AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene03172

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene03172.t1 MTR_2g029180 100.000 263 0 0 1 263 146 408 0.0 526
MS.gene03172.t1 MTR_3g049400 55.200 250 107 4 1 248 153 399 4.31e-82 252
MS.gene03172.t1 MTR_2g022700 54.800 250 108 4 1 248 147 393 1.65e-81 250
MS.gene03172.t1 MTR_4g131800 50.741 270 109 5 1 247 144 412 2.86e-67 225
MS.gene03172.t1 MTR_4g105630 44.048 252 135 4 4 252 131 379 5.31e-59 192
MS.gene03172.t1 MTR_6g005480 46.154 260 135 4 3 258 158 416 1.06e-58 192
MS.gene03172.t1 MTR_4g088350 42.045 264 138 6 2 261 32 284 1.38e-57 186
MS.gene03172.t1 MTR_5g044220 40.625 256 142 5 5 256 151 400 2.55e-56 186
MS.gene03172.t1 MTR_4g088350 42.045 264 138 6 2 261 143 395 5.07e-56 185
MS.gene03172.t1 MTR_4g105630 43.210 243 132 4 4 243 131 370 5.31e-55 181
MS.gene03172.t1 MTR_3g077640 44.531 256 136 4 4 256 156 408 4.55e-54 180
MS.gene03172.t1 MTR_4g105630 40.816 196 110 4 4 196 131 323 1.32e-34 127
MS.gene03172.t1 MTR_4g105630 41.143 175 95 3 4 170 131 305 1.17e-31 119
MS.gene03172.t1 MTR_3g072380 29.046 241 164 4 7 245 67 302 1.01e-19 87.4
MS.gene03172.t1 MTR_1g030320 28.099 242 165 6 7 245 66 301 1.16e-17 81.6
MS.gene03172.t1 MTR_3g070000 24.800 250 181 5 7 253 77 322 9.61e-15 73.2
MS.gene03172.t1 MTR_4g101860 28.571 217 147 4 40 253 139 350 1.24e-14 73.2
MS.gene03172.t1 MTR_4g018760 26.383 235 167 4 16 248 75 305 1.60e-14 72.4
MS.gene03172.t1 MTR_5g081710 25.806 217 155 4 39 253 94 306 1.37e-13 69.7
MS.gene03172.t1 MTR_3g462070 24.434 221 157 6 39 256 95 308 1.18e-12 67.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene03172.t1 AT5G17630 83.650 263 43 0 1 263 155 417 2.07e-160 452
MS.gene03172.t1 AT5G54800 55.200 250 107 4 1 248 140 386 2.88e-82 252
MS.gene03172.t1 AT1G61800 52.800 250 113 4 1 248 140 386 1.86e-80 247
MS.gene03172.t1 AT1G61800 52.610 249 113 4 1 247 140 385 2.10e-79 245
MS.gene03172.t1 AT5G46110 39.623 265 150 5 2 262 39 297 1.15e-57 186
MS.gene03172.t1 AT5G46110 39.623 265 150 5 2 262 152 410 1.86e-56 186
MS.gene03172.t1 AT5G46110 40.530 264 142 6 2 261 152 404 3.21e-55 183
MS.gene03172.t1 AT5G46110 38.491 265 142 6 2 262 152 399 3.85e-52 175
MS.gene03172.t1 AT3G01550 44.177 249 130 4 3 248 124 366 6.10e-52 174
MS.gene03172.t1 AT3G01550 44.177 249 135 3 3 248 124 371 6.30e-52 174
MS.gene03172.t1 AT5G33320 41.406 256 146 3 3 256 153 406 2.44e-48 165
MS.gene03172.t1 AT4G03950 36.864 236 103 7 27 257 67 261 2.18e-33 122
MS.gene03172.t1 AT1G77610 30.769 208 138 3 39 245 94 296 5.85e-20 88.2
MS.gene03172.t1 AT1G21870 27.801 241 167 4 7 245 67 302 5.37e-19 85.5
MS.gene03172.t1 AT1G12500 26.667 225 154 5 40 261 145 361 9.50e-15 73.6
MS.gene03172.t1 AT5G05820 24.603 252 179 6 7 253 63 308 5.03e-13 68.2
MS.gene03172.t1 AT3G11320 25.114 219 154 5 39 253 96 308 2.60e-12 65.9

Find 40 sgRNAs with CRISPR-Local

Find 57 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGATCTGCCATTGCTATTCT+TGG 0.173141 2.1:+62026847 MS.gene03172:CDS
CCATTTGGATGCTTGTTCTT+TGG 0.202656 2.1:+62026140 None:intergenic
AGTGATTGTGTCTTCGATTT+TGG 0.242143 2.1:+62026789 MS.gene03172:CDS
TTTCCAACAGAGAAAGTTAA+TGG 0.242242 2.1:-62026748 None:intergenic
AGCTTGTGTTTCATTCTCTA+AGG 0.279265 2.1:+62026255 MS.gene03172:CDS
TGGTGATAGGTATCCAATTC+AGG 0.283536 2.1:+62026348 MS.gene03172:CDS
CAAAATTTCAAAGAAGTTGA+TGG 0.305953 2.1:+62026514 MS.gene03172:CDS
GTTGATGGTTTGAACTTATA+TGG 0.310417 2.1:+62026529 MS.gene03172:CDS
CCAAGTAGTGCAAAGATAAA+AGG 0.314629 2.1:-62026199 None:intergenic
ATTGAAAGCCAAACCTGAAT+TGG 0.343853 2.1:-62026361 None:intergenic
GTTAGGCCTCTTAATGGTCT+TGG 0.367474 2.1:+62026826 MS.gene03172:CDS
TTTCTTCTGTTCTTGGTGAT+AGG 0.374490 2.1:+62026335 MS.gene03172:CDS
GATCTGCCATTGCTATTCTT+GGG 0.384636 2.1:+62026848 MS.gene03172:CDS
CCTGCTTTGTTTCACACAAT+AGG 0.391158 2.1:+62026223 MS.gene03172:CDS
TAAGAGGCCTAACCGGATTC+CGG 0.403937 2.1:-62026816 None:intergenic
ATGGATTCCAGGGTATTATA+AGG 0.414035 2.1:+62026615 MS.gene03172:CDS
GAAGGTTCTCAATGGATTCC+AGG 0.417158 2.1:+62026604 MS.gene03172:CDS
AAAGAACAACCAAGCACAAT+TGG 0.428671 2.1:-62026388 None:intergenic
ATAGGTATCCAATTCAGGTT+TGG 0.441304 2.1:+62026353 MS.gene03172:CDS
AATCCGGTTAGGCCTCTTAA+TGG 0.445202 2.1:+62026820 MS.gene03172:CDS
GAGGTATCTTTCAATGTTGG+AGG 0.458201 2.1:+62026424 MS.gene03172:CDS
AGTCCATTAACTTTCTCTGT+TGG 0.459007 2.1:+62026745 MS.gene03172:CDS
AGACCATTAAGAGGCCTAAC+CGG 0.467988 2.1:-62026823 None:intergenic
AAGAAAGCAAAGAAAATTGA+AGG 0.478846 2.1:+62026901 MS.gene03172:CDS
TTCTTTAGCTGCTGTTACTG+AGG 0.482713 2.1:+62026405 MS.gene03172:CDS
TATAAGGCGCTTGAAGCGAT+TGG 0.482837 2.1:+62026631 MS.gene03172:CDS
ATGGTTTGAACTTATATGGT+TGG 0.489171 2.1:+62026533 MS.gene03172:CDS
TGTGCACTTATTAGCAATGT+TGG 0.491248 2.1:+62026454 MS.gene03172:CDS
CTTTCAATGTTGGAGGATTG+TGG 0.498343 2.1:+62026431 MS.gene03172:CDS
ACTGAGGTATCTTTCAATGT+TGG 0.506410 2.1:+62026421 MS.gene03172:CDS
TCAATCATCTTATCAAGCAT+TGG 0.516384 2.1:+62026714 MS.gene03172:CDS
TGGTGTTCCGGAATCCGGTT+AGG 0.528399 2.1:+62026809 MS.gene03172:CDS
GCAGATCCAAGACCATTAAG+AGG 0.528834 2.1:-62026832 None:intergenic
AGAAAGCAAAGAAAATTGAA+GGG 0.581786 2.1:+62026902 MS.gene03172:CDS
AAGGTTCTCAATGGATTCCA+GGG 0.590612 2.1:+62026605 MS.gene03172:CDS
CCTATTGTGTGAAACAAAGC+AGG 0.603409 2.1:-62026223 None:intergenic
TGGAAATACAATGAAGAGAG+TGG 0.612192 2.1:+62026765 MS.gene03172:CDS
AAAAGTCCCAAGAATAGCAA+TGG 0.616189 2.1:-62026854 None:intergenic
GAAAGCAAAGAAAATTGAAG+GGG 0.622560 2.1:+62026903 MS.gene03172:CDS
TCAAGCGCCTTATAATACCC+TGG 0.633740 2.1:-62026622 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATAAAAGGTTTTGAGATTTT+TGG - chr2.1:62026187-62026206 None:intergenic 20.0%
!!! TTCATTTATGTATCTTTTTC+CGG + chr2.1:62026567-62026586 MS.gene03172:CDS 20.0%
! AAGAAAGCAAAGAAAATTGA+AGG + chr2.1:62026901-62026920 MS.gene03172:CDS 25.0%
! AGAAAGCAAAGAAAATTGAA+GGG + chr2.1:62026902-62026921 MS.gene03172:CDS 25.0%
! CAAAATTTCAAAGAAGTTGA+TGG + chr2.1:62026514-62026533 MS.gene03172:CDS 25.0%
! GAAAATATGACAGAAAAAAC+AGG - chr2.1:62026319-62026338 None:intergenic 25.0%
!!! GACTTTTTATATTTGGGTTT+TGG + chr2.1:62026663-62026682 MS.gene03172:CDS 25.0%
ACCCAAATATAAAAAGTCGA+AGG - chr2.1:62026661-62026680 None:intergenic 30.0%
ATGGTTTGAACTTATATGGT+TGG + chr2.1:62026533-62026552 MS.gene03172:CDS 30.0%
GAAAGCAAAGAAAATTGAAG+GGG + chr2.1:62026903-62026922 MS.gene03172:CDS 30.0%
TCAATCATCTTATCAAGCAT+TGG + chr2.1:62026714-62026733 MS.gene03172:CDS 30.0%
TTTCCAACAGAGAAAGTTAA+TGG - chr2.1:62026751-62026770 None:intergenic 30.0%
! GCCTTCGACTTTTTATATTT+GGG + chr2.1:62026657-62026676 MS.gene03172:CDS 30.0%
! GTCATATTTTCTTCTGTTCT+TGG + chr2.1:62026328-62026347 MS.gene03172:CDS 30.0%
! TCAATTTTACCAATTGTGCT+TGG + chr2.1:62026379-62026398 MS.gene03172:CDS 30.0%
! TTTTTGTAGAAGGTTCTCAA+TGG + chr2.1:62026596-62026615 MS.gene03172:CDS 30.0%
!! GTTGATGGTTTGAACTTATA+TGG + chr2.1:62026529-62026548 MS.gene03172:CDS 30.0%
!!! TATATTTGGGTTTTGGTTTC+TGG + chr2.1:62026670-62026689 MS.gene03172:CDS 30.0%
AAAAGTCCCAAGAATAGCAA+TGG - chr2.1:62026857-62026876 None:intergenic 35.0%
AAAGAACAACCAAGCACAAT+TGG - chr2.1:62026391-62026410 None:intergenic 35.0%
AGCTTGTGTTTCATTCTCTA+AGG + chr2.1:62026255-62026274 MS.gene03172:CDS 35.0%
AGTCCATTAACTTTCTCTGT+TGG + chr2.1:62026745-62026764 MS.gene03172:CDS 35.0%
ATTGAAAGCCAAACCTGAAT+TGG - chr2.1:62026364-62026383 None:intergenic 35.0%
CCAAGTAGTGCAAAGATAAA+AGG - chr2.1:62026202-62026221 None:intergenic 35.0%
TGGAAATACAATGAAGAGAG+TGG + chr2.1:62026765-62026784 MS.gene03172:CDS 35.0%
TGTGCACTTATTAGCAATGT+TGG + chr2.1:62026454-62026473 MS.gene03172:CDS 35.0%
! ACTGAGGTATCTTTCAATGT+TGG + chr2.1:62026421-62026440 MS.gene03172:CDS 35.0%
! AGTGATTGTGTCTTCGATTT+TGG + chr2.1:62026789-62026808 MS.gene03172:CDS 35.0%
! ATAGGTATCCAATTCAGGTT+TGG + chr2.1:62026353-62026372 MS.gene03172:CDS 35.0%
! ATGGATTCCAGGGTATTATA+AGG + chr2.1:62026615-62026634 MS.gene03172:CDS 35.0%
! CCTTTTATCTTTGCACTACT+TGG + chr2.1:62026199-62026218 MS.gene03172:CDS 35.0%
! CGCCTTCGACTTTTTATATT+TGG + chr2.1:62026656-62026675 MS.gene03172:CDS 35.0%
! TTTCTTCTGTTCTTGGTGAT+AGG + chr2.1:62026335-62026354 MS.gene03172:CDS 35.0%
!!! GGTTTTGAGATTTTTGGACA+AGG - chr2.1:62026181-62026200 None:intergenic 35.0%
CCTATTGTGTGAAACAAAGC+AGG - chr2.1:62026226-62026245 None:intergenic 40.0%
CCTTCTACAAAAATCGCTAC+CGG - chr2.1:62026589-62026608 None:intergenic 40.0%
CTTTCAATGTTGGAGGATTG+TGG + chr2.1:62026431-62026450 MS.gene03172:CDS 40.0%
TGGTGATAGGTATCCAATTC+AGG + chr2.1:62026348-62026367 MS.gene03172:CDS 40.0%
TTCTTTAGCTGCTGTTACTG+AGG + chr2.1:62026405-62026424 MS.gene03172:CDS 40.0%
! AAGGTTCTCAATGGATTCCA+GGG + chr2.1:62026605-62026624 MS.gene03172:CDS 40.0%
! GAGGTATCTTTCAATGTTGG+AGG + chr2.1:62026424-62026443 MS.gene03172:CDS 40.0%
! GATCTGCCATTGCTATTCTT+GGG + chr2.1:62026848-62026867 MS.gene03172:CDS 40.0%
!! CCTGCTTTGTTTCACACAAT+AGG + chr2.1:62026223-62026242 MS.gene03172:CDS 40.0%
!!! GCAATGTTGGTTTTGTGTTG+AGG + chr2.1:62026467-62026486 MS.gene03172:CDS 40.0%
!!! TGTCTTCGATTTTGGTGTTC+CGG + chr2.1:62026797-62026816 MS.gene03172:CDS 40.0%
AATCCGGTTAGGCCTCTTAA+TGG + chr2.1:62026820-62026839 MS.gene03172:CDS 45.0%
AGACCATTAAGAGGCCTAAC+CGG - chr2.1:62026826-62026845 None:intergenic 45.0%
GCAGATCCAAGACCATTAAG+AGG - chr2.1:62026835-62026854 None:intergenic 45.0%
GTTAGGCCTCTTAATGGTCT+TGG + chr2.1:62026826-62026845 MS.gene03172:CDS 45.0%
TCAAGCGCCTTATAATACCC+TGG - chr2.1:62026625-62026644 None:intergenic 45.0%
! CCGGTAGCGATTTTTGTAGA+AGG + chr2.1:62026586-62026605 MS.gene03172:CDS 45.0%
! GAAGGTTCTCAATGGATTCC+AGG + chr2.1:62026604-62026623 MS.gene03172:CDS 45.0%
! GGATCTGCCATTGCTATTCT+TGG + chr2.1:62026847-62026866 MS.gene03172:CDS 45.0%
! TATAAGGCGCTTGAAGCGAT+TGG + chr2.1:62026631-62026650 MS.gene03172:CDS 45.0%
!!! GATTTTGGTGTTCCGGAATC+CGG + chr2.1:62026804-62026823 MS.gene03172:CDS 45.0%
TAAGAGGCCTAACCGGATTC+CGG - chr2.1:62026819-62026838 None:intergenic 50.0%
TGGTGTTCCGGAATCCGGTT+AGG + chr2.1:62026809-62026828 MS.gene03172:CDS 55.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 62026148 62026939 62026148 ID=MS.gene03172
chr2.1 mRNA 62026148 62026939 62026148 ID=MS.gene03172.t1;Parent=MS.gene03172
chr2.1 exon 62026148 62026939 62026148 ID=MS.gene03172.t1.exon1;Parent=MS.gene03172.t1
chr2.1 CDS 62026148 62026939 62026148 ID=cds.MS.gene03172.t1;Parent=MS.gene03172.t1
Gene Sequence

>MS.gene03172

ATGCTTGTTCTTTGGTCTTTAAAGCTTCAACCTTGTCCAAAAATCTCAAAACCTTTTATCTTTGCACTACTTGGACCTGCTTTGTTTCACACAATAGGTCACATTTCAGCTTGTGTTTCATTCTCTAAGGTTGCTGTGTCTTTCACACATGTTATTAAATCAGCAGAACCTGTTTTTTCTGTCATATTTTCTTCTGTTCTTGGTGATAGGTATCCAATTCAGGTTTGGCTTTCAATTTTACCAATTGTGCTTGGTTGTTCTTTAGCTGCTGTTACTGAGGTATCTTTCAATGTTGGAGGATTGTGGTGTGCACTTATTAGCAATGTTGGTTTTGTGTTGAGGAACATTTATTCGAAAAAAAGTTTACAAAATTTCAAAGAAGTTGATGGTTTGAACTTATATGGTTGGATTACTATACTTTCATTTATGTATCTTTTTCCGGTAGCGATTTTTGTAGAAGGTTCTCAATGGATTCCAGGGTATTATAAGGCGCTTGAAGCGATTGGAACGCCTTCGACTTTTTATATTTGGGTTTTGGTTTCTGGTCTGTTTTATCATCTTTATAATCAATCATCTTATCAAGCATTGGATGAAATTAGTCCATTAACTTTCTCTGTTGGAAATACAATGAAGAGAGTGGTAGTGATTGTGTCTTCGATTTTGGTGTTCCGGAATCCGGTTAGGCCTCTTAATGGTCTTGGATCTGCCATTGCTATTCTTGGGACTTTTCTGTATTCACAAGCTACAGCTGCAAAGAAAGCAAAGAAAATTGAAGGGGAAAAGAGTAGTTAG
Protein sequence

>MS.gene03172.t1

MLVLWSLKLQPCPKISKPFIFALLGPALFHTIGHISACVSFSKVAVSFTHVIKSAEPVFSVIFSSVLGDRYPIQVWLSILPIVLGCSLAAVTEVSFNVGGLWCALISNVGFVLRNIYSKKSLQNFKEVDGLNLYGWITILSFMYLFPVAIFVEGSQWIPGYYKALEAIGTPSTFYIWVLVSGLFYHLYNQSSYQALDEISPLTFSVGNTMKRVVVIVSSILVFRNPVRPLNGLGSAIAILGTFLYSQATAAKKAKKIEGEKSS