AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1400470


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1400470 MtrunA17_Chr1g0195991 98.990 99 1 0 1 99 1 99 3.54e-69 201
Msa1400470 MtrunA17_Chr1g0195981 95.960 99 4 0 1 99 1 99 3.18e-68 199
Msa1400470 MtrunA17_Chr7g0268711 76.531 98 23 0 1 98 1 98 2.74e-57 171
Msa1400470 MtrunA17_Chr2g0286251 56.842 95 41 0 1 95 1 95 4.02e-39 125
Msa1400470 MtrunA17_Chr1g0195971 52.041 98 47 0 1 98 1 98 4.82e-36 118
Msa1400470 MtrunA17_Chr2g0286271 54.737 95 43 0 1 95 1 95 1.08e-35 117
Msa1400470 MtrunA17_Chr7g0222541 51.042 96 46 1 1 95 30 125 5.05e-34 114
Msa1400470 MtrunA17_Chr7g0222551 50.000 96 47 1 1 95 30 125 1.49e-33 112
Msa1400470 MtrunA17_Chr7g0224091 51.042 96 46 1 1 95 22 117 3.31e-33 111
Msa1400470 MtrunA17_Chr7g0222491 50.000 96 47 1 1 95 30 125 1.21e-32 110
Msa1400470 MtrunA17_Chr4g0066791 50.000 96 47 1 1 95 1 96 5.84e-32 107
Msa1400470 MtrunA17_Chr4g0066801 50.000 96 47 1 1 95 1 96 5.84e-32 107
Msa1400470 MtrunA17_Chr4g0066811 50.000 96 47 1 1 95 1 96 5.84e-32 107
Msa1400470 MtrunA17_Chr7g0268731 49.474 95 47 1 1 94 1 95 1.31e-30 104
Msa1400470 MtrunA17_Chr7g0268721 48.421 95 48 1 1 94 1 95 8.76e-30 102
Msa1400470 MtrunA17_Chr7g0268751 41.053 95 56 0 1 95 1 95 7.44e-26 92.4
Msa1400470 MtrunA17_Chr1g0195951 38.298 94 58 0 1 94 1 94 4.42e-25 90.5
Msa1400470 MtrunA17_Chr1g0195931 42.857 98 56 0 1 98 1 98 1.45e-21 81.6
Msa1400470 MtrunA17_Chr2g0303741 39.796 98 55 1 2 95 40 137 3.25e-21 81.6
Msa1400470 MtrunA17_Chr7g0268761 40.426 94 56 0 1 94 1 94 2.60e-20 78.2
Msa1400470 MtrunA17_Chr2g0325001 38.542 96 52 2 4 95 41 133 1.18e-19 77.8
Msa1400470 MtrunA17_Chr2g0282951 36.170 94 60 0 2 95 27 120 6.54e-19 75.5
Msa1400470 MtrunA17_Chr3g0117411 35.789 95 61 0 1 95 18 112 1.03e-16 69.7
Msa1400470 MtrunA17_Chr4g0040601 38.710 93 52 3 6 95 58 148 4.19e-16 68.9
Msa1400470 MtrunA17_Chr3g0117391 34.043 94 62 0 1 94 21 114 4.94e-16 68.2
Msa1400470 MtrunA17_Chr7g0228311 37.234 94 59 0 1 94 3 96 7.85e-16 67.0
Msa1400470 MtrunA17_Chr1g0151231 36.170 94 58 1 3 94 48 141 5.78e-14 63.2
Msa1400470 MtrunA17_Chr1g0182971 32.979 94 62 1 2 94 84 177 6.48e-14 63.9
Msa1400470 MtrunA17_Chr3g0135811 35.484 93 54 3 3 94 23 110 3.11e-13 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1400470 AT2G47880.1 72.449 98 27 0 1 98 1 98 2.04e-52 159
Msa1400470 AT1G06830.1 73.196 97 26 0 1 97 1 97 8.45e-52 158
Msa1400470 AT2G30540.1 66.327 98 33 0 1 98 1 98 2.72e-51 157
Msa1400470 AT3G62960.1 70.408 98 29 0 1 98 1 98 8.50e-51 155
Msa1400470 AT3G62950.1 51.042 96 46 1 1 95 1 96 2.05e-36 119
Msa1400470 AT2G47870.1 54.167 96 43 1 1 95 1 96 6.63e-36 118
Msa1400470 AT4G15670.1 50.526 95 47 0 1 95 1 95 3.04e-34 114
Msa1400470 AT4G15680.1 51.579 95 46 0 1 95 1 95 1.06e-33 112
Msa1400470 AT4G15660.1 49.485 97 49 0 1 97 1 97 1.11e-33 112
Msa1400470 AT4G15700.1 51.579 95 46 0 1 95 1 95 1.21e-33 112
Msa1400470 AT3G21460.1 53.684 95 44 0 1 95 1 95 1.32e-33 112
Msa1400470 AT4G15690.1 50.526 95 47 0 1 95 1 95 5.36e-33 110
Msa1400470 AT5G18600.1 46.316 95 51 0 1 95 1 95 8.06e-31 105
Msa1400470 AT5G14070.1 42.718 103 51 2 1 95 31 133 8.83e-26 93.6
Msa1400470 AT3G62930.1 41.053 95 56 0 1 95 1 95 1.57e-25 92.0
Msa1400470 AT1G03020.1 43.158 95 54 0 1 95 1 95 8.46e-25 90.1
Msa1400470 AT3G02000.1 42.424 99 51 1 3 95 31 129 2.42e-24 89.7
Msa1400470 AT1G28480.1 36.735 98 58 2 2 95 33 130 2.38e-17 72.0
Msa1400470 AT4G33040.1 39.175 97 53 2 3 94 41 136 3.13e-16 69.3
Msa1400470 AT5G40370.1 35.106 94 61 0 1 94 3 96 1.06e-15 67.0
Msa1400470 AT5G11930.1 41.935 93 44 4 3 94 57 140 5.30e-15 66.2
Msa1400470 AT4G28730.1 31.915 94 63 1 2 94 71 164 1.23e-13 63.2
Msa1400470 AT5G63030.1 37.805 82 51 0 13 94 31 112 3.67e-13 60.8
Msa1400470 AT5G20500.1 29.670 91 64 0 4 94 35 125 2.84e-11 56.2
Msa1400470 AT2G20270.1 31.915 94 63 1 2 94 76 169 2.86e-11 57.0
Msa1400470 AT1G03850.2 34.884 86 52 2 10 95 62 143 4.69e-11 56.2

Find 35 sgRNAs with CRISPR-Local

Find 33 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAGGGTACACTCCAATTTCT+TGG 0.312373 tig0022456:-46904 None:intergenic
TTCTCCATTTCTTTCCCATC+AGG 0.358196 tig0022456:-46950 None:intergenic
GGAGAAAGCTATAACAAAGT+TGG 0.418322 tig0022456:+46967 Msa1400470:CDS
AGATCCTGATGGGAAAGAAA+TGG 0.430695 tig0022456:+46946 Msa1400470:CDS
CCTGTCCCTGCAGTATTCAT+TGG 0.431206 tig0022456:+47001 Msa1400470:CDS
GTGTAGGGACATTACTTCAT+TGG 0.438643 tig0022456:-47044 None:intergenic
TGATCAAAGTAAGCTAAATT+CGG 0.447173 tig0022456:-47102 None:intergenic
GAGAAAGCTATAACAAAGTT+GGG 0.448427 tig0022456:+46968 Msa1400470:CDS
TTGTCAATTTCATGAATCAC+AGG 0.463222 tig0022456:-46923 None:intergenic
CTTCCTCCAATGAATACTGC+AGG 0.488474 tig0022456:-47007 None:intergenic
GATGAGGCTAGCTACAGAAA+AGG 0.500022 tig0022456:+46823 Msa1400470:CDS
GCATAGACAACAAGAGCTCT+TGG 0.505172 tig0022456:-46861 None:intergenic
TCATTGGAGGAAGGCTGGTG+GGG 0.511910 tig0022456:+47017 Msa1400470:CDS
TTCATTGGAGGAAGGCTGGT+GGG 0.512409 tig0022456:+47016 Msa1400470:CDS
CCAATGAATACTGCAGGGAC+AGG 0.522380 tig0022456:-47001 None:intergenic
GTTCACTTGTTCCACTACTC+AGG 0.536048 tig0022456:+47074 Msa1400470:CDS
AGTATTCATTGGAGGAAGGC+TGG 0.536333 tig0022456:+47012 Msa1400470:CDS
ATGAGGCTAGCTACAGAAAA+GGG 0.537218 tig0022456:+46824 Msa1400470:CDS
GTCCCTGCAGTATTCATTGG+AGG 0.543693 tig0022456:+47004 Msa1400470:CDS
GAAATTGACAAAGATCCTGA+TGG 0.544778 tig0022456:+46935 Msa1400470:CDS
AAAGTAAGCTAAATTCGGTA+TGG 0.551896 tig0022456:-47097 None:intergenic
TAGGGACATTACTTCATTGG+TGG 0.552920 tig0022456:-47041 None:intergenic
ATTCGGTATGGCCTGAGTAG+TGG 0.556723 tig0022456:-47085 None:intergenic
CAAGTGAACCACTTAGGTGT+AGG 0.571843 tig0022456:-47060 None:intergenic
ATTCATTGGAGGAAGGCTGG+TGG 0.573512 tig0022456:+47015 Msa1400470:CDS
AAGTGAACCACTTAGGTGTA+GGG 0.580489 tig0022456:-47059 None:intergenic
GTGGAACAAGTGAACCACTT+AGG 0.593219 tig0022456:-47066 None:intergenic
AGCTACAGAAAAGGGTGTGG+TGG 0.593409 tig0022456:+46832 Msa1400470:CDS
CTGCAGTATTCATTGGAGGA+AGG 0.598971 tig0022456:+47008 Msa1400470:CDS
GTAATGTCCCTACACCTAAG+TGG 0.609456 tig0022456:+47052 Msa1400470:CDS
AAATTGACAAAGATCCTGAT+GGG 0.612548 tig0022456:+46936 Msa1400470:CDS
TTCCTCCAATGAATACTGCA+GGG 0.637919 tig0022456:-47006 None:intergenic
GCTAGCTACAGAAAAGGGTG+TGG 0.645043 tig0022456:+46829 Msa1400470:CDS
TGTCAATTTCATGAATCACA+GGG 0.646979 tig0022456:-46922 None:intergenic
TTAAGATGGAGAAGGTGATG+AGG 0.659848 tig0022456:+46807 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACATTTTGTTCCAAGAAAT+TGG + tig0022456:46893-46912 Msa1400470:CDS 25.0%
TGTCAATTTCATGAATCACA+GGG - tig0022456:46925-46944 None:intergenic 30.0%
TTGTCAATTTCATGAATCAC+AGG - tig0022456:46926-46945 None:intergenic 30.0%
AAATTGACAAAGATCCTGAT+GGG + tig0022456:46936-46955 Msa1400470:CDS 30.0%
GAGAAAGCTATAACAAAGTT+GGG + tig0022456:46968-46987 Msa1400470:CDS 30.0%
GAAATTGACAAAGATCCTGA+TGG + tig0022456:46935-46954 Msa1400470:CDS 35.0%
GGAGAAAGCTATAACAAAGT+TGG + tig0022456:46967-46986 Msa1400470:CDS 35.0%
! ATGAGGCTAGCTACAGAAAA+GGG + tig0022456:46824-46843 Msa1400470:CDS 40.0%
AGATCCTGATGGGAAAGAAA+TGG + tig0022456:46946-46965 Msa1400470:CDS 40.0%
TTCTCCATTTCTTTCCCATC+AGG - tig0022456:46953-46972 None:intergenic 40.0%
TTCCTCCAATGAATACTGCA+GGG - tig0022456:47009-47028 None:intergenic 40.0%
TAGGGACATTACTTCATTGG+TGG - tig0022456:47044-47063 None:intergenic 40.0%
GTGTAGGGACATTACTTCAT+TGG - tig0022456:47047-47066 None:intergenic 40.0%
AAGTGAACCACTTAGGTGTA+GGG - tig0022456:47062-47081 None:intergenic 40.0%
! GATGAGGCTAGCTACAGAAA+AGG + tig0022456:46823-46842 Msa1400470:CDS 45.0%
GCATAGACAACAAGAGCTCT+TGG - tig0022456:46864-46883 None:intergenic 45.0%
CAGGGTACACTCCAATTTCT+TGG - tig0022456:46907-46926 None:intergenic 45.0%
CTTCCTCCAATGAATACTGC+AGG - tig0022456:47010-47029 None:intergenic 45.0%
CTGCAGTATTCATTGGAGGA+AGG + tig0022456:47008-47027 Msa1400470:CDS 45.0%
AGTATTCATTGGAGGAAGGC+TGG + tig0022456:47012-47031 Msa1400470:CDS 45.0%
GTAATGTCCCTACACCTAAG+TGG + tig0022456:47052-47071 Msa1400470:CDS 45.0%
CAAGTGAACCACTTAGGTGT+AGG - tig0022456:47063-47082 None:intergenic 45.0%
GTGGAACAAGTGAACCACTT+AGG - tig0022456:47069-47088 None:intergenic 45.0%
GTTCACTTGTTCCACTACTC+AGG + tig0022456:47074-47093 Msa1400470:CDS 45.0%
GCTAGCTACAGAAAAGGGTG+TGG + tig0022456:46829-46848 Msa1400470:CDS 50.0%
! AGCTACAGAAAAGGGTGTGG+TGG + tig0022456:46832-46851 Msa1400470:CDS 50.0%
CCAATGAATACTGCAGGGAC+AGG - tig0022456:47004-47023 None:intergenic 50.0%
CCTGTCCCTGCAGTATTCAT+TGG + tig0022456:47001-47020 Msa1400470:CDS 50.0%
GTCCCTGCAGTATTCATTGG+AGG + tig0022456:47004-47023 Msa1400470:CDS 50.0%
ATTCATTGGAGGAAGGCTGG+TGG + tig0022456:47015-47034 Msa1400470:CDS 50.0%
TTCATTGGAGGAAGGCTGGT+GGG + tig0022456:47016-47035 Msa1400470:CDS 50.0%
ATTCGGTATGGCCTGAGTAG+TGG - tig0022456:47088-47107 None:intergenic 50.0%
TCATTGGAGGAAGGCTGGTG+GGG + tig0022456:47017-47036 Msa1400470:CDS 55.0%
Chromosome Type Strat End Strand Name
tig0022456 gene 46812 47111 46812 ID=Msa1400470;Name=Msa1400470
tig0022456 mRNA 46812 47111 46812 ID=Msa1400470-mRNA-1;Parent=Msa1400470;Name=Msa1400470-mRNA-1;_AED=0.29;_eAED=0.29;_QI=0|-1|0|1|-1|1|1|0|99
tig0022456 exon 46812 47111 46812 ID=Msa1400470-mRNA-1:exon:17724;Parent=Msa1400470-mRNA-1
tig0022456 CDS 46812 47111 46812 ID=Msa1400470-mRNA-1:cds;Parent=Msa1400470-mRNA-1
Gene Sequence

>Msa1400470

ATGGAGAAGGTGATGAGGCTAGCTACAGAAAAGGGTGTGGTGGTATTCACCAAGAGCTCTTGTTGTCTATGCTATGCAGTGAACATTTTGTTCCAAGAAATTGGAGTGTACCCTGTGATTCATGAAATTGACAAAGATCCTGATGGGAAAGAAATGGAGAAAGCTATAACAAAGTTGGGTTGTAATGCACCTGTCCCTGCAGTATTCATTGGAGGAAGGCTGGTGGGGTCCACCAATGAAGTAATGTCCCTACACCTAAGTGGTTCACTTGTTCCACTACTCAGGCCATACCGAATTTAG

Protein sequence

>Msa1400470

MEKVMRLATEKGVVVFTKSSCCLCYAVNILFQEIGVYPVIHEIDKDPDGKEMEKAITKLGCNAPVPAVFIGGRLVGSTNEVMSLHLSGSLVPLLRPYRI*