21046574 Msa0013620:CDS 55.0%
TGGCGAGGATAGAGCTTGGA+AGG - chr1_1:21047006-21047025 Msa0013620:CDS 55.0%
! GGGTTGGCGAGGATAGAGCT+TGG - chr1_1:21047002-21047021 Msa0013620:CDS 60.0%
! GGGTTGGCGAGGATAGAGCT+TGG - chr1_1:21047002-21047021 Msa0013620:CDS 60.0%
Chromosome Type Strat End Strand Name
chr1_1 gene 21045905 21047048 21045905 ID=Msa0013620;Name=Msa0013620
chr1_1 mRNA 21045905 21047048 21045905 ID=Msa0013620-mRNA-1;Parent=Msa0013620;Name=Msa0013620-mRNA-1;_AED=0.29;_eAED=0.30;_QI=0|0|0|1|0.33|0.5|4|0|158
chr1_1 exon 21046967 21047048 21046967 ID=Msa0013620-mRNA-1:exon:7493;Parent=Msa0013620-mRNA-1
chr1_1 exon 21046817 21046875 21046817 ID=Msa0013620-mRNA-1:exon:7492;Parent=Msa0013620-mRNA-1
chr1_1 exon 21046506 21046733 21046506 ID=Msa0013620-mRNA-1:exon:7491;Parent=Msa0013620-mRNA-1
chr1_1 exon 21045905 21046012 21045905 ID=Msa0013620-mRNA-1:exon:7490;Parent=Msa0013620-mRNA-1
chr1_1 CDS 21046967 21047048 21046967 ID=Msa0013620-mRNA-1:cds;Parent=Msa0013620-mRNA-1
chr1_1 CDS 21046817 21046875 21046817 ID=Msa0013620-mRNA-1:cds;Parent=Msa0013620-mRNA-1
chr1_1 CDS 21046506 21046733 21046506 ID=Msa0013620-mRNA-1:cds;Parent=Msa0013620-mRNA-1
chr1_1 CDS 21045905 21046012 21045905 ID=Msa0013620-mRNA-1:cds;Parent=Msa0013620-mRNA-1
Gene Sequence

>Msa0013620

ATGCCAGAAGAAGATATGGAATATGTGAGCAATTTTGGAGAACGAATTTCAAACAGAAGCCCAAAAACACATGGTCTCAGGAATTCTGTAAGTCCGAATTTACATGACAAATTCAAGGTTTTTGTAACATCATTAGACAAGTTGGTTGTACTACCAAGTGAGCTGTTAAAAAGACATGATATATTTAGTGGAAATTCGGTGGAGTTGAAAGTAGAGGAAGAAACATGGTTTGTGGAGGTGAGTTGTAATGAGCATCTCGACTATGGGTGGTTCACTGAAGGCTGGCAAGAATTTGTAAGAGATTGCAAAGTAAAGACTGGAGACACTTGCTTGTTTGAGATGATTGATGTGCAAAATCATGTGTTCAAGTGCATACCAACTCTGTTTACGAAAGAATACTCGAACGAGTTTGAAGGGACCAAAAGAATAAGGGTTGGCGAGGATAGAGCTTGGAAGGTGAATATGAGGTTTGATTAA

Protein sequence

>Msa0013620

MPEEDMEYVSNFGERISNRSPKTHGLRNSVSPNLHDKFKVFVTSLDKLVVLPSELLKRHDIFSGNSVELKVEEETWFVEVSCNEHLDYGWFTEGWQEFVRDCKVKTGDTCLFEMIDVQNHVFKCIPTLFTKEYSNEFEGTKRIRVGEDRAWKVNMRFD*