AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0585090

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0585090 MtrunA17_Chr4g0014031 86.486 111 15 0 1 111 1 111 2.08e-60 184
Msa0585090 MtrunA17_Chr4g0014121 85.586 111 16 0 1 111 29 139 8.72e-58 176
Msa0585090 MtrunA17_Chr4g0014131 86.486 111 15 0 1 111 1 111 9.45e-58 177
Msa0585090 MtrunA17_Chr4g0014321 71.171 111 32 0 1 111 1 111 1.33e-53 167
Msa0585090 MtrunA17_Chr4g0013041 69.369 111 32 1 1 111 1 109 3.86e-50 157
Msa0585090 MtrunA17_Chr8g0351751 75.248 101 23 1 1 99 1 101 4.30e-50 159
Msa0585090 MtrunA17_Chr3g0110131 68.182 110 35 0 1 110 1 110 1.88e-46 149
Msa0585090 MtrunA17_Chr2g0296831 72.072 111 31 0 1 111 1 111 3.48e-46 144
Msa0585090 MtrunA17_Chr3g0107381 58.716 109 45 0 1 109 1 109 1.14e-44 144
Msa0585090 MtrunA17_Chr3g0107331 53.704 108 50 0 3 110 2 109 2.90e-39 128
Msa0585090 MtrunA17_Chr5g0432691 51.376 109 53 0 1 109 1 109 4.52e-37 123
Msa0585090 MtrunA17_Chr3g0107341 50.926 108 53 0 3 110 2 109 4.92e-35 117
Msa0585090 MtrunA17_Chr3g0107361 49.074 108 55 0 3 110 2 109 9.06e-35 117
Msa0585090 MtrunA17_Chr5g0420351 49.550 111 55 1 1 111 1 110 1.19e-34 116
Msa0585090 MtrunA17_Chr3g0107351 50.000 108 54 0 3 110 2 109 2.05e-34 116
Msa0585090 MtrunA17_Chr2g0283941 49.541 109 55 0 1 109 1 109 4.07e-33 115
Msa0585090 MtrunA17_Chr3g0107461 44.144 111 62 0 1 111 1 111 1.17e-31 109
Msa0585090 MtrunA17_Chr1g0188681 45.455 110 59 1 1 110 1 109 5.61e-31 107
Msa0585090 MtrunA17_Chr1g0197321 44.144 111 61 1 1 111 1 110 1.65e-30 106
Msa0585090 MtrunA17_Chr1g0197261 45.946 111 59 1 1 111 1 110 2.27e-30 105
Msa0585090 MtrunA17_Chr1g0197461 47.525 101 52 1 3 103 2 101 1.46e-29 103
Msa0585090 MtrunA17_Chr7g0218151 48.649 111 56 1 1 111 1 110 7.24e-29 102
Msa0585090 MtrunA17_Chr1g0188651 50.450 111 54 1 1 111 1 110 6.57e-28 99.8
Msa0585090 MtrunA17_Chr1g0188661 47.273 110 57 1 1 110 1 109 1.30e-27 99.0
Msa0585090 MtrunA17_Chr4g0012761 46.847 111 58 1 1 111 1 110 1.73e-27 98.6
Msa0585090 MtrunA17_Chr1g0193311 48.649 111 56 1 1 111 1 110 2.57e-27 98.2
Msa0585090 MtrunA17_Chr3g0105791 48.148 81 42 0 29 109 1 81 6.30e-25 91.7
Msa0585090 MtrunA17_Chr4g0008701 41.667 108 63 0 3 110 6 113 2.85e-24 95.5
Msa0585090 MtrunA17_Chr7g0267601 41.667 108 63 0 3 110 6 113 5.97e-24 94.7
Msa0585090 MtrunA17_Chr2g0296861 37.895 95 59 0 1 95 1 95 8.19e-23 86.7
Msa0585090 MtrunA17_Chr4g0031421 46.914 81 43 0 29 109 1 81 4.09e-22 84.3
Msa0585090 MtrunA17_Chr3g0128721 37.037 108 68 0 3 110 6 113 4.14e-21 86.7
Msa0585090 MtrunA17_Chr3g0106421 44.444 81 45 0 29 109 1 81 1.95e-19 79.3
Msa0585090 MtrunA17_Chr3g0106501 39.506 81 49 0 29 109 1 81 1.18e-17 73.6
Msa0585090 MtrunA17_Chr6g0449861 37.168 113 64 4 1 107 9 120 1.92e-13 64.7
Msa0585090 MtrunA17_Chr1g0212151 32.743 113 69 3 1 107 1 112 2.45e-13 64.3
Msa0585090 MtrunA17_Chr6g0457851 35.398 113 66 4 1 107 11 122 3.33e-13 63.9
Msa0585090 MtrunA17_Chr6g0449851 36.283 113 65 4 1 107 1 112 1.23e-11 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0585090 AT5G48670.1 60.909 110 43 0 1 110 1 110 2.38e-37 128
Msa0585090 AT1G65300.1 50.476 105 52 0 5 109 4 108 3.11e-34 119
Msa0585090 AT1G65330.1 51.402 107 52 0 3 109 2 108 8.52e-34 118
Msa0585090 AT5G27960.1 51.887 106 51 0 5 110 3 108 1.76e-33 118
Msa0585090 AT5G26650.1 51.887 106 51 0 5 110 3 108 1.88e-33 119
Msa0585090 AT3G05860.2 44.144 111 62 0 1 111 1 111 2.87e-31 110
Msa0585090 AT3G05860.3 44.144 111 62 0 1 111 1 111 1.06e-30 109
Msa0585090 AT3G05860.1 44.144 111 62 0 1 111 1 111 1.64e-30 109
Msa0585090 AT5G27810.1 56.098 82 36 0 29 110 1 82 3.46e-29 102
Msa0585090 AT1G31630.1 43.519 108 60 1 3 110 2 108 1.04e-28 106
Msa0585090 AT1G31640.1 46.296 108 57 1 3 110 2 108 1.29e-28 107
Msa0585090 AT5G26630.1 53.636 110 51 0 1 110 1 110 3.31e-28 102
Msa0585090 AT1G22590.2 40.367 109 65 0 1 109 1 109 1.02e-25 94.7
Msa0585090 AT2G28700.1 40.909 110 65 0 1 110 1 110 1.42e-24 95.1
Msa0585090 AT5G26580.1 41.818 110 50 1 1 110 1 96 1.09e-23 93.2
Msa0585090 AT5G06500.1 37.615 109 64 1 1 109 1 105 2.41e-20 82.8
Msa0585090 AT2G40210.1 38.614 101 62 0 1 101 1 101 3.64e-18 78.6
Msa0585090 AT5G58890.1 42.056 107 53 4 6 105 6 110 1.07e-16 73.6
Msa0585090 AT5G55690.1 44.872 78 36 2 1 71 1 78 6.20e-15 68.9
Msa0585090 AT5G55690.2 44.872 78 36 2 1 71 1 78 6.20e-15 68.9
Msa0585090 AT5G27944.1 38.095 84 48 2 24 103 41 124 8.54e-12 59.7
Msa0585090 AT5G27090.1 34.444 90 58 1 7 95 23 112 1.16e-11 58.9
Msa0585090 AT2G15660.1 32.990 97 50 2 11 106 18 100 1.70e-11 59.3

Find 26 sgRNAs with CRISPR-Local

Find 30 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAGAGACTTTCTTGACAAAA+AGG 0.228423 4_2:+5617206 Msa0585090:CDS
TGAAACAAAGAAAAGATAAT+AGG 0.275750 4_2:+5617254 Msa0585090:CDS
CACAACCATGGCTAGAAATA+AGG 0.308050 4_2:+5616943 None:intergenic
AACGAAGGGTCTATTGAAAA+AGG 0.335070 4_2:+5617021 Msa0585090:CDS
ATGAGCCTCAACCTGAGATT+TGG 0.345571 4_2:+5617101 Msa0585090:CDS
ATCTCAGGTTGAGGCTCATA+AGG 0.373927 4_2:-5617097 None:intergenic
GAAACAAAGAAAAGATAATA+GGG 0.419680 4_2:+5617255 Msa0585090:CDS
TCTGGTGAAGGCCAAATCTC+AGG 0.467267 4_2:-5617112 None:intergenic
CTCATAAGGGCCATACACTA+TGG 0.468858 4_2:-5617083 None:intergenic
TTTAACCTTATTTCTAGCCA+TGG 0.493379 4_2:-5616948 None:intergenic
TCTCAGGTTGAGGCTCATAA+GGG 0.533923 4_2:-5617096 None:intergenic
ACTTGCCTTCATTGTCAATG+AGG 0.536135 4_2:+5616970 Msa0585090:CDS
TCATTGTCAATGAGGCTACA+AGG 0.551605 4_2:+5616978 Msa0585090:CDS
TGTAGCCTCATTGACAATGA+AGG 0.553670 4_2:-5616975 None:intergenic
GAAGCCTGTGCCATAGTGTA+TGG 0.559714 4_2:+5617073 Msa0585090:CDS
GAGATTTGGCCTTCACCAGA+GGG 0.565461 4_2:+5617115 Msa0585090:CDS
GATTTGGCCTTCACCAGAGG+GGG 0.573799 4_2:+5617117 Msa0585090:CDS
GAAGGCCAAATCTCAGGTTG+AGG 0.598100 4_2:-5617106 None:intergenic
ACAGGCTTCAATGCCACAGA+GGG 0.601811 4_2:-5617059 None:intergenic
TGAGATTTGGCCTTCACCAG+AGG 0.614269 4_2:+5617114 Msa0585090:CDS
ATCATACAAGAAAAGAACGA+AGG 0.618898 4_2:+5617006 Msa0585090:CDS
TCATACAAGAAAAGAACGAA+GGG 0.620354 4_2:+5617007 Msa0585090:CDS
AGGGCCATACACTATGGCAC+AGG 0.641363 4_2:-5617077 None:intergenic
AGATTTGGCCTTCACCAGAG+GGG 0.650878 4_2:+5617116 Msa0585090:CDS
GCTGAACTTAGCACCCTCTG+TGG 0.677042 4_2:+5617046 Msa0585090:CDS
CACAGGCTTCAATGCCACAG+AGG 0.696692 4_2:-5617060 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGAAACAAAGAAAAGATAAT+AGG + chr4_2:5617254-5617273 Msa0585090:CDS 20.0%
!! GAAACAAAGAAAAGATAATA+GGG + chr4_2:5617255-5617274 Msa0585090:CDS 20.0%
ATCATACAAGAAAAGAACGA+AGG + chr4_2:5617006-5617025 Msa0585090:CDS 30.0%
TCATACAAGAAAAGAACGAA+GGG + chr4_2:5617007-5617026 Msa0585090:CDS 30.0%
!! TGAATTTTGAGAGAACAGAT+TGG - chr4_2:5617144-5617163 None:intergenic 30.0%
! TTTTTGTCAAGAAAGTCTCT+TGG - chr4_2:5617207-5617226 None:intergenic 30.0%
AAGAGACTTTCTTGACAAAA+AGG + chr4_2:5617206-5617225 Msa0585090:CDS 30.0%
AGAGACTTTCTTGACAAAAA+GGG + chr4_2:5617207-5617226 Msa0585090:CDS 30.0%
AACGAAGGGTCTATTGAAAA+AGG + chr4_2:5617021-5617040 Msa0585090:CDS 35.0%
ACTTGCCTTCATTGTCAATG+AGG + chr4_2:5616970-5616989 Msa0585090:CDS 40.0%
TGTAGCCTCATTGACAATGA+AGG - chr4_2:5616978-5616997 None:intergenic 40.0%
TCATTGTCAATGAGGCTACA+AGG + chr4_2:5616978-5616997 Msa0585090:CDS 40.0%
! CTTGACAAAAAGGGTTCTGA+AGG + chr4_2:5617216-5617235 Msa0585090:CDS 40.0%
CTCATAAGGGCCATACACTA+TGG - chr4_2:5617086-5617105 None:intergenic 45.0%
!! TCTCAGGTTGAGGCTCATAA+GGG - chr4_2:5617099-5617118 None:intergenic 45.0%
!! ATCTCAGGTTGAGGCTCATA+AGG - chr4_2:5617100-5617119 None:intergenic 45.0%
ATGAGCCTCAACCTGAGATT+TGG + chr4_2:5617101-5617120 Msa0585090:CDS 45.0%
ACAGGCTTCAATGCCACAGA+GGG - chr4_2:5617062-5617081 None:intergenic 50.0%
GAAGCCTGTGCCATAGTGTA+TGG + chr4_2:5617073-5617092 Msa0585090:CDS 50.0%
! GAAGGCCAAATCTCAGGTTG+AGG - chr4_2:5617109-5617128 None:intergenic 50.0%
TCTGGTGAAGGCCAAATCTC+AGG - chr4_2:5617115-5617134 None:intergenic 50.0%
! TGAGATTTGGCCTTCACCAG+AGG + chr4_2:5617114-5617133 Msa0585090:CDS 50.0%
! GAGATTTGGCCTTCACCAGA+GGG + chr4_2:5617115-5617134 Msa0585090:CDS 50.0%
! AGATTTGGCCTTCACCAGAG+GGG + chr4_2:5617116-5617135 Msa0585090:CDS 50.0%
GCTGAACTTAGCACCCTCTG+TGG + chr4_2:5617046-5617065 Msa0585090:CDS 55.0%
CACAGGCTTCAATGCCACAG+AGG - chr4_2:5617063-5617082 None:intergenic 55.0%
AGGGCCATACACTATGGCAC+AGG - chr4_2:5617080-5617099 None:intergenic 55.0%
! GATTTGGCCTTCACCAGAGG+GGG + chr4_2:5617117-5617136 Msa0585090:CDS 55.0%
AGAACAGATTGGACCCCCTC+TGG - chr4_2:5617133-5617152 None:intergenic 55.0%
GATTGGACCCCCTCTGGTGA+AGG - chr4_2:5617127-5617146 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 5616950 5617285 5616950 ID=Msa0585090;Name=Msa0585090
chr4_2 mRNA 5616950 5617285 5616950 ID=Msa0585090-mRNA-1;Parent=Msa0585090;Name=Msa0585090-mRNA-1;_AED=0.42;_eAED=0.42;_QI=0|-1|0|1|-1|1|1|0|111
chr4_2 exon 5616950 5617285 5616950 ID=Msa0585090-mRNA-1:exon:1359;Parent=Msa0585090-mRNA-1
chr4_2 CDS 5616950 5617285 5616950 ID=Msa0585090-mRNA-1:cds;Parent=Msa0585090-mRNA-1
Gene Sequence

>Msa0585090

ATGGCTAGAAATAAGGTTAAACTTGCCTTCATTGTCAATGAGGCTACAAGGAAAGCATCATACAAGAAAAGAACGAAGGGTCTATTGAAAAAGGTTGCTGAACTTAGCACCCTCTGTGGCATTGAAGCCTGTGCCATAGTGTATGGCCCTTATGAGCCTCAACCTGAGATTTGGCCTTCACCAGAGGGGGTCCAATCTGTTCTCTCAAAATTCATGACGATGCACGAGTTTCAAAAGTGCAAGAAAATGATGAACCAAGAGACTTTCTTGACAAAAAGGGTTCTGAAGGCTGAAGAGAAATTGATGAAACAAAGAAAAGATAATAGGGAGCAATAG
Protein sequence

>Msa0585090

MARNKVKLAFIVNEATRKASYKKRTKGLLKKVAELSTLCGIEACAIVYGPYEPQPEIWPSPEGVQSVLSKFMTMHEFQKCKKMMNQETFLTKRVLKAEEKLMKQRKDNREQ*