AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0869090

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0869090 MtrunA17_Chr6g0450121 96.685 181 5 1 1 180 1 181 1.21e-119 335
Msa0869090 MtrunA17_Chr8g0372561 32.984 191 100 5 14 179 7 194 3.07e-19 80.9
Msa0869090 MtrunA17_Chr7g0234831 35.878 131 74 2 59 179 86 216 1.73e-14 68.6
Msa0869090 MtrunA17_Chr2g0293431 32.624 141 85 3 47 177 12 152 5.43e-14 67.0
Msa0869090 MtrunA17_Chr2g0293341 49.254 67 34 0 109 175 119 185 1.20e-13 65.9
Msa0869090 MtrunA17_Chr2g0310131 33.588 131 77 2 59 179 85 215 1.72e-12 63.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0869090 AT3G27850.1 59.783 184 68 3 1 180 6 187 1.03e-53 169
Msa0869090 AT3G27830.2 64.596 161 49 3 28 180 31 191 3.05e-52 166
Msa0869090 AT3G27830.1 64.596 161 49 3 28 180 31 191 3.05e-52 166
Msa0869090 AT3G27840.1 50.898 167 64 3 31 179 26 192 6.62e-44 144
Msa0869090 AT4G36420.1 36.301 146 79 3 48 179 33 178 1.34e-18 79.3
Msa0869090 AT4G37660.1 32.877 146 96 1 36 179 21 166 5.31e-14 66.6
Msa0869090 AT3G06040.3 35.200 125 78 1 54 175 57 181 6.79e-14 67.0
Msa0869090 AT3G06040.2 35.200 125 78 1 54 175 57 181 6.79e-14 67.0
Msa0869090 AT3G06040.1 35.200 125 78 1 54 175 57 181 6.79e-14 67.0
Msa0869090 AT1G70190.2 36.029 136 71 3 59 179 73 207 5.64e-13 64.7
Msa0869090 AT1G70190.1 36.029 136 71 3 59 179 73 207 5.64e-13 64.7

