AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0868730

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0868730 MtrunA17_Chr6g0449641 99.310 145 1 0 1 145 1 145 1.38e-106 300
Msa0868730 MtrunA17_Chr6g0449651 92.143 140 11 0 1 140 59 198 9.60e-95 272
Msa0868730 MtrunA17_Chr7g0227511 68.675 166 32 4 2 149 4 167 7.45e-72 213
Msa0868730 MtrunA17_Chr3g0117121 64.151 159 30 2 1 132 1 159 8.67e-66 198
Msa0868730 MtrunA17_Chr4g0058651 83.810 105 17 0 7 111 9 113 3.35e-64 194
Msa0868730 MtrunA17_Chr4g0043421 56.522 138 56 3 8 141 14 151 1.11e-49 157
Msa0868730 MtrunA17_Chr2g0311601 61.607 112 42 1 8 118 12 123 2.86e-49 155
Msa0868730 MtrunA17_Chr5g0437571 57.377 122 52 0 7 128 4 125 8.94e-49 154
Msa0868730 MtrunA17_Chr5g0402611 67.290 107 35 0 3 109 2 108 1.21e-48 159
Msa0868730 MtrunA17_Chr8g0353981 69.643 112 32 1 1 112 1 110 6.13e-48 154
Msa0868730 MtrunA17_Chr3g0115431 66.972 109 36 0 1 109 1 109 8.19e-48 154
Msa0868730 MtrunA17_Chr3g0114061 51.613 155 65 4 6 151 5 158 1.07e-46 149
Msa0868730 MtrunA17_Chr3g0097221 65.455 110 38 0 4 113 2 111 1.30e-46 153
Msa0868730 MtrunA17_Chr3g0106101 56.637 113 49 0 7 119 5 117 7.14e-46 147
Msa0868730 MtrunA17_Chr5g0437401 64.151 106 38 0 6 111 8 113 1.80e-44 144
Msa0868730 MtrunA17_Chr3g0113891 68.041 97 31 0 6 102 11 107 5.80e-44 143
Msa0868730 MtrunA17_Chr5g0438091 60.577 104 41 0 6 109 36 139 9.64e-43 140
Msa0868730 MtrunA17_Chr3g0129071 59.615 104 42 0 8 111 46 149 2.79e-42 140
Msa0868730 MtrunA17_Chr4g0030001 47.015 134 70 1 8 140 23 156 3.77e-40 133
Msa0868730 MtrunA17_Chr1g0200201 51.327 113 55 0 10 122 73 185 1.20e-38 130
Msa0868730 MtrunA17_Chr5g0432451 56.637 113 49 0 8 120 42 154 2.24e-38 130
Msa0868730 MtrunA17_Chr7g0260971 56.881 109 46 1 2 109 7 115 1.19e-37 127
Msa0868730 MtrunA17_Chr1g0184281 49.296 142 64 4 6 139 12 153 1.20e-36 125
Msa0868730 MtrunA17_Chr8g0351701 55.882 102 44 1 9 109 23 124 1.87e-34 120
Msa0868730 MtrunA17_Chr8g0351721 54.717 106 47 1 9 113 18 123 4.09e-34 119
Msa0868730 MtrunA17_Chr7g0245871 58.947 95 38 1 9 102 27 121 6.05e-34 119
Msa0868730 MtrunA17_Chr6g0460951 48.276 116 57 2 8 120 39 154 1.33e-33 117
Msa0868730 MtrunA17_Chr7g0225111 48.039 102 53 0 8 109 4 105 3.75e-32 110
Msa0868730 MtrunA17_Chr5g0435641 52.577 97 45 1 8 103 6 102 4.10e-32 113
Msa0868730 MtrunA17_Chr8g0374601 49.074 108 54 1 9 115 26 133 1.42e-31 114
Msa0868730 MtrunA17_Chr7g0261031 54.082 98 44 1 6 102 5 102 2.30e-31 112
Msa0868730 MtrunA17_Chr5g0444351 48.113 106 48 1 10 115 6 104 7.19e-31 108
Msa0868730 MtrunA17_Chr1g0184271 51.579 95 45 1 9 102 12 106 2.01e-30 109
Msa0868730 MtrunA17_Chr8g0374591 43.689 103 58 0 9 111 8 110 5.61e-28 100
Msa0868730 MtrunA17_Chr6g0452661 45.918 98 52 1 7 103 7 104 7.35e-28 103
Msa0868730 MtrunA17_Chr7g0245861 54.348 92 39 2 7 95 10 101 7.56e-28 100
Msa0868730 MtrunA17_Chr4g0059901 47.000 100 53 0 10 109 11 110 1.04e-27 103
Msa0868730 MtrunA17_Chr8g0374581 47.115 104 54 1 9 111 8 111 2.38e-26 99.4
Msa0868730 MtrunA17_Chr6g0460941 48.864 88 44 1 9 95 7 94 7.35e-26 94.0
Msa0868730 MtrunA17_Chr6g0452671 41.000 100 59 0 6 105 8 107 1.70e-25 96.3
Msa0868730 MtrunA17_Chr6g0452691 42.857 105 59 1 6 109 6 110 1.38e-24 93.6
Msa0868730 MtrunA17_Chr2g0330201 42.000 100 58 0 6 105 16 115 7.66e-24 94.0
Msa0868730 MtrunA17_Chr8g0342351 40.385 104 62 0 6 109 9 112 9.71e-24 93.2
Msa0868730 MtrunA17_Chr4g0040831 41.935 93 54 0 10 102 16 108 1.84e-21 85.9
Msa0868730 MtrunA17_Chr2g0326041 58.621 58 24 0 1 58 25 82 4.22e-21 81.6
Msa0868730 MtrunA17_Chr4g0055441 40.000 95 56 1 10 103 3 97 4.37e-21 83.6
Msa0868730 MtrunA17_Chr5g0439111 41.837 98 56 1 7 103 7 104 1.59e-20 84.0
Msa0868730 MtrunA17_Chr2g0326051 50.725 69 34 0 54 122 5 73 1.41e-16 71.2
Msa0868730 MtrunA17_Chr4g0046201 31.111 90 62 0 8 97 5 94 2.55e-15 70.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0868730 AT3G27650.1 76.423 123 25 1 3 121 33 155 2.47e-67 201
Msa0868730 AT5G63090.4 75.591 127 29 1 1 125 1 127 9.81e-65 196
Msa0868730 AT5G63090.3 75.591 127 29 1 1 125 1 127 9.81e-65 196
Msa0868730 AT5G63090.2 75.591 127 29 1 1 125 1 127 9.81e-65 196
Msa0868730 AT5G63090.1 75.591 127 29 1 1 125 1 127 9.81e-65 196
Msa0868730 AT2G30130.1 60.169 118 47 0 7 124 6 123 1.77e-49 157
Msa0868730 AT1G65620.1 66.379 116 39 0 1 116 1 116 2.14e-48 155
Msa0868730 AT1G65620.4 66.379 116 39 0 1 116 1 116 2.14e-48 155
Msa0868730 AT1G65620.3 66.379 116 39 0 1 116 1 116 2.14e-48 155
Msa0868730 AT1G65620.5 66.379 116 39 0 1 116 1 116 2.14e-48 155
Msa0868730 AT1G65620.2 66.379 116 39 0 1 116 1 116 2.14e-48 155
Msa0868730 AT5G66870.1 66.055 109 35 1 1 109 1 107 5.20e-48 157
Msa0868730 AT2G23660.2 64.762 105 37 0 6 110 2 106 7.69e-48 157
Msa0868730 AT2G23660.3 64.762 105 37 0 6 110 2 106 7.69e-48 157
Msa0868730 AT2G23660.1 64.762 105 37 0 6 110 2 106 7.69e-48 157
Msa0868730 AT1G31320.1 69.318 88 27 0 8 95 12 99 7.74e-44 142
Msa0868730 AT1G07900.1 54.783 115 52 0 8 122 32 146 1.36e-43 142
Msa0868730 AT2G30340.1 55.752 113 50 0 8 120 51 163 1.98e-43 144
Msa0868730 AT2G30340.2 55.752 113 50 0 8 120 52 164 1.98e-43 144
Msa0868730 AT1G16530.1 62.617 107 39 1 8 113 13 119 3.02e-43 140
Msa0868730 AT2G28500.1 55.652 115 51 0 8 122 54 168 1.11e-42 141
Msa0868730 AT3G11090.1 58.559 111 44 1 6 116 8 116 1.31e-41 136
Msa0868730 AT2G40470.2 60.185 108 43 0 8 115 19 126 1.26e-40 135
Msa0868730 AT2G40470.1 60.185 108 43 0 8 115 44 151 2.54e-40 135
Msa0868730 AT3G26660.1 55.000 100 45 0 10 109 6 105 2.03e-38 127
Msa0868730 AT3G26620.1 55.000 100 45 0 10 109 6 105 2.24e-38 127
Msa0868730 AT2G42430.1 52.500 120 54 2 6 124 12 129 1.08e-35 124
Msa0868730 AT3G03760.1 54.808 104 46 1 8 110 50 153 2.04e-35 124
Msa0868730 AT4G00220.1 56.311 103 44 1 12 113 20 122 4.97e-34 119
Msa0868730 AT5G06080.1 54.639 97 43 1 8 103 6 102 1.89e-33 116
Msa0868730 AT4G00210.1 54.717 106 47 1 9 113 11 116 2.07e-33 117
Msa0868730 AT2G45420.1 55.340 103 45 1 12 113 40 142 5.52e-33 117
Msa0868730 AT3G58190.1 52.083 96 45 1 9 103 11 106 2.57e-31 112
Msa0868730 AT2G31310.1 52.083 96 45 1 8 102 6 101 2.72e-31 111
Msa0868730 AT2G45410.1 56.566 99 42 1 12 109 19 117 3.66e-31 110
Msa0868730 AT2G42440.1 49.495 99 49 1 6 103 4 102 9.33e-31 111
Msa0868730 AT3G50510.1 46.602 103 55 0 7 109 10 112 1.00e-29 107
Msa0868730 AT3G50510.2 46.602 103 55 0 7 109 10 112 1.00e-29 107
Msa0868730 AT3G13850.1 43.617 94 53 0 10 103 37 130 3.07e-25 97.4
Msa0868730 AT5G35900.1 45.000 100 55 0 10 109 6 105 3.69e-25 95.9
Msa0868730 AT3G47870.1 39.423 104 63 0 6 109 33 136 1.00e-24 97.4
Msa0868730 AT1G72980.1 41.346 104 61 0 6 109 10 113 2.10e-22 89.0
Msa0868730 AT1G06280.1 45.161 93 50 1 10 102 25 116 5.12e-21 85.1
Msa0868730 AT4G22700.1 34.921 126 71 4 10 134 6 121 6.84e-17 73.9
Msa0868730 AT2G19820.1 38.542 96 57 2 6 100 9 103 2.36e-16 70.9
Msa0868730 AT5G15060.1 36.986 73 44 1 10 80 18 90 1.22e-12 61.6

Find 25 sgRNAs with CRISPR-Local

Find 26 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCAAATGTTCACAAAATATT+TGG 0.192290 6_1:+2476666 Msa0868730:CDS
GCAAACTTATGAGGCTCTTC+TGG 0.277156 6_1:-2476645 None:intergenic
GGCTCTTCTGGTGGGAAATA+AGG 0.304156 6_1:-2476633 None:intergenic
GGTTCTTCTTCTCTTGGTCT+TGG 0.305065 6_1:+2476897 Msa0868730:CDS
CATCAAGGTTCTTCTTCTCT+TGG 0.331910 6_1:+2476891 Msa0868730:CDS
TTATATATCACCTTTGTTGT+AGG 0.350339 6_1:-2476985 None:intergenic
TGAACATTTGCAAACTTATG+AGG 0.383834 6_1:-2476654 None:intergenic
GAATCATTGCTCAAATTAGA+TGG 0.418926 6_1:-2476951 None:intergenic
CTTGGACATGTTCATTCTGA+TGG 0.439607 6_1:+2476915 Msa0868730:CDS
ATGATTTAAGCGAATCAAAT+CGG 0.450299 6_1:-2476871 None:intergenic
ATTTGAGCAATGATTCTTGT+GGG 0.463152 6_1:+2476958 Msa0868730:CDS
TTGATTCGCTTAAATCATCA+AGG 0.486236 6_1:+2476876 Msa0868730:CDS
ACAACTCATTAAGCTTCAAA+AGG 0.501141 6_1:+2476830 Msa0868730:CDS
TGTGGGGATTCCTACAACAA+AGG 0.509877 6_1:+2476975 Msa0868730:CDS
AGGATTAAAGATCCAGTGTA+TGG 0.525146 6_1:+2476777 Msa0868730:CDS
AACTTATGAGGCTCTTCTGG+TGG 0.540828 6_1:-2476642 None:intergenic
AATTTGAGCAATGATTCTTG+TGG 0.553273 6_1:+2476957 Msa0868730:CDS
ACTGTATCTTCTCTTTGATG+AGG 0.567592 6_1:-2476726 None:intergenic
GATCCAGTGTATGGTTGTGT+TGG 0.578362 6_1:+2476786 Msa0868730:CDS
AGAAACTTGCAAGCAGCACA+TGG 0.591215 6_1:-2476576 None:intergenic
ACTTATGAGGCTCTTCTGGT+GGG 0.610191 6_1:-2476641 None:intergenic
TTTGAGCAATGATTCTTGTG+GGG 0.613138 6_1:+2476959 Msa0868730:CDS
TAGCTTATGAAGCTGAAGCA+AGG 0.625096 6_1:+2476757 Msa0868730:CDS
TGGAGAATTTGAGTAGCTTG+AGG 0.626001 6_1:-2476556 None:intergenic
GCTCCAACACAACCATACAC+TGG 0.629286 6_1:-2476789 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! GCAAATGTTCACAAAATATT+TGG + chr6_1:2476666-2476685 Msa0868730:CDS 25.0%
! ATGATTTAAGCGAATCAAAT+CGG - chr6_1:2476874-2476893 None:intergenic 25.0%
!! TTATATATCACCTTTGTTGT+AGG - chr6_1:2476988-2477007 None:intergenic 25.0%
TGAACATTTGCAAACTTATG+AGG - chr6_1:2476657-2476676 None:intergenic 30.0%
ACAACTCATTAAGCTTCAAA+AGG + chr6_1:2476830-2476849 Msa0868730:CDS 30.0%
! TTGATTCGCTTAAATCATCA+AGG + chr6_1:2476876-2476895 Msa0868730:CDS 30.0%
GAATCATTGCTCAAATTAGA+TGG - chr6_1:2476954-2476973 None:intergenic 30.0%
AATTTGAGCAATGATTCTTG+TGG + chr6_1:2476957-2476976 Msa0868730:CDS 30.0%
ATTTGAGCAATGATTCTTGT+GGG + chr6_1:2476958-2476977 Msa0868730:CDS 30.0%
AAGGTGCAAAAATGCAATCT+TGG - chr6_1:2476617-2476636 None:intergenic 35.0%
ACTGTATCTTCTCTTTGATG+AGG - chr6_1:2476729-2476748 None:intergenic 35.0%
AGGATTAAAGATCCAGTGTA+TGG + chr6_1:2476777-2476796 Msa0868730:CDS 35.0%
TTTGAGCAATGATTCTTGTG+GGG + chr6_1:2476959-2476978 Msa0868730:CDS 35.0%
TGGAGAATTTGAGTAGCTTG+AGG - chr6_1:2476559-2476578 None:intergenic 40.0%
TAGCTTATGAAGCTGAAGCA+AGG + chr6_1:2476757-2476776 Msa0868730:CDS 40.0%
CATCAAGGTTCTTCTTCTCT+TGG + chr6_1:2476891-2476910 Msa0868730:CDS 40.0%
CTTGGACATGTTCATTCTGA+TGG + chr6_1:2476915-2476934 Msa0868730:CDS 40.0%
AGAAACTTGCAAGCAGCACA+TGG - chr6_1:2476579-2476598 None:intergenic 45.0%
ACTTATGAGGCTCTTCTGGT+GGG - chr6_1:2476644-2476663 None:intergenic 45.0%
AACTTATGAGGCTCTTCTGG+TGG - chr6_1:2476645-2476664 None:intergenic 45.0%
GCAAACTTATGAGGCTCTTC+TGG - chr6_1:2476648-2476667 None:intergenic 45.0%
GATCCAGTGTATGGTTGTGT+TGG + chr6_1:2476786-2476805 Msa0868730:CDS 45.0%
GGTTCTTCTTCTCTTGGTCT+TGG + chr6_1:2476897-2476916 Msa0868730:CDS 45.0%
TGTGGGGATTCCTACAACAA+AGG + chr6_1:2476975-2476994 Msa0868730:CDS 45.0%
GGCTCTTCTGGTGGGAAATA+AGG - chr6_1:2476636-2476655 None:intergenic 50.0%
GCTCCAACACAACCATACAC+TGG - chr6_1:2476792-2476811 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr6_1 gene 2476552 2477007 2476552 ID=Msa0868730;Name=Msa0868730
chr6_1 mRNA 2476552 2477007 2476552 ID=Msa0868730-mRNA-1;Parent=Msa0868730;Name=Msa0868730-mRNA-1;_AED=0.30;_eAED=0.30;_QI=0|-1|0|1|-1|1|1|0|151
chr6_1 exon 2476552 2477007 2476552 ID=Msa0868730-mRNA-1:exon:708;Parent=Msa0868730-mRNA-1
chr6_1 CDS 2476552 2477007 2476552 ID=Msa0868730-mRNA-1:cds;Parent=Msa0868730-mRNA-1
Gene Sequence

>Msa0868730

ATGGCCTCAAGCTACTCAAATTCTCCATGTGCTGCTTGCAAGTTTCTAAGAAGAAAATGCAACCAAGATTGCATTTTTGCACCTTATTTCCCACCAGAAGAGCCTCATAAGTTTGCAAATGTTCACAAAATATTTGGTGCAAGCAATGTTAGCAAAATTCTTAATGAAGTTTTACCTCATCAAAGAGAAGATACAGTGAATTCTCTAGCTTATGAAGCTGAAGCAAGGATTAAAGATCCAGTGTATGGTTGTGTTGGAGCTATTTCAGTGCTTCAAAGACAACTCATTAAGCTTCAAAAGGAACTTGATGCTACAAATGCCGATTTGATTCGCTTAAATCATCAAGGTTCTTCTTCTCTTGGTCTTGGACATGTTCATTCTGATGGTTTTTTTAATTGTCCATCTAATTTGAGCAATGATTCTTGTGGGGATTCCTACAACAAAGGTGATATATAA
Protein sequence

>Msa0868730

MASSYSNSPCAACKFLRRKCNQDCIFAPYFPPEEPHKFANVHKIFGASNVSKILNEVLPHQREDTVNSLAYEAEARIKDPVYGCVGAISVLQRQLIKLQKELDATNADLIRLNHQGSSSLGLGHVHSDGFFNCPSNLSNDSCGDSYNKGDI*