AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene054730

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene054730.t1 MTR_3g101810 95.604 273 9 3 1 272 1 271 0.0 521
MS.gene054730.t1 MTR_5g017210 61.491 161 57 3 91 250 56 212 6.54e-48 159
MS.gene054730.t1 MTR_8g093500 76.923 91 21 0 146 236 87 177 1.92e-46 157
MS.gene054730.t1 MTR_2g100490 63.441 93 33 1 145 236 261 353 1.71e-27 109
MS.gene054730.t1 MTR_8g015450 56.311 103 41 1 145 243 296 398 4.12e-27 109
MS.gene054730.t1 MTR_7g069590 68.519 54 17 0 179 232 32 85 1.89e-21 88.2
MS.gene054730.t1 MTR_5g079500 62.500 56 21 0 180 235 225 280 1.94e-18 83.6
MS.gene054730.t1 MTR_1g018090 62.963 54 20 0 182 235 283 336 1.17e-17 82.0
MS.gene054730.t1 MTR_1g106460 50.746 67 33 0 169 235 234 300 2.32e-17 80.9
MS.gene054730.t1 MTR_5g005110 61.111 54 21 0 182 235 233 286 5.65e-17 79.7
MS.gene054730.t1 MTR_1g106470 46.914 81 43 0 182 262 205 285 7.11e-17 79.0
MS.gene054730.t1 MTR_3g103030 53.968 63 29 0 173 235 229 291 5.89e-16 76.6
MS.gene054730.t1 MTR_4g131160 55.385 65 28 1 180 243 203 267 1.07e-14 73.6
MS.gene054730.t1 MTR_4g131160 55.385 65 28 1 180 243 206 270 1.13e-14 73.6
MS.gene054730.t1 MTR_1g080890 46.835 79 41 1 166 243 186 264 1.89e-14 72.8
MS.gene054730.t1 MTR_1g106480 58.000 50 21 0 186 235 82 131 1.66e-13 67.0
MS.gene054730.t1 MTR_2g067000 49.333 75 31 1 169 236 146 220 2.94e-13 68.9
MS.gene054730.t1 MTR_1g060700 57.407 54 23 0 183 236 357 410 2.46e-12 67.0
MS.gene054730.t1 MTR_4g033295 56.140 57 24 1 183 238 128 184 9.32e-12 63.2
MS.gene054730.t1 MTR_2g089070 51.852 54 26 0 183 236 146 199 1.82e-11 63.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene054730.t1 AT3G50330 73.016 126 26 3 136 254 77 201 5.76e-47 157
MS.gene054730.t1 AT5G67060 87.234 94 12 0 146 239 83 176 3.32e-46 155
MS.gene054730.t1 AT5G67060 87.234 94 12 0 146 239 95 188 4.51e-46 155
MS.gene054730.t1 AT4G00120 69.663 89 27 0 148 236 87 175 2.40e-37 131
MS.gene054730.t1 AT3G21330 65.217 92 32 0 145 236 241 332 1.12e-36 134
MS.gene054730.t1 AT5G09750 75.556 90 22 0 146 235 92 181 2.25e-34 124
MS.gene054730.t1 AT5G01305 56.579 76 33 0 174 249 38 113 1.89e-21 89.0
MS.gene054730.t1 AT5G43175 50.725 69 34 0 167 235 126 194 1.37e-18 82.4
MS.gene054730.t1 AT4G33880 64.815 54 19 0 182 235 275 328 2.11e-18 84.0
MS.gene054730.t1 AT5G37800 53.333 75 28 1 168 235 189 263 3.86e-18 82.8
MS.gene054730.t1 AT1G27740 52.941 68 32 0 168 235 162 229 4.87e-18 81.6
MS.gene054730.t1 AT1G66470 63.636 55 20 0 181 235 203 257 7.76e-18 81.6
MS.gene054730.t1 AT2G14760 62.963 54 20 0 182 235 246 299 2.43e-17 80.9
MS.gene054730.t1 AT4G30980 54.054 74 33 1 170 242 127 200 6.15e-16 76.6
MS.gene054730.t1 AT2G24260 53.165 79 29 3 171 242 28 105 7.10e-16 75.5
MS.gene054730.t1 AT4G30980 53.333 75 34 1 169 242 174 248 1.16e-15 76.3
MS.gene054730.t1 AT2G24260 53.165 79 29 3 171 242 131 208 1.74e-15 75.9
MS.gene054730.t1 AT5G58010 50.000 76 37 1 170 244 96 171 2.13e-14 72.0
MS.gene054730.t1 AT2G14760 50.746 67 20 1 182 235 246 312 4.54e-14 71.6

Find 52 sgRNAs with CRISPR-Local

Find 57 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACAGTTGCTGGTTCAGGATT+AGG 0.247420 5.3:-33100257 MS.gene054730:CDS
GATTCTGGGTCTATGTAAAT+TGG 0.284997 5.3:+33100515 None:intergenic
CCGTTAGATGAAGAAAATTC+AGG 0.301231 5.3:+33100914 None:intergenic
GATCGTAATGTTGATCGTTA+TGG 0.304956 5.3:-33100203 MS.gene054730:CDS
TGTTGTTGTTGGAACATTAA+TGG 0.311513 5.3:+33100677 None:intergenic
AACAGGACAGTTGCTGGTTC+AGG 0.321831 5.3:-33100263 MS.gene054730:CDS
CAGTTGCTGGTTCAGGATTA+GGG 0.322129 5.3:-33100256 MS.gene054730:CDS
AGAGATTGTGTTTGTGTTTG+TGG 0.340639 5.3:+33100724 None:intergenic
TCACTGCAGGAACGTGCTTC+AGG 0.355705 5.3:-33100296 MS.gene054730:CDS
TAAGGCTTAGGCAATGAAAC+AGG 0.373028 5.3:+33100230 None:intergenic
CTTCAGGAGCCAACAATAAC+AGG 0.382936 5.3:-33100280 MS.gene054730:CDS
CTCGAATTAGAAAATATTAA+CGG 0.384561 5.3:+33100647 None:intergenic
GAAGACCATGGTATTGGATT+AGG 0.391268 5.3:+33100782 None:intergenic
AACAATAACAGGACAGTTGC+TGG 0.393832 5.3:-33100269 MS.gene054730:CDS
TGGTGTAGTAGAGTTGTTAT+TGG 0.394604 5.3:+33100697 None:intergenic
ATCGTAATGTTGATCGTTAT+GGG 0.398296 5.3:-33100202 MS.gene054730:CDS
ATGATGAAGATGACTTTAAC+TGG 0.403724 5.3:+33100984 None:intergenic
ACGGTGTTGTTTGTTGTTGT+TGG 0.421243 5.3:+33100666 None:intergenic
AACGATCAACATTACGATCT+TGG 0.428866 5.3:+33100207 None:intergenic
AGCAACTGTCCTGTTATTGT+TGG 0.439967 5.3:+33100271 None:intergenic
GACCATGGTATTGGATTAGG+AGG 0.459342 5.3:+33100785 None:intergenic
GAAGATGAAGACCATGGTAT+TGG 0.485579 5.3:+33100776 None:intergenic
GCTCAGAATACGAACCATTA+CGG 0.497476 5.3:-33100614 MS.gene054730:CDS
CGTTAGATGAAGAAAATTCA+GGG 0.499125 5.3:+33100915 None:intergenic
GTGTTTGTGGTGGATTGTGA+AGG 0.504020 5.3:+33100737 None:intergenic
AAACTCGATGGCGGCGATGA+GGG 0.510188 5.3:-33100567 MS.gene054730:CDS
AATAAGAATACTGCAAAGAA+TGG 0.517132 5.3:-33100402 MS.gene054730:CDS
GGTACCAGGTGGAACTAAGA+TGG 0.521420 5.3:-33100381 MS.gene054730:CDS
ATCGAGTTTCTCTTCTCAGA+TGG 0.533422 5.3:+33100581 None:intergenic
TGACGGTGGAAATTGATTGA+TGG 0.535291 5.3:+33100877 None:intergenic
GATTGTGTTTGTGTTTGTGG+TGG 0.537734 5.3:+33100727 None:intergenic
TTACGATCTTGGTAAGGCTT+AGG 0.545623 5.3:+33100218 None:intergenic
ATGGCAACGCAGTACCGTAA+TGG 0.563985 5.3:+33100600 None:intergenic
GATGGATACTGCATCAATGT+TGG 0.564818 5.3:-33100363 MS.gene054730:CDS
TGGAAATTGATTGATGGTGT+TGG 0.574025 5.3:+33100883 None:intergenic
TCATAGAATTGTTGATCTGA+CGG 0.575452 5.3:+33100860 None:intergenic
TCAACATTACGATCTTGGTA+AGG 0.575828 5.3:+33100212 None:intergenic
GACACAACTTAAGTCACTGC+AGG 0.578655 5.3:-33100309 MS.gene054730:CDS
GAAACTCGATGGCGGCGATG+AGG 0.584557 5.3:-33100568 MS.gene054730:CDS
ATCTGAGAAGAGAAACTCGA+TGG 0.628326 5.3:-33100579 MS.gene054730:CDS
GTCATCTTCATCATCATCAG+AGG 0.630073 5.3:-33100975 MS.gene054730:CDS
TTATCTATTAAATCTGCAAG+AGG 0.636966 5.3:+33100809 None:intergenic
GTATCCATCTTAGTTCCACC+TGG 0.642640 5.3:+33100377 None:intergenic
AAGGCTTAGGCAATGAAACA+GGG 0.655130 5.3:+33100231 None:intergenic
ACCATGGTATTGGATTAGGA+GGG 0.660517 5.3:+33100786 None:intergenic
TAGAATTGTTGATCTGACGG+TGG 0.670211 5.3:+33100863 None:intergenic
ATACTGCAAAGAATGGTACC+AGG 0.680757 5.3:-33100395 MS.gene054730:CDS
TGAGAAGAGAAACTCGATGG+CGG 0.685272 5.3:-33100576 MS.gene054730:CDS
ACCCTCCTAATCCAATACCA+TGG 0.687624 5.3:-33100787 MS.gene054730:CDS
TGTCTAGCTGCAATACTCTG+AGG 0.695596 5.3:+33100449 None:intergenic
CTGCAAAGAATGGTACCAGG+TGG 0.704915 5.3:-33100392 MS.gene054730:CDS
AATGATGAAGATGAAGACCA+TGG 0.757666 5.3:+33100770 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CTCGAATTAGAAAATATTAA+CGG + chr5.3:33100550-33100569 None:intergenic 20.0%
! AATAAGAATACTGCAAAGAA+TGG - chr5.3:33100792-33100811 MS.gene054730:CDS 25.0%
! TTATCTATTAAATCTGCAAG+AGG + chr5.3:33100388-33100407 None:intergenic 25.0%
ATCGTAATGTTGATCGTTAT+GGG - chr5.3:33100992-33101011 MS.gene054730:CDS 30.0%
ATGATGAAGATGACTTTAAC+TGG + chr5.3:33100213-33100232 None:intergenic 30.0%
CGTTAGATGAAGAAAATTCA+GGG + chr5.3:33100282-33100301 None:intergenic 30.0%
TCATAGAATTGTTGATCTGA+CGG + chr5.3:33100337-33100356 None:intergenic 30.0%
! ATCTTCACGTTTCTTCTTTT+TGG + chr5.3:33100715-33100734 None:intergenic 30.0%
! CCTGAATTTTCTTCATCTAA+CGG - chr5.3:33100280-33100299 MS.gene054730:CDS 30.0%
! TGTTGTTGTTGGAACATTAA+TGG + chr5.3:33100520-33100539 None:intergenic 30.0%
AACGATCAACATTACGATCT+TGG + chr5.3:33100990-33101009 None:intergenic 35.0%
AATGATGAAGATGAAGACCA+TGG + chr5.3:33100427-33100446 None:intergenic 35.0%
AGAGATTGTGTTTGTGTTTG+TGG + chr5.3:33100473-33100492 None:intergenic 35.0%
CCGTTAGATGAAGAAAATTC+AGG + chr5.3:33100283-33100302 None:intergenic 35.0%
GATCGTAATGTTGATCGTTA+TGG - chr5.3:33100991-33101010 MS.gene054730:CDS 35.0%
GATTCTGGGTCTATGTAAAT+TGG + chr5.3:33100682-33100701 None:intergenic 35.0%
TCAACATTACGATCTTGGTA+AGG + chr5.3:33100985-33101004 None:intergenic 35.0%
TGGTGTAGTAGAGTTGTTAT+TGG + chr5.3:33100500-33100519 None:intergenic 35.0%
! TTCACGTTTCTTCTTTTTGG+TGG + chr5.3:33100712-33100731 None:intergenic 35.0%
!! TGGAAATTGATTGATGGTGT+TGG + chr5.3:33100314-33100333 None:intergenic 35.0%
!!! TTGGTGGTTTTACTGATTCT+GGG + chr5.3:33100696-33100715 None:intergenic 35.0%
!!! TTTGGTGGTTTTACTGATTC+TGG + chr5.3:33100697-33100716 None:intergenic 35.0%
AACAATAACAGGACAGTTGC+TGG - chr5.3:33100925-33100944 MS.gene054730:CDS 40.0%
AAGGCTTAGGCAATGAAACA+GGG + chr5.3:33100966-33100985 None:intergenic 40.0%
AGCAACTGTCCTGTTATTGT+TGG + chr5.3:33100926-33100945 None:intergenic 40.0%
ATACTGCAAAGAATGGTACC+AGG - chr5.3:33100799-33100818 MS.gene054730:CDS 40.0%
ATCGAGTTTCTCTTCTCAGA+TGG + chr5.3:33100616-33100635 None:intergenic 40.0%
ATCTGAGAAGAGAAACTCGA+TGG - chr5.3:33100615-33100634 MS.gene054730:CDS 40.0%
GAAGATGAAGACCATGGTAT+TGG + chr5.3:33100421-33100440 None:intergenic 40.0%
GATGGATACTGCATCAATGT+TGG - chr5.3:33100831-33100850 MS.gene054730:CDS 40.0%
GATTGTGTTTGTGTTTGTGG+TGG + chr5.3:33100470-33100489 None:intergenic 40.0%
GCTCAGAATACGAACCATTA+CGG - chr5.3:33100580-33100599 MS.gene054730:CDS 40.0%
GTCATCTTCATCATCATCAG+AGG - chr5.3:33100219-33100238 MS.gene054730:CDS 40.0%
TAAGGCTTAGGCAATGAAAC+AGG + chr5.3:33100967-33100986 None:intergenic 40.0%
TAGAATTGTTGATCTGACGG+TGG + chr5.3:33100334-33100353 None:intergenic 40.0%
TGACGGTGGAAATTGATTGA+TGG + chr5.3:33100320-33100339 None:intergenic 40.0%
TTACGATCTTGGTAAGGCTT+AGG + chr5.3:33100979-33100998 None:intergenic 40.0%
! ACCATGGTATTGGATTAGGA+GGG + chr5.3:33100411-33100430 None:intergenic 40.0%
! GAAGACCATGGTATTGGATT+AGG + chr5.3:33100415-33100434 None:intergenic 40.0%
!! ACGGTGTTGTTTGTTGTTGT+TGG + chr5.3:33100531-33100550 None:intergenic 40.0%
ACCCTCCTAATCCAATACCA+TGG - chr5.3:33100407-33100426 MS.gene054730:CDS 45.0%
CTTCAGGAGCCAACAATAAC+AGG - chr5.3:33100914-33100933 MS.gene054730:CDS 45.0%
GACACAACTTAAGTCACTGC+AGG - chr5.3:33100885-33100904 MS.gene054730:CDS 45.0%
GTATCCATCTTAGTTCCACC+TGG + chr5.3:33100820-33100839 None:intergenic 45.0%
TGAGAAGAGAAACTCGATGG+CGG - chr5.3:33100618-33100637 MS.gene054730:CDS 45.0%
TGTCTAGCTGCAATACTCTG+AGG + chr5.3:33100748-33100767 None:intergenic 45.0%
! GACCATGGTATTGGATTAGG+AGG + chr5.3:33100412-33100431 None:intergenic 45.0%
!! ACAGTTGCTGGTTCAGGATT+AGG - chr5.3:33100937-33100956 MS.gene054730:CDS 45.0%
!! CAGTTGCTGGTTCAGGATTA+GGG - chr5.3:33100938-33100957 MS.gene054730:CDS 45.0%
!! GTGTTTGTGGTGGATTGTGA+AGG + chr5.3:33100460-33100479 None:intergenic 45.0%
ATGGCAACGCAGTACCGTAA+TGG + chr5.3:33100597-33100616 None:intergenic 50.0%
CTGCAAAGAATGGTACCAGG+TGG - chr5.3:33100802-33100821 MS.gene054730:CDS 50.0%
GGTACCAGGTGGAACTAAGA+TGG - chr5.3:33100813-33100832 MS.gene054730:CDS 50.0%
!! AACAGGACAGTTGCTGGTTC+AGG - chr5.3:33100931-33100950 MS.gene054730:CDS 50.0%
TCACTGCAGGAACGTGCTTC+AGG - chr5.3:33100898-33100917 MS.gene054730:CDS 55.0%
! AAACTCGATGGCGGCGATGA+GGG - chr5.3:33100627-33100646 MS.gene054730:CDS 55.0%
! GAAACTCGATGGCGGCGATG+AGG - chr5.3:33100626-33100645 MS.gene054730:CDS 60.0%


Chromosome Type Strat End Strand Name
chr5.3 gene 33100199 33101017 33100199 ID=MS.gene054730
chr5.3 mRNA 33100199 33101017 33100199 ID=MS.gene054730.t1;Parent=MS.gene054730
chr5.3 exon 33100199 33101017 33100199 ID=MS.gene054730.t1.exon1;Parent=MS.gene054730.t1
chr5.3 CDS 33100199 33101017 33100199 ID=cds.MS.gene054730.t1;Parent=MS.gene054730.t1
Gene Sequence

>MS.gene054730

ATGGACTGTAACCAGTTAAAGTCATCTTCATCATCATCAGAGGATCAAATTGACATGATGTTAATGATGATGATGCAACTCCCTGAATTTTCTTCATCTAACGGTAATAATACCAACACCATCAATCAATTTCCACCGTCAGATCAACAATTCTATGAAGCTTCAAATGCTTCTAACAATACACGTCCTCTTGCAGATTTAATAGATAACCCTCCTAATCCAATACCATGGTCTTCATCTTCATCATTCACTCATTTACCTTCACAATCCACCACAAACACAAACACAATCTCTTTCACCAATAACAACTCTACTACACCATTAATGTTCCAACAACAACAAACAACACCGTTAATATTTTCTAATTCGAGCAACGAGATTGCTCAGAATACGAACCATTACGGTACTGCGTTGCCATCTGAGAAGAGAAACTCGATGGCGGCGATGAGGGAGATGATATTCAGAATAGCAGCTATGCAACCAATTTACATAGACCCAGAATCAGTAAAACCACCAAAAAGAAGAAACGTGAAGATTTCAAAAGATCCTCAGAGTATTGCAGCTAGACACAGAAGAGAAAGAATAAGCGAGAAAATAAGAATACTGCAAAGAATGGTACCAGGTGGAACTAAGATGGATACTGCATCAATGTTGGATGAAGCTATTCATTATGTTAAGTTTCTCAAGACACAACTTAAGTCACTGCAGGAACGTGCTTCAGGAGCCAACAATAACAGGACAGTTGCTGGTTCAGGATTAGGGTTCCCTGTTTCATTGCCTAAGCCTTACCAAGATCGTAATGTTGATCGTTATGGGTGA
Protein sequence

>MS.gene054730.t1

MDCNQLKSSSSSSEDQIDMMLMMMMQLPEFSSSNGNNTNTINQFPPSDQQFYEASNASNNTRPLADLIDNPPNPIPWSSSSSFTHLPSQSTTNTNTISFTNNNSTTPLMFQQQQTTPLIFSNSSNEIAQNTNHYGTALPSEKRNSMAAMREMIFRIAAMQPIYIDPESVKPPKRRNVKISKDPQSIAARHRRERISEKIRILQRMVPGGTKMDTASMLDEAIHYVKFLKTQLKSLQERASGANNNRTVAGSGLGFPVSLPKPYQDRNVDRYG