Find 49 sgRNAs with CRISPR-Local

Find 65 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGCAGCGGCGACGGCGGCGG+CGG 0.240866 6_1:+2911904 None:intergenic
GGGAGCAGCGGCGACGGCGG+CGG 0.290611 6_1:+2911901 None:intergenic
GAGGTAGTCGACGAGGTCTT+TGG 0.313141 6_1:+2911964 None:intergenic
GCAGCGGCGACGGCGGCGGC+GGG 0.315412 6_1:+2911905 None:intergenic
GGAGATGGAGAGGGGTTTGG+AGG 0.336690 6_1:+2912081 None:intergenic
GGCGGCGGGAGCAGCGGCGA+CGG 0.343764 6_1:+2911895 None:intergenic
GTTAGAGCTTTGACGAGTTT+AGG 0.347699 6_1:-2911785 Msa0869090:CDS
TTCAATCACAACATCGAATT+CGG 0.351658 6_1:+2911847 None:intergenic
GGAGACGAGTGCGGTGGTGG+GGG 0.366760 6_1:+2912059 None:intergenic
GACGGAGACGAGTGCGGTGG+TGG 0.372523 6_1:+2912056 None:intergenic
TTCTTCGACTACTGCAACTT+CGG 0.382145 6_1:+2911874 None:intergenic
CGGAGACGAGTGCGGTGGTG+GGG 0.384508 6_1:+2912058 None:intergenic
ACACCTTCTTTAAATTTCTT+CGG 0.390394 6_1:+2911728 None:intergenic
GGGAAATTGAGAGTGGAGAT+TGG 0.393088 6_1:+2912103 None:intergenic
GGCGGGAGCAGCGGCGACGG+CGG 0.408129 6_1:+2911898 None:intergenic
GCCGCAATTCTCGCGTTACT+AGG 0.408930 6_1:+2911818 None:intergenic
GTCGACGAGGTCTTTGGCTT+GGG 0.415248 6_1:+2911970 None:intergenic
TTCAGTGGCCACGGCGGAGA+TGG 0.416551 6_1:+2912033 None:intergenic
AGATGGAGAGGGGTTTGGAG+GGG 0.422416 6_1:+2912083 None:intergenic
GGCGGCGGGAGCGAAGGAAG+CGG 0.435068 6_1:+2911919 None:intergenic
AACTTCGGCGGCGGGAGCAG+CGG 0.438188 6_1:+2911889 None:intergenic
AGTCGACGAGGTCTTTGGCT+TGG 0.457705 6_1:+2911969 None:intergenic
GAAGCGAAGGAATTGATTGA+AGG 0.470442 6_1:-2911755 Msa0869090:CDS
GACTACTGCAACTTCGGCGG+CGG 0.472198 6_1:+2911880 None:intergenic
GACGGCGGCGGCGGGAGCGA+AGG 0.479033 6_1:+2911913 None:intergenic
ACGGAGACGAGTGCGGTGGT+GGG 0.493453 6_1:+2912057 None:intergenic
TTGCCGAAGAAATTTAAAGA+AGG 0.505106 6_1:-2911731 Msa0869090:CDS
ACTACTGCAACTTCGGCGGC+GGG 0.506435 6_1:+2911881 None:intergenic
GAGATGGAGAGGGGTTTGGA+GGG 0.507359 6_1:+2912082 None:intergenic
TCCTAGTAACGCGAGAATTG+CGG 0.528323 6_1:-2911819 Msa0869090:CDS
TCAGTGGCCACGGCGGAGAT+GGG 0.542642 6_1:+2912034 None:intergenic
GAGACGAGTGCGGTGGTGGG+GGG 0.556105 6_1:+2912060 None:intergenic
GGCTTGGGAGAGAGTGAGGT+CGG 0.562669 6_1:+2911985 None:intergenic
AAGAAACAACTTGAAGCTGC+AGG 0.564071 6_1:-2911680 Msa0869090:CDS
TGGCCACGGCGGAGATGGGA+CGG 0.564429 6_1:+2912038 None:intergenic
TTTAGGATTGAAAGAAGCGA+AGG 0.566913 6_1:-2911768 Msa0869090:CDS
TTTGGAGGGGAAATTGAGAG+TGG 0.570125 6_1:+2912096 None:intergenic
CTTTGGCTTGGGAGAGAGTG+AGG 0.572512 6_1:+2911981 None:intergenic
CGAAACCCTAAATTAAGCAA+TGG 0.594710 6_1:+2911646 None:intergenic
TTCGACTACTGCAACTTCGG+CGG 0.600582 6_1:+2911877 None:intergenic
GGGTGTGGTGAGAAAGTGTG+AGG 0.616452 6_1:+2912140 None:intergenic
GGTGTGGTGAGAAAGTGTGA+GGG 0.616748 6_1:+2912141 None:intergenic
GAGAATTGCGGCGATTAAAG+CGG 0.638455 6_1:-2911807 Msa0869090:CDS
TTCTATTTCAGTGGCCACGG+CGG 0.638885 6_1:+2912027 None:intergenic
TCTCCGTCCCATCTCCGCCG+TGG 0.646628 6_1:-2912041 Msa0869090:CDS
AGATGGGACGGAGACGAGTG+CGG 0.648615 6_1:+2912050 None:intergenic
GGTTGAGATAGTTGTGAAAG+CGG 0.650535 6_1:+2912162 None:intergenic
TTTCTTGGAGGTAGTCGACG+AGG 0.676894 6_1:+2911957 None:intergenic
TGGGACGGAGACGAGTGCGG+TGG 0.682439 6_1:+2912053 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! ACACCTTCTTTAAATTTCTT+CGG + chr6_1:2912111-2912130 None:intergenic 25.0%
TTCAATCACAACATCGAATT+CGG + chr6_1:2911992-2912011 None:intergenic 30.0%
TTGCCGAAGAAATTTAAAGA+AGG - chr6_1:2912105-2912124 Msa0869090:CDS 30.0%
!!! AGATTGGTTTTTTTGAGAGG+GGG + chr6_1:2911720-2911739 None:intergenic 35.0%
!!! GAGATTGGTTTTTTTGAGAG+GGG + chr6_1:2911721-2911740 None:intergenic 35.0%
!!! GGAGATTGGTTTTTTTGAGA+GGG + chr6_1:2911722-2911741 None:intergenic 35.0%
!!! TGGAGATTGGTTTTTTTGAG+AGG + chr6_1:2911723-2911742 None:intergenic 35.0%
! TTTTTCTATTTCAGTGGCCA+CGG + chr6_1:2911815-2911834 None:intergenic 35.0%
GCCACTGAAATAGAAAAACT+CGG - chr6_1:2911817-2911836 Msa0869090:CDS 35.0%
! TTTAGGATTGAAAGAAGCGA+AGG - chr6_1:2912068-2912087 Msa0869090:CDS 35.0%
GGTTGAGATAGTTGTGAAAG+CGG + chr6_1:2911677-2911696 None:intergenic 40.0%
!!! GATTGGTTTTTTTGAGAGGG+GGG + chr6_1:2911719-2911738 None:intergenic 40.0%
! GCCGAGTTTTTCTATTTCAG+TGG + chr6_1:2911821-2911840 None:intergenic 40.0%
GACTACCTCCAAGAAAAACT+CGG - chr6_1:2911886-2911905 Msa0869090:CDS 40.0%
TTCTTCGACTACTGCAACTT+CGG + chr6_1:2911965-2911984 None:intergenic 40.0%
! GTTAGAGCTTTGACGAGTTT+AGG - chr6_1:2912051-2912070 Msa0869090:CDS 40.0%
GAAGCGAAGGAATTGATTGA+AGG - chr6_1:2912081-2912100 Msa0869090:CDS 40.0%
AAGAAACAACTTGAAGCTGC+AGG - chr6_1:2912156-2912175 Msa0869090:CDS 40.0%
GGGAAATTGAGAGTGGAGAT+TGG + chr6_1:2911736-2911755 None:intergenic 45.0%
TTTGGAGGGGAAATTGAGAG+TGG + chr6_1:2911743-2911762 None:intergenic 45.0%
TCCTAGTAACGCGAGAATTG+CGG - chr6_1:2912017-2912036 Msa0869090:CDS 45.0%
GAGAATTGCGGCGATTAAAG+CGG - chr6_1:2912029-2912048 Msa0869090:CDS 45.0%
! GGTGTGGTGAGAAAGTGTGA+GGG + chr6_1:2911698-2911717 None:intergenic 50.0%
!!! GTTTTTTTGAGAGGGGGGTG+TGG + chr6_1:2911714-2911733 None:intergenic 50.0%
TTCTATTTCAGTGGCCACGG+CGG + chr6_1:2911812-2911831 None:intergenic 50.0%
TTTCTTGGAGGTAGTCGACG+AGG + chr6_1:2911882-2911901 None:intergenic 50.0%
! TGACGCCGAGTTTTTCTTGG+AGG + chr6_1:2911894-2911913 None:intergenic 50.0%
! CAGTGACGCCGAGTTTTTCT+TGG + chr6_1:2911897-2911916 None:intergenic 50.0%
TTCGACTACTGCAACTTCGG+CGG + chr6_1:2911962-2911981 None:intergenic 50.0%
! GGGTGTGGTGAGAAAGTGTG+AGG + chr6_1:2911699-2911718 None:intergenic 55.0%
AGATGGAGAGGGGTTTGGAG+GGG + chr6_1:2911756-2911775 None:intergenic 55.0%
GAGATGGAGAGGGGTTTGGA+GGG + chr6_1:2911757-2911776 None:intergenic 55.0%
!! CTTTGGCTTGGGAGAGAGTG+AGG + chr6_1:2911858-2911877 None:intergenic 55.0%
! GTCGACGAGGTCTTTGGCTT+GGG + chr6_1:2911869-2911888 None:intergenic 55.0%
AGTCGACGAGGTCTTTGGCT+TGG + chr6_1:2911870-2911889 None:intergenic 55.0%
GAGGTAGTCGACGAGGTCTT+TGG + chr6_1:2911875-2911894 None:intergenic 55.0%
GCCGCAATTCTCGCGTTACT+AGG + chr6_1:2912021-2912040 None:intergenic 55.0%
GGAGATGGAGAGGGGTTTGG+AGG + chr6_1:2911758-2911777 None:intergenic 60.0%
AGATGGGACGGAGACGAGTG+CGG + chr6_1:2911789-2911808 None:intergenic 60.0%
GGCTTGGGAGAGAGTGAGGT+CGG + chr6_1:2911854-2911873 None:intergenic 60.0%
ACTACTGCAACTTCGGCGGC+GGG + chr6_1:2911958-2911977 None:intergenic 60.0%
GACTACTGCAACTTCGGCGG+CGG + chr6_1:2911959-2911978 None:intergenic 60.0%
GGGGGAGATGGAGAGGGGTT+TGG + chr6_1:2911761-2911780 None:intergenic 65.0%
TGGTGGGGGGAGATGGAGAG+GGG + chr6_1:2911766-2911785 None:intergenic 65.0%
! GTGGTGGGGGGAGATGGAGA+GGG + chr6_1:2911767-2911786 None:intergenic 65.0%
ACGGAGACGAGTGCGGTGGT+GGG + chr6_1:2911782-2911801 None:intergenic 65.0%
TCAGTGGCCACGGCGGAGAT+GGG + chr6_1:2911805-2911824 None:intergenic 65.0%
TTCAGTGGCCACGGCGGAGA+TGG + chr6_1:2911806-2911825 None:intergenic 65.0%
!! GGTGGTGGGGGGAGATGGAG+AGG + chr6_1:2911768-2911787 None:intergenic 70.0%
!! AGTGCGGTGGTGGGGGGAGA+TGG + chr6_1:2911773-2911792 None:intergenic 70.0%
!! GAGACGAGTGCGGTGGTGGG+GGG + chr6_1:2911779-2911798 None:intergenic 70.0%
! GGAGACGAGTGCGGTGGTGG+GGG + chr6_1:2911780-2911799 None:intergenic 70.0%
CGGAGACGAGTGCGGTGGTG+GGG + chr6_1:2911781-2911800 None:intergenic 70.0%
GACGGAGACGAGTGCGGTGG+TGG + chr6_1:2911783-2911802 None:intergenic 70.0%
TGGGACGGAGACGAGTGCGG+TGG + chr6_1:2911786-2911805 None:intergenic 70.0%
TCTCCGTCCCATCTCCGCCG+TGG - chr6_1:2911795-2911814 Msa0869090:CDS 70.0%
TGGCCACGGCGGAGATGGGA+CGG + chr6_1:2911801-2911820 None:intergenic 70.0%
AACTTCGGCGGCGGGAGCAG+CGG + chr6_1:2911950-2911969 None:intergenic 70.0%
GGCGGCGGGAGCGAAGGAAG+CGG + chr6_1:2911920-2911939 None:intergenic 75.0%
! GACGGCGGCGGCGGGAGCGA+AGG + chr6_1:2911926-2911945 None:intergenic 85.0%
! AGCAGCGGCGACGGCGGCGG+CGG + chr6_1:2911935-2911954 None:intergenic 85.0%
! GGGAGCAGCGGCGACGGCGG+CGG + chr6_1:2911938-2911957 None:intergenic 85.0%
! GGCGGGAGCAGCGGCGACGG+CGG + chr6_1:2911941-2911960 None:intergenic 85.0%
! GGCGGCGGGAGCAGCGGCGA+CGG + chr6_1:2911944-2911963 None:intergenic 85.0%
! GCAGCGGCGACGGCGGCGGC+GGG + chr6_1:2911934-2911953 None:intergenic 90.0%
Chromosome Type Strat End Strand Name
chr6_1 gene 2911658 2912200 2911658 ID=Msa0869090;Name=Msa0869090
chr6_1 mRNA 2911658 2912200 2911658 ID=Msa0869090-mRNA-1;Parent=Msa0869090;Name=Msa0869090-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|180
chr6_1 exon 2911658 2912200 2911658 ID=Msa0869090-mRNA-1:exon:924;Parent=Msa0869090-mRNA-1
chr6_1 CDS 2911658 2912200 2911658 ID=Msa0869090-mRNA-1:cds;Parent=Msa0869090-mRNA-1
Gene Sequence

>Msa0869090

ATGGCATTATCAACAACCGCTTTCACAACTATCTCAACCCTCACACTTTCTCACCACACCCCCCTCTCAAAAAAACCAATCTCCACTCTCAATTTCCCCTCCAAACCCCTCTCCATCTCCCCCCACCACCGCACTCGTCTCCGTCCCATCTCCGCCGTGGCCACTGAAATAGAAAAACTCGGCAACGACATCTCCGACCTCACTCTCTCCCAAGCCAAAGACCTCGTCGACTACCTCCAAGAAAAACTCGGCGTCACTGCCGCTTCCTTCGCTCCCGCCGCCGCCGTCGCCGCTGCTCCCGCCGCCGAAGTTGCAGTAGTCGAAGAAAAGACCGAATTCGATGTTGTGATTGAAGAAGTTCCTAGTAACGCGAGAATTGCGGCGATTAAAGCGGTTAGAGCTTTGACGAGTTTAGGATTGAAAGAAGCGAAGGAATTGATTGAAGGTTTGCCGAAGAAATTTAAAGAAGGTGTGAGTAAAGATGAAGCTGATGATGCTAAGAAACAACTTGAAGCTGCAGGTGCTAAAGTTACCATTGCTTAA
Protein sequence

>Msa0869090

MALSTTAFTTISTLTLSHHTPLSKKPISTLNFPSKPLSISPHHRTRLRPISAVATEIEKLGNDISDLTLSQAKDLVDYLQEKLGVTAASFAPAAAVAAAPAAEVAVVEEKTEFDVVIEEVPSNARIAAIKAVRALTSLGLKEAKELIEGLPKKFKEGVSKDEADDAKKQLEAAGAKVTIA*