AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene003243

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene003243.t1 MTR_2g029180 99.240 263 2 0 1 263 146 408 0.0 520
MS.gene003243.t1 MTR_3g049400 55.200 250 107 4 1 248 153 399 6.10e-82 251
MS.gene003243.t1 MTR_2g022700 54.800 250 108 4 1 248 147 393 2.07e-81 250
MS.gene003243.t1 MTR_4g131800 51.111 270 108 5 1 247 144 412 2.69e-67 225
MS.gene003243.t1 MTR_4g105630 44.444 252 134 4 4 252 131 379 2.60e-60 195
MS.gene003243.t1 MTR_6g005480 46.538 260 134 4 3 258 158 416 5.75e-60 195
MS.gene003243.t1 MTR_4g088350 42.424 264 137 6 2 261 32 284 4.58e-59 189
MS.gene003243.t1 MTR_5g044220 41.016 256 141 5 5 256 151 400 1.01e-57 189
MS.gene003243.t1 MTR_4g088350 42.424 264 137 6 2 261 143 395 1.87e-57 188
MS.gene003243.t1 MTR_4g105630 43.621 243 131 4 4 243 131 370 2.25e-56 185
MS.gene003243.t1 MTR_3g077640 44.922 256 135 4 4 256 156 408 2.23e-55 183
MS.gene003243.t1 MTR_4g105630 41.327 196 109 4 4 196 131 323 5.45e-36 131
MS.gene003243.t1 MTR_4g105630 41.714 175 94 3 4 170 131 305 6.58e-33 122
MS.gene003243.t1 MTR_3g072380 29.461 241 163 4 7 245 67 302 2.21e-20 89.4
MS.gene003243.t1 MTR_1g030320 28.099 242 165 6 7 245 66 301 9.31e-18 82.0
MS.gene003243.t1 MTR_3g070000 24.800 250 181 5 7 253 77 322 9.34e-15 73.2
MS.gene003243.t1 MTR_4g018760 26.496 234 166 4 16 247 75 304 1.30e-14 72.8
MS.gene003243.t1 MTR_4g101860 28.571 217 147 4 40 253 139 350 1.45e-14 72.8
MS.gene003243.t1 MTR_5g081710 25.806 217 155 4 39 253 94 306 1.34e-13 69.7
MS.gene003243.t1 MTR_3g462070 24.434 221 157 6 39 256 95 308 1.49e-12 66.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene003243.t1 AT5G17630 83.270 263 44 0 1 263 155 417 1.11e-158 447
MS.gene003243.t1 AT5G54800 55.600 250 106 4 1 248 140 386 6.11e-83 254
MS.gene003243.t1 AT1G61800 52.800 250 113 4 1 248 140 386 2.19e-80 247
MS.gene003243.t1 AT1G61800 52.610 249 113 4 1 247 140 385 2.96e-79 245
MS.gene003243.t1 AT5G46110 40.000 265 149 5 2 262 39 297 3.72e-59 190
MS.gene003243.t1 AT5G46110 40.000 265 149 5 2 262 152 410 6.94e-58 190
MS.gene003243.t1 AT5G46110 40.909 264 141 6 2 261 152 404 1.37e-56 187
MS.gene003243.t1 AT3G01550 44.578 249 129 4 3 248 124 366 1.80e-53 177
MS.gene003243.t1 AT3G01550 44.578 249 134 3 3 248 124 371 1.84e-53 177
MS.gene003243.t1 AT5G46110 38.868 265 141 6 2 262 152 399 2.01e-53 178
MS.gene003243.t1 AT5G33320 41.634 257 144 4 3 256 153 406 1.28e-49 168
MS.gene003243.t1 AT4G03950 37.083 240 97 8 27 257 67 261 6.96e-34 124
MS.gene003243.t1 AT1G77610 30.288 208 139 3 39 245 94 296 1.84e-19 86.7
MS.gene003243.t1 AT1G21870 28.365 208 143 3 39 245 100 302 2.25e-18 83.6
MS.gene003243.t1 AT1G12500 26.667 225 154 5 40 261 145 361 9.14e-15 73.6
MS.gene003243.t1 AT5G05820 24.603 252 179 6 7 253 63 308 4.19e-13 68.2
MS.gene003243.t1 AT3G11320 25.114 219 154 5 39 253 96 308 2.43e-12 66.2
MS.gene003243.t1 AT3G10290 24.766 214 149 5 39 247 143 349 4.22e-11 62.8

Find 40 sgRNAs with CRISPR-Local

Find 58 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTTCTGCCATTGCTATTCT+TGG 0.179095 2.4:+60626366 MS.gene003243:CDS
CCATTTGGATGCTTGTTCTT+TGG 0.202656 2.4:+60625659 None:intergenic
AGTGATTGTGTCTTCGATTT+TGG 0.242143 2.4:+60626308 MS.gene003243:CDS
TTTCCAACAGAGAAAGTTAA+TGG 0.242242 2.4:-60626267 None:intergenic
AGCTTGTGTTTCATTCTCTA+AGG 0.279265 2.4:+60625774 MS.gene003243:CDS
TGGTGATAGGTATCCAATTC+AGG 0.283536 2.4:+60625867 MS.gene003243:CDS
GTTGATGGTTTGAACTTATA+TGG 0.310417 2.4:+60626048 MS.gene003243:CDS
CAGAATTTCAAAGAAGTTGA+TGG 0.312773 2.4:+60626033 MS.gene003243:CDS
CCAAGTAGTGCAAAGATAAA+AGG 0.314629 2.4:-60625718 None:intergenic
ATTGAAAGCCAAACCTGAAT+TGG 0.343853 2.4:-60625880 None:intergenic
TATAAGGCGCTTGAAACTAT+TGG 0.351508 2.4:+60626150 MS.gene003243:CDS
GTTAGGCCTCTTAATGGTCT+TGG 0.361838 2.4:+60626345 MS.gene003243:CDS
TTTCTTCTGTTCTTGGTGAT+AGG 0.374490 2.4:+60625854 MS.gene003243:CDS
CCTGCTTTGTTTCACACAAT+AGG 0.391158 2.4:+60625742 MS.gene003243:CDS
GTTCTGCCATTGCTATTCTT+GGG 0.400152 2.4:+60626367 MS.gene003243:CDS
TAAGAGGCCTAACCGGATTC+CGG 0.403937 2.4:-60626335 None:intergenic
ATGGATTCCAGGGTATTATA+AGG 0.414035 2.4:+60626134 MS.gene003243:CDS
GAAGGTTCTCAATGGATTCC+AGG 0.417158 2.4:+60626123 MS.gene003243:CDS
AAAGAACAACCAAGCACAAT+TGG 0.428671 2.4:-60625907 None:intergenic
ATAGGTATCCAATTCAGGTT+TGG 0.441304 2.4:+60625872 MS.gene003243:CDS
AATCCGGTTAGGCCTCTTAA+TGG 0.445202 2.4:+60626339 MS.gene003243:CDS
GAGGTATCTTTCAATGTTGG+AGG 0.458201 2.4:+60625943 MS.gene003243:CDS
AGTCCATTAACTTTCTCTGT+TGG 0.459007 2.4:+60626264 MS.gene003243:CDS
AGACCATTAAGAGGCCTAAC+CGG 0.471343 2.4:-60626342 None:intergenic
AAGAAAGCAAAGAAAATTGA+AGG 0.478846 2.4:+60626420 MS.gene003243:CDS
TTCTTTAGCTGCTGTTACTG+AGG 0.482713 2.4:+60625924 MS.gene003243:CDS
ATGGTTTGAACTTATATGGT+TGG 0.489171 2.4:+60626052 MS.gene003243:CDS
TGTGCACTTATTAGCAATGT+TGG 0.491248 2.4:+60625973 MS.gene003243:CDS
CTTTCAATGTTGGAGGATTG+TGG 0.498343 2.4:+60625950 MS.gene003243:CDS
ACTGAGGTATCTTTCAATGT+TGG 0.506410 2.4:+60625940 MS.gene003243:CDS
TCAATCATCTTATCAAGCAT+TGG 0.516384 2.4:+60626233 MS.gene003243:CDS
TGGTGTTCCGGAATCCGGTT+AGG 0.528399 2.4:+60626328 MS.gene003243:CDS
GCAGAACCAAGACCATTAAG+AGG 0.535866 2.4:-60626351 None:intergenic
AGAAAGCAAAGAAAATTGAA+GGG 0.581786 2.4:+60626421 MS.gene003243:CDS
AAGGTTCTCAATGGATTCCA+GGG 0.590612 2.4:+60626124 MS.gene003243:CDS
CCTATTGTGTGAAACAAAGC+AGG 0.603409 2.4:-60625742 None:intergenic
TGGAAATACAATGAAGAGAG+TGG 0.612192 2.4:+60626284 MS.gene003243:CDS
AAAAGTCCCAAGAATAGCAA+TGG 0.616189 2.4:-60626373 None:intergenic
GAAAGCAAAGAAAATTGAAG+GGG 0.622560 2.4:+60626422 MS.gene003243:CDS
TCAAGCGCCTTATAATACCC+TGG 0.644150 2.4:-60626141 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GAAAATATAACAGAAAAAAC+AGG - chr2.4:60625838-60625857 None:intergenic 20.0%
!!! ATAAAAGGTTTTGAGATTTT+TGG - chr2.4:60625706-60625725 None:intergenic 20.0%
!!! TTCATTTATGTATCTTTTTC+CGG + chr2.4:60626086-60626105 MS.gene003243:CDS 20.0%
! AAGAAAGCAAAGAAAATTGA+AGG + chr2.4:60626420-60626439 MS.gene003243:CDS 25.0%
! AGAAAGCAAAGAAAATTGAA+GGG + chr2.4:60626421-60626440 MS.gene003243:CDS 25.0%
!! GTTATATTTTCTTCTGTTCT+TGG + chr2.4:60625847-60625866 MS.gene003243:CDS 25.0%
!!! GACTTTTTATATTTGGGTTT+TGG + chr2.4:60626182-60626201 MS.gene003243:CDS 25.0%
ACCCAAATATAAAAAGTCGA+AGG - chr2.4:60626180-60626199 None:intergenic 30.0%
ATGGTTTGAACTTATATGGT+TGG + chr2.4:60626052-60626071 MS.gene003243:CDS 30.0%
CAGAATTTCAAAGAAGTTGA+TGG + chr2.4:60626033-60626052 MS.gene003243:CDS 30.0%
GAAAGCAAAGAAAATTGAAG+GGG + chr2.4:60626422-60626441 MS.gene003243:CDS 30.0%
TCAATCATCTTATCAAGCAT+TGG + chr2.4:60626233-60626252 MS.gene003243:CDS 30.0%
TTTCCAACAGAGAAAGTTAA+TGG - chr2.4:60626270-60626289 None:intergenic 30.0%
! GCCTTCGACTTTTTATATTT+GGG + chr2.4:60626176-60626195 MS.gene003243:CDS 30.0%
! TCAATTTTACCAATTGTGCT+TGG + chr2.4:60625898-60625917 MS.gene003243:CDS 30.0%
! TTTTTGTAGAAGGTTCTCAA+TGG + chr2.4:60626115-60626134 MS.gene003243:CDS 30.0%
!! GTTGATGGTTTGAACTTATA+TGG + chr2.4:60626048-60626067 MS.gene003243:CDS 30.0%
!!! ATATTTGGGTTTTGGTTTCT+GGG + chr2.4:60626190-60626209 MS.gene003243:CDS 30.0%
!!! TATATTTGGGTTTTGGTTTC+TGG + chr2.4:60626189-60626208 MS.gene003243:CDS 30.0%
AAAAGTCCCAAGAATAGCAA+TGG - chr2.4:60626376-60626395 None:intergenic 35.0%
AAAGAACAACCAAGCACAAT+TGG - chr2.4:60625910-60625929 None:intergenic 35.0%
AGCTTGTGTTTCATTCTCTA+AGG + chr2.4:60625774-60625793 MS.gene003243:CDS 35.0%
AGTCCATTAACTTTCTCTGT+TGG + chr2.4:60626264-60626283 MS.gene003243:CDS 35.0%
ATTGAAAGCCAAACCTGAAT+TGG - chr2.4:60625883-60625902 None:intergenic 35.0%
CCAAGTAGTGCAAAGATAAA+AGG - chr2.4:60625721-60625740 None:intergenic 35.0%
TGGAAATACAATGAAGAGAG+TGG + chr2.4:60626284-60626303 MS.gene003243:CDS 35.0%
TGTGCACTTATTAGCAATGT+TGG + chr2.4:60625973-60625992 MS.gene003243:CDS 35.0%
! ACTGAGGTATCTTTCAATGT+TGG + chr2.4:60625940-60625959 MS.gene003243:CDS 35.0%
! AGTGATTGTGTCTTCGATTT+TGG + chr2.4:60626308-60626327 MS.gene003243:CDS 35.0%
! ATAGGTATCCAATTCAGGTT+TGG + chr2.4:60625872-60625891 MS.gene003243:CDS 35.0%
! ATGGATTCCAGGGTATTATA+AGG + chr2.4:60626134-60626153 MS.gene003243:CDS 35.0%
! CCTTTTATCTTTGCACTACT+TGG + chr2.4:60625718-60625737 MS.gene003243:CDS 35.0%
! CGCCTTCGACTTTTTATATT+TGG + chr2.4:60626175-60626194 MS.gene003243:CDS 35.0%
! TATAAGGCGCTTGAAACTAT+TGG + chr2.4:60626150-60626169 MS.gene003243:CDS 35.0%
! TTTCTTCTGTTCTTGGTGAT+AGG + chr2.4:60625854-60625873 MS.gene003243:CDS 35.0%
CCTATTGTGTGAAACAAAGC+AGG - chr2.4:60625745-60625764 None:intergenic 40.0%
CCTTCTACAAAAATCGCTAC+CGG - chr2.4:60626108-60626127 None:intergenic 40.0%
CTTTCAATGTTGGAGGATTG+TGG + chr2.4:60625950-60625969 MS.gene003243:CDS 40.0%
TGGTGATAGGTATCCAATTC+AGG + chr2.4:60625867-60625886 MS.gene003243:CDS 40.0%
TTCTTTAGCTGCTGTTACTG+AGG + chr2.4:60625924-60625943 MS.gene003243:CDS 40.0%
! AAGGTTCTCAATGGATTCCA+GGG + chr2.4:60626124-60626143 MS.gene003243:CDS 40.0%
! GAGGTATCTTTCAATGTTGG+AGG + chr2.4:60625943-60625962 MS.gene003243:CDS 40.0%
! GTTCTGCCATTGCTATTCTT+GGG + chr2.4:60626367-60626386 MS.gene003243:CDS 40.0%
!! CCTGCTTTGTTTCACACAAT+AGG + chr2.4:60625742-60625761 MS.gene003243:CDS 40.0%
!!! GCAATGTTGGTTTTGTGTTG+AGG + chr2.4:60625986-60626005 MS.gene003243:CDS 40.0%
!!! GGTTTTGAGATTTTTGGACG+AGG - chr2.4:60625700-60625719 None:intergenic 40.0%
!!! TGTCTTCGATTTTGGTGTTC+CGG + chr2.4:60626316-60626335 MS.gene003243:CDS 40.0%
AATCCGGTTAGGCCTCTTAA+TGG + chr2.4:60626339-60626358 MS.gene003243:CDS 45.0%
AGACCATTAAGAGGCCTAAC+CGG - chr2.4:60626345-60626364 None:intergenic 45.0%
GCAGAACCAAGACCATTAAG+AGG - chr2.4:60626354-60626373 None:intergenic 45.0%
GTTAGGCCTCTTAATGGTCT+TGG + chr2.4:60626345-60626364 MS.gene003243:CDS 45.0%
TCAAGCGCCTTATAATACCC+TGG - chr2.4:60626144-60626163 None:intergenic 45.0%
! CCGGTAGCGATTTTTGTAGA+AGG + chr2.4:60626105-60626124 MS.gene003243:CDS 45.0%
! GAAGGTTCTCAATGGATTCC+AGG + chr2.4:60626123-60626142 MS.gene003243:CDS 45.0%
! GGTTCTGCCATTGCTATTCT+TGG + chr2.4:60626366-60626385 MS.gene003243:CDS 45.0%
!!! GATTTTGGTGTTCCGGAATC+CGG + chr2.4:60626323-60626342 MS.gene003243:CDS 45.0%
TAAGAGGCCTAACCGGATTC+CGG - chr2.4:60626338-60626357 None:intergenic 50.0%
TGGTGTTCCGGAATCCGGTT+AGG + chr2.4:60626328-60626347 MS.gene003243:CDS 55.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 60625667 60626458 60625667 ID=MS.gene003243
chr2.4 mRNA 60625667 60626458 60625667 ID=MS.gene003243.t1;Parent=MS.gene003243
chr2.4 exon 60625667 60626458 60625667 ID=MS.gene003243.t1.exon1;Parent=MS.gene003243.t1
chr2.4 CDS 60625667 60626458 60625667 ID=cds.MS.gene003243.t1;Parent=MS.gene003243.t1
Gene Sequence

>MS.gene003243

ATGCTTGTTCTTTGGTCTTTAAAGCTTCAACCTCGTCCAAAAATCTCAAAACCTTTTATCTTTGCACTACTTGGACCTGCTTTGTTTCACACAATAGGTCACATTTCAGCTTGTGTTTCATTCTCTAAGGTTGCTGTGTCTTTCACACATGTTATAAAATCTGCAGAACCTGTTTTTTCTGTTATATTTTCTTCTGTTCTTGGTGATAGGTATCCAATTCAGGTTTGGCTTTCAATTTTACCAATTGTGCTTGGTTGTTCTTTAGCTGCTGTTACTGAGGTATCTTTCAATGTTGGAGGATTGTGGTGTGCACTTATTAGCAATGTTGGTTTTGTGTTGAGGAACATTTATTCGAAAAAAAGTTTACAGAATTTCAAAGAAGTTGATGGTTTGAACTTATATGGTTGGATTACTATACTTTCATTTATGTATCTTTTTCCGGTAGCGATTTTTGTAGAAGGTTCTCAATGGATTCCAGGGTATTATAAGGCGCTTGAAACTATTGGAACGCCTTCGACTTTTTATATTTGGGTTTTGGTTTCTGGGCTGTTTTATCATCTTTATAATCAATCATCTTATCAAGCATTGGATGAAATTAGTCCATTAACTTTCTCTGTTGGAAATACAATGAAGAGAGTGGTAGTGATTGTGTCTTCGATTTTGGTGTTCCGGAATCCGGTTAGGCCTCTTAATGGTCTTGGTTCTGCCATTGCTATTCTTGGGACTTTTCTGTATTCACAAGCTACAGCTGCAAAGAAAGCAAAGAAAATTGAAGGGGAAAAGAGTAGTTAG
Protein sequence

>MS.gene003243.t1

MLVLWSLKLQPRPKISKPFIFALLGPALFHTIGHISACVSFSKVAVSFTHVIKSAEPVFSVIFSSVLGDRYPIQVWLSILPIVLGCSLAAVTEVSFNVGGLWCALISNVGFVLRNIYSKKSLQNFKEVDGLNLYGWITILSFMYLFPVAIFVEGSQWIPGYYKALETIGTPSTFYIWVLVSGLFYHLYNQSSYQALDEISPLTFSVGNTMKRVVVIVSSILVFRNPVRPLNGLGSAIAILGTFLYSQATAAKKAKKIEGEKSS