AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG042403

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG042403 MtrunA17_Chr8g0351881 86.967 399 19 4 1 374 1 391 0.0 669
MsaG042403 MtrunA17_Chr3g0087771 51.807 415 113 16 18 373 10 396 1.71e-114 339
MsaG042403 MtrunA17_Chr1g0174271 38.338 373 191 10 28 371 8 370 9.97e-58 192
MsaG042403 MtrunA17_Chr2g0329041 35.208 409 183 13 32 371 8 403 2.38e-50 174
MsaG042403 MtrunA17_Chr4g0032951 41.445 263 119 10 130 372 181 428 1.19e-49 172
MsaG042403 MtrunA17_Chr7g0258181 34.254 362 179 7 22 371 1 315 3.83e-42 149
MsaG042403 MtrunA17_Chr4g0014771 67.045 88 27 1 285 372 106 191 3.45e-34 125
MsaG042403 MtrunA17_Chr1g0213791 51.562 128 43 3 246 371 227 337 3.80e-32 124
MsaG042403 MtrunA17_Chr4g0074161 55.072 69 30 1 298 366 205 272 1.08e-16 80.9
MsaG042403 MtrunA17_Chr1g0190731 53.623 69 31 1 298 366 192 259 4.23e-15 75.9
MsaG042403 MtrunA17_Chr3g0144641 46.753 77 41 0 287 363 179 255 1.79e-13 71.2
MsaG042403 MtrunA17_Chr7g0234761 49.231 65 33 0 299 363 317 381 2.25e-13 71.2
MsaG042403 MtrunA17_Chr8g0339091 49.231 65 33 0 299 363 291 355 2.80e-13 70.9
MsaG042403 MtrunA17_Chr3g0131771 50.769 65 32 0 299 363 147 211 3.31e-13 70.1
MsaG042403 MtrunA17_Chr1g0152131 41.860 86 42 1 278 363 247 324 3.58e-13 70.5
MsaG042403 MtrunA17_Chr8g0365941 49.231 65 33 0 299 363 305 369 7.69e-13 69.7
MsaG042403 MtrunA17_Chr5g0421111 43.590 78 36 1 286 363 360 429 1.74e-12 68.6
MsaG042403 MtrunA17_Chr4g0035101 47.692 65 34 0 299 363 143 207 3.00e-12 67.0
MsaG042403 MtrunA17_Chr8g0363921 47.692 65 34 0 299 363 151 215 3.04e-12 66.6
MsaG042403 MtrunA17_Chr5g0415291 47.692 65 34 0 299 363 112 176 1.07e-11 64.3
MsaG042403 MtrunA17_Chr7g0258161 43.284 67 38 0 297 363 171 237 1.37e-11 65.1
MsaG042403 MtrunA17_Chr5g0393721 48.485 66 33 1 298 363 223 287 2.27e-11 64.3
MsaG042403 MtrunA17_Chr8g0385911 46.154 65 35 0 299 363 145 209 2.36e-11 64.3
MsaG042403 MtrunA17_Chr1g0152651 48.485 66 33 1 298 363 273 337 2.85e-11 64.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG042403 AT2G42280.1 36.413 368 167 11 40 371 15 351 2.52e-51 175
MsaG042403 AT2G42280.3 36.034 358 162 11 40 361 15 341 2.33e-46 162
MsaG042403 AT1G51140.1 32.031 384 199 12 32 373 15 378 2.32e-41 149
MsaG042403 AT2G43140.2 40.234 256 123 7 122 371 72 303 4.84e-39 141
MsaG042403 AT2G43140.1 43.784 185 79 4 188 371 46 206 1.15e-37 135
MsaG042403 AT1G05805.1 32.368 380 172 11 36 371 17 355 1.57e-36 136
MsaG042403 AT1G35460.1 63.218 87 30 1 285 371 169 253 8.54e-32 121
MsaG042403 AT4G09180.1 53.153 111 52 0 261 371 146 256 3.20e-31 119
MsaG042403 AT2G42280.2 31.731 312 146 11 40 315 15 295 1.09e-22 97.4
MsaG042403 AT2G24260.2 55.072 69 30 1 298 366 34 101 4.90e-17 80.5
MsaG042403 AT2G24260.1 55.072 69 30 1 298 366 137 204 1.32e-16 80.5
MsaG042403 AT4G30980.1 53.623 69 31 1 298 366 129 196 3.82e-16 79.0
MsaG042403 AT1G35460.2 64.286 56 18 1 285 340 169 222 4.50e-16 77.0
MsaG042403 AT4G30980.2 53.623 69 31 1 298 366 177 244 6.02e-16 79.0
MsaG042403 AT5G58010.1 52.174 69 32 1 298 366 98 165 6.68e-16 77.8
MsaG042403 AT4G34530.1 52.308 65 31 0 299 363 172 236 4.37e-14 73.2
MsaG042403 AT1G68920.3 43.011 93 48 1 276 363 274 366 1.70e-13 72.0
MsaG042403 AT1G68920.1 43.011 93 48 1 276 363 275 367 1.83e-13 72.0
MsaG042403 AT1G68920.4 43.011 93 48 1 276 363 275 367 1.83e-13 72.0
MsaG042403 AT1G68920.2 43.011 93 48 1 276 363 275 367 1.83e-13 72.0
MsaG042403 AT3G07340.1 49.231 65 33 0 299 363 258 322 8.65e-13 69.7
MsaG042403 AT3G07340.2 49.231 65 33 0 299 363 258 322 9.96e-13 69.7
MsaG042403 AT1G10120.2 41.379 87 43 1 277 363 192 270 1.08e-12 68.9
MsaG042403 AT1G10120.1 41.379 87 43 1 277 363 192 270 1.08e-12 68.9
MsaG042403 AT1G26260.5 50.769 65 32 0 299 363 201 265 1.29e-12 68.9
MsaG042403 AT1G26260.4 50.769 65 32 0 299 363 223 287 1.30e-12 68.9
MsaG042403 AT1G26260.1 50.769 65 32 0 299 363 223 287 1.30e-12 68.9
MsaG042403 AT1G26260.6 50.769 65 32 0 299 363 223 287 1.30e-12 68.9
MsaG042403 AT1G26260.2 50.769 65 32 0 299 363 223 287 1.30e-12 68.9
MsaG042403 AT1G26260.3 50.769 65 32 0 299 363 172 236 1.58e-12 68.6
MsaG042403 AT5G50915.1 47.692 65 34 0 299 363 136 200 2.19e-12 67.4
MsaG042403 AT5G50915.2 47.692 65 34 0 299 363 136 200 2.19e-12 67.4
MsaG042403 AT5G50915.3 47.692 65 34 0 299 363 136 200 2.30e-12 67.0
MsaG042403 AT5G50915.4 47.692 65 34 0 299 363 136 200 2.30e-12 67.0
MsaG042403 AT5G48560.1 47.692 65 34 0 299 363 301 365 2.32e-12 68.6
MsaG042403 AT5G48560.2 47.692 65 34 0 299 363 301 365 2.48e-12 68.6
MsaG042403 AT4G33880.1 45.349 86 42 2 278 363 249 329 3.24e-12 67.4
MsaG042403 AT3G57800.2 44.776 67 37 0 297 363 202 268 4.22e-12 67.4
MsaG042403 AT4G36540.2 40.476 84 50 0 280 363 122 205 4.45e-12 66.6
MsaG042403 AT4G36540.1 40.476 84 50 0 280 363 122 205 4.52e-12 66.6
MsaG042403 AT2G42300.1 44.776 67 37 0 297 363 183 249 4.79e-12 67.0
MsaG042403 AT2G18300.1 46.154 65 35 0 299 363 185 249 4.94e-12 67.0
MsaG042403 AT2G18300.2 46.154 65 35 0 299 363 185 249 5.05e-12 67.0
MsaG042403 AT3G23690.1 46.154 65 35 0 299 363 191 255 5.26e-12 67.0
MsaG042403 AT2G42300.4 44.776 67 37 0 297 363 183 249 5.63e-12 66.2
MsaG042403 AT2G18300.3 46.154 65 35 0 299 363 185 249 5.68e-12 67.0
MsaG042403 AT1G59640.1 47.692 65 34 0 299 363 136 200 8.10e-12 65.5
MsaG042403 AT1G59640.2 47.692 65 34 0 299 363 136 200 1.28e-11 65.9
MsaG042403 AT1G27740.1 47.143 70 36 1 294 363 162 230 1.73e-11 64.3
MsaG042403 AT1G73830.2 46.154 65 35 0 299 363 147 211 1.85e-11 64.3
MsaG042403 AT1G73830.1 46.154 65 35 0 299 363 147 211 1.96e-11 64.3
MsaG042403 AT1G25330.1 43.243 74 41 1 299 371 104 177 2.62e-11 63.2

Find 64 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACAGAAATGGATTCAAAATT+TGG 0.143373 8:-21338743 MsaT042403.1:CDS
TATTGTATTCCATGTGAAAA+AGG 0.176835 8:+21338479 None:intergenic
ACACTTCCTACCTCTCTTAA+TGG 0.183445 8:+21336994 None:intergenic
AGTTGCCAGAATGTAGATTT+TGG 0.208118 8:-21336150 MsaT042403.1:intron
ACCCTCTCTGCAATGCTTCT+AGG 0.208569 8:+21335991 None:intergenic
ACCACTATCAACCGAATAAT+TGG 0.239497 8:+21338292 None:intergenic
GGATTTCCAAATGGTTCTTT+AGG 0.260650 8:-21338398 MsaT042403.1:CDS
CAATACAATGATTACTCTTA+TGG 0.263413 8:-21338461 MsaT042403.1:CDS
TATATTACCTTATCTGCATT+TGG 0.272226 8:+21335821 None:intergenic
CAATTTGCTTGAAGAGCTTC+AGG 0.284637 8:+21336868 None:intergenic
AGAGAGGTAGGAAGTGTAAA+TGG 0.308528 8:-21336988 MsaT042403.1:CDS
TTCTTCCAAGATGGCTACTA+TGG 0.309052 8:-21336082 MsaT042403.1:CDS
ATCCTTGATTATGTTGAGTT+TGG 0.317397 8:+21338417 None:intergenic
GCGTTAAGCCGGAATTGTTT+TGG 0.328492 8:+21338693 None:intergenic
GTGAGTGGCAAAGCCTCTTT+TGG 0.336425 8:+21336014 None:intergenic
ATATTACCTTATCTGCATTT+GGG 0.367954 8:+21335822 None:intergenic
TCCAATTATTCGGTTGATAG+TGG 0.369287 8:-21338293 MsaT042403.1:intron
CCCTCTCTGCAATGCTTCTA+GGG 0.373214 8:+21335992 None:intergenic
CTTCTCCATAGTAGCCATCT+TGG 0.374024 8:+21336077 None:intergenic
CCTTATCTGCATTTGGGAAA+AGG 0.380651 8:+21335828 None:intergenic
ACTACATCATCTAGTGGATA+TGG 0.382484 8:-21336958 MsaT042403.1:CDS
CATTGTCTCCAAAACAATTC+CGG 0.388810 8:-21338701 MsaT042403.1:CDS
CACTGACAAAGATTCAGAAT+TGG 0.412608 8:+21338520 None:intergenic
AGAAACATGGGAAATGATAA+TGG 0.418925 8:-21336835 MsaT042403.1:CDS
TCAACACCTAAAGAACCATT+TGG 0.425199 8:+21338392 None:intergenic
TTCAATGAAGAACACAGAAA+TGG 0.438657 8:-21338756 MsaT042403.1:CDS
GTCAGTGAAACAAGAAGAAA+AGG 0.444248 8:-21338504 MsaT042403.1:CDS
CCCTAGAAGCATTGCAGAGA+GGG 0.444514 8:-21335992 MsaT042403.1:intron
AATGGTTCTTTAGGTGTTGA+AGG 0.450234 8:-21338389 MsaT042403.1:CDS
TGTAAAATTCGTGCCAAAAG+AGG 0.450273 8:-21336027 MsaT042403.1:CDS
GTCAAATGCTTTGGAAAGTC+AGG 0.462075 8:-21336701 MsaT042403.1:intron
CTAGCTTCACCAATGACTAC+TGG 0.472078 8:-21336792 MsaT042403.1:CDS
ATAATTGCTCCAATCTCATT+AGG 0.473532 8:-21338343 MsaT042403.1:CDS
AGACCTCAGGAAACAACTTA+AGG 0.479589 8:-21335527 MsaT042403.1:intron
AACCTATGTTTGTGTCTACA+AGG 0.486036 8:+21338636 None:intergenic
AGCTAGGCAGACTCAAATGA+TGG 0.490931 8:+21336106 None:intergenic
CATAATCAAGGATTTCCAAA+TGG 0.493678 8:-21338407 MsaT042403.1:CDS
AGAACTATCCCAGTAGTCAT+TGG 0.496050 8:+21336783 None:intergenic
AACTAGCACTGCTGATATGT+TGG 0.496568 8:-21335572 MsaT042403.1:CDS
TACCAAACTCAACATAATCA+AGG 0.522748 8:-21338419 MsaT042403.1:CDS
TTGAGTACATTAAAGACCTC+AGG 0.529279 8:