AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0082550


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0082550 MtrunA17_Chr1g0195991 98.990 99 1 0 1 99 1 99 3.54e-69 201
Msa0082550 MtrunA17_Chr1g0195981 95.960 99 4 0 1 99 1 99 3.18e-68 199
Msa0082550 MtrunA17_Chr7g0268711 76.531 98 23 0 1 98 1 98 2.74e-57 171
Msa0082550 MtrunA17_Chr2g0286251 56.842 95 41 0 1 95 1 95 4.02e-39 125
Msa0082550 MtrunA17_Chr1g0195971 52.041 98 47 0 1 98 1 98 4.82e-36 118
Msa0082550 MtrunA17_Chr2g0286271 54.737 95 43 0 1 95 1 95 1.08e-35 117
Msa0082550 MtrunA17_Chr7g0222541 51.042 96 46 1 1 95 30 125 5.05e-34 114
Msa0082550 MtrunA17_Chr7g0222551 50.000 96 47 1 1 95 30 125 1.49e-33 112
Msa0082550 MtrunA17_Chr7g0224091 51.042 96 46 1 1 95 22 117 3.31e-33 111
Msa0082550 MtrunA17_Chr7g0222491 50.000 96 47 1 1 95 30 125 1.21e-32 110
Msa0082550 MtrunA17_Chr4g0066791 50.000 96 47 1 1 95 1 96 5.84e-32 107
Msa0082550 MtrunA17_Chr4g0066801 50.000 96 47 1 1 95 1 96 5.84e-32 107
Msa0082550 MtrunA17_Chr4g0066811 50.000 96 47 1 1 95 1 96 5.84e-32 107
Msa0082550 MtrunA17_Chr7g0268731 49.474 95 47 1 1 94 1 95 1.31e-30 104
Msa0082550 MtrunA17_Chr7g0268721 48.421 95 48 1 1 94 1 95 8.76e-30 102
Msa0082550 MtrunA17_Chr7g0268751 41.053 95 56 0 1 95 1 95 7.44e-26 92.4
Msa0082550 MtrunA17_Chr1g0195951 38.298 94 58 0 1 94 1 94 4.42e-25 90.5
Msa0082550 MtrunA17_Chr1g0195931 42.857 98 56 0 1 98 1 98 1.45e-21 81.6
Msa0082550 MtrunA17_Chr2g0303741 39.796 98 55 1 2 95 40 137 3.25e-21 81.6
Msa0082550 MtrunA17_Chr7g0268761 40.426 94 56 0 1 94 1 94 2.60e-20 78.2
Msa0082550 MtrunA17_Chr2g0325001 38.542 96 52 2 4 95 41 133 1.18e-19 77.8
Msa0082550 MtrunA17_Chr2g0282951 36.170 94 60 0 2 95 27 120 6.54e-19 75.5
Msa0082550 MtrunA17_Chr3g0117411 35.789 95 61 0 1 95 18 112 1.03e-16 69.7
Msa0082550 MtrunA17_Chr4g0040601 38.710 93 52 3 6 95 58 148 4.19e-16 68.9
Msa0082550 MtrunA17_Chr3g0117391 34.043 94 62 0 1 94 21 114 4.94e-16 68.2
Msa0082550 MtrunA17_Chr7g0228311 37.234 94 59 0 1 94 3 96 7.85e-16 67.0
Msa0082550 MtrunA17_Chr1g0151231 36.170 94 58 1 3 94 48 141 5.78e-14 63.2
Msa0082550 MtrunA17_Chr1g0182971 32.979 94 62 1 2 94 84 177 6.48e-14 63.9
Msa0082550 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
Msa0082550 AT2G47880.1 72.449 98 27 0 1 98 1 98 2.04e-52 159
Msa0082550 AT1G06830.1 73.196 97 26 0 1 97 1 97 8.45e-52 158
Msa0082550 AT2G30540.1 66.327 98 33 0 1 98 1 98 2.72e-51 157
Msa0082550 AT3G62960.1 70.408 98 29 0 1 98 1 98 8.50e-51 155
Msa0082550 AT3G62950.1 51.042 96 46 1 1 95 1 96 2.05e-36 119
Msa0082550 AT2G47870.1 54.167 96 43 1 1 95 1 96 6.63e-36 118
Msa0082550 AT4G15670.1 50.526 95 47 0 1 95 1 95 3.04e-34 114
Msa0082550 AT4G15680.1 51.579 95 46 0 1 95 1 95 1.06e-33 112
Msa0082550 AT4G15660.1 49.485 97 49 0 1 97 1 97 1.11e-33 112
Msa0082550 AT4G15700.1 51.579 95 46 0 1 95 1 95 1.21e-33 112
Msa0082550 AT3G21460.1 53.684 95 44 0 1 95 1 95 1.32e-33 112
Msa0082550 AT4G15690.1 50.526 95 47 0 1 95 1 95 5.36e-33 110
Msa0082550 AT5G18600.1 46.316 95 51 0 1 95 1 95 8.06e-31 105
Msa0082550 AT5G14070.1 42.718 103 51 2 1 95 31 133 8.83e-26 93.6
Msa0082550 AT3G62930.1 41.053 95 56 0 1 95 1 95 1.57e-25 92.0
Msa0082550 AT1G03020.1 43.158 95 54 0 1 95 1 95 8.46e-25 90.1
Msa0082550 AT3G02000.1 42.424 99 51 1 3 95 31 129 2.42e-24 89.7
Msa0082550 AT1G28480.1 36.735 98 58 2 2 95 33 130 2.38e-17 72.0
Msa0082550 AT4G33040.1 39.175 97 53 2 3 94 41 136 3.13e-16 69.3
Msa0082550 AT5G40370.1 35.106 94 61 0 1 94 3 96 1.06e-15 67.0
Msa0082550 AT5G11930.1 41.935 93 44 4 3 94 57 140 5.30e-15 66.2
Msa0082550 AT4G28730.1 31.915 94 63 1 2 94 71 164 1.23e-13 63.2
Msa0082550 AT5G63030.1 37.805 82 51 0 13 94 31 112 3.67e-13 60.8
Msa0082550 AT5G20500.1 29.670 91 64 0 4 94 35 125 2.84e-11 56.2
Msa0082550 AT2G20270.1 31.915 94 63 1 2 94 76 169 2.86e-11 57.0
Msa0082550 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 1_2:-61386366 None:intergenic
TTCTCCATTTCTTTCCCATC+AGG 0.358196 1_2:-61386412 None:intergenic
GGAGAAAGCTATAACAAAGT+TGG 0.418322 1_2:+61386429 Msa0082550:CDS
AGATCCTGATGGGAAAGAAA+TGG 0.430695 1_2:+61386408 Msa0082550:CDS
CCTGTCCCTGCAGTATTCAT+TGG 0.431206 1_2:+61386463 Msa0082550:CDS
GTGTAGGGACATTACTTCAT+TGG 0.438643 1_2:-61386506 None:intergenic
TGATCAAAGTAAGCTAAATT+CGG 0.447173 1_2:-61386564 None:intergenic
GAGAAAGCTATAACAAAGTT+GGG 0.448427 1_2:+61386430 Msa0082550:CDS
TTGTCAATTTCATGAATCAC+AGG 0.463222 1_2:-61386385 None:intergenic
CTTCCTCCAATGAATACTGC+AGG 0.488474 1_2:-61386469 None:intergenic
GATGAGGCTAGCTACAGAAA+AGG 0.500022 1_2:+61386285 Msa0082550:CDS
GCATAGACAACAAGAGCTCT+TGG 0.505172 1_2:-61386323 None:intergenic
TCATTGGAGGAAGGCTGGTG+GGG 0.511910 1_2:+61386479 Msa0082550:CDS
TTCATTGGAGGAAGGCTGGT+GGG 0.512409 1_2:+61386478 Msa0082550:CDS
CCAATGAATACTGCAGGGAC+AGG 0.522380 1_2:-61386463 None:intergenic
GTTCACTTGTTCCACTACTC+AGG 0.536048 1_2:+61386536 Msa0082550:CDS
AGTATTCATTGGAGGAAGGC+TGG 0.536333 1_2:+61386474 Msa0082550:CDS
ATGAGGCTAGCTACAGAAAA+GGG 0.537218 1_2:+61386286 Msa0082550:CDS
GTCCCTGCAGTATTCATTGG+AGG 0.543693 1_2:+61386466 Msa0082550:CDS
GAAATTGACAAAGATCCTGA+TGG 0.544778 1_2:+61386397 Msa0082550:CDS
AAAGTAAGCTAAATTCGGTA+TGG 0.551896 1_2:-61386559 None:intergenic
TAGGGACATTACTTCATTGG+TGG 0.552920 1_2:-61386503 None:intergenic
ATTCGGTATGGCCTGAGTAG+TGG 0.556723 1_2:-61386547 None:intergenic
CAAGTGAACCACTTAGGTGT+AGG 0.571843 1_2:-61386522 None:intergenic
ATTCATTGGAGGAAGGCTGG+TGG 0.573512 1_2:+61386477 Msa0082550:CDS
AAGTGAACCACTTAGGTGTA+GGG 0.580489 1_2:-61386521 None:intergenic
GTGGAACAAGTGAACCACTT+AGG 0.593219 1_2:-61386528 None:intergenic
AGCTACAGAAAAGGGTGTGG+TGG 0.593409 1_2:+61386294 Msa0082550:CDS
CTGCAGTATTCATTGGAGGA+AGG 0.598971 1_2:+61386470 Msa0082550:CDS
GTAATGTCCCTACACCTAAG+TGG 0.609456 1_2:+61386514 Msa0082550:CDS
AAATTGACAAAGATCCTGAT+GGG 0.612548 1_2:+61386398 Msa0082550:CDS
TTCCTCCAATGAATACTGCA+GGG 0.637919 1_2:-61386468 None:intergenic
GCTAGCTACAGAAAAGGGTG+TGG 0.645043 1_2:+61386291 Msa0082550:CDS
TGTCAATTTCATGAATCACA+GGG 0.646979 1_2:-61386384 None:intergenic
TTAAGATGGAGAAGGTGATG+AGG 0.659848 1_2:+61386269 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACATTTTGTTCCAAGAAAT+TGG + chr1_2:61386355-61386374 Msa0082550:CDS 25.0%
TGTCAATTTCATGAATCACA+GGG - chr1_2:61386387-61386406 None:intergenic 30.0%
TTGTCAATTTCATGAATCAC+AGG - chr1_2:61386388-61386407 None:intergenic 30.0%
AAATTGACAAAGATCCTGAT+GGG + chr1_2:61386398-61386417 Msa0082550:CDS 30.0%
GAGAAAGCTATAACAAAGTT+GGG + chr1_2:61386430-61386449 Msa0082550:CDS 30.0%
GAAATTGACAAAGATCCTGA+TGG + chr1_2:61386397-61386416 Msa0082550:CDS 35.0%
GGAGAAAGCTATAACAAAGT+TGG + chr1_2:61386429-61386448 Msa0082550:CDS 35.0%
! ATGAGGCTAGCTACAGAAAA+GGG + chr1_2:61386286-61386305 Msa0082550:CDS 40.0%
AGATCCTGATGGGAAAGAAA+TGG + chr1_2:61386408-61386427 Msa0082550:CDS 40.0%
TTCTCCATTTCTTTCCCATC+AGG - chr1_2:61386415-61386434 None:intergenic 40.0%
TTCCTCCAATGAATACTGCA+GGG - chr1_2:61386471-61386490 None:intergenic 40.0%
TAGGGACATTACTTCATTGG+TGG - chr1_2:61386506-61386525 None:intergenic 40.0%
GTGTAGGGACATTACTTCAT+TGG - chr1_2:61386509-61386528 None:intergenic 40.0%
AAGTGAACCACTTAGGTGTA+GGG - chr1_2:61386524-61386543 None:intergenic 40.0%
! GATGAGGCTAGCTACAGAAA+AGG + chr1_2:61386285-61386304 Msa0082550:CDS 45.0%
GCATAGACAACAAGAGCTCT+TGG - chr1_2:61386326-61386345 None:intergenic 45.0%
CAGGGTACACTCCAATTTCT+TGG - chr1_2:61386369-61386388 None:intergenic 45.0%
CTTCCTCCAATGAATACTGC+AGG - chr1_2:61386472-61386491 None:intergenic 45.0%
CTGCAGTATTCATTGGAGGA+AGG + chr1_2:61386470-61386489 Msa0082550:CDS 45.0%
AGTATTCATTGGAGGAAGGC+TGG + chr1_2:61386474-61386493 Msa0082550:CDS 45.0%
GTAATGTCCCTACACCTAAG+TGG + chr1_2:61386514-61386533 Msa0082550:CDS 45.0%
CAAGTGAACCACTTAGGTGT+AGG - chr1_2:61386525-61386544 None:intergenic 45.0%
GTGGAACAAGTGAACCACTT+AGG - chr1_2:61386531-61386550 None:intergenic 45.0%
GTTCACTTGTTCCACTACTC+AGG + chr1_2:61386536-61386555 Msa0082550:CDS 45.0%
GCTAGCTACAGAAAAGGGTG+TGG + chr1_2:61386291-61386310 Msa0082550:CDS 50.0%
! AGCTACAGAAAAGGGTGTGG+TGG + chr1_2:61386294-61386313 Msa0082550:CDS 50.0%
CCAATGAATACTGCAGGGAC+AGG - chr1_2:61386466-61386485 None:intergenic 50.0%
CCTGTCCCTGCAGTATTCAT+TGG + chr1_2:61386463-61386482 Msa0082550:CDS 50.0%
GTCCCTGCAGTATTCATTGG+AGG + chr1_2:61386466-61386485 Msa0082550:CDS 50.0%
ATTCATTGGAGGAAGGCTGG+TGG + chr1_2:61386477-61386496 Msa0082550:CDS 50.0%
TTCATTGGAGGAAGGCTGGT+GGG + chr1_2:61386478-61386497 Msa0082550:CDS 50.0%
ATTCGGTATGGCCTGAGTAG+TGG - chr1_2:61386550-61386569 None:intergenic 50.0%
TCATTGGAGGAAGGCTGGTG+GGG + chr1_2:61386479-61386498 Msa0082550:CDS 55.0%
Chromosome Type Strat End Strand Name
chr1_2 gene 61386274 61386573 61386274 ID=Msa0082550;Name=Msa0082550
chr1_2 mRNA 61386274 61386573 61386274 ID=Msa0082550-mRNA-1;Parent=Msa0082550;Name=Msa0082550-mRNA-1;_AED=0.29;_eAED=0.29;_QI=0|-1|0|1|-1|1|1|0|99
chr1_2 exon 61386274 61386573 61386274 ID=Msa0082550-mRNA-1:exon:20293;Parent=Msa0082550-mRNA-1
chr1_2 CDS 61386274 61386573 61386274 ID=Msa0082550-mRNA-1:cds;Parent=Msa0082550-mRNA-1
Gene Sequence

>Msa0082550

ATGGAGAAGGTGATGAGGCTAGCTACAGAAAAGGGTGTGGTGGTATTCACCAAGAGCTCTTGTTGTCTATGCTATGCAGTGAACATTTTGTTCCAAGAAATTGGAGTGTACCCTGTGATTCATGAAATTGACAAAGATCCTGATGGGAAAGAAATGGAGAAAGCTATAACAAAGTTGGGTTGTAATGCACCTGTCCCTGCAGTATTCATTGGAGGAAGGCTGGTGGGGTCCACCAATGAAGTAATGTCCCTACACCTAAGTGGTTCACTTGTTCCACTACTCAGGCCATACCGAATTTAG

Protein sequence

>Msa0082550

MEKVMRLATEKGVVVFTKSSCCLCYAVNILFQEIGVYPVIHEIDKDPDGKEMEKAITKLGCNAPVPAVFIGGRLVGSTNEVMSLHLSGSLVPLLRPYRI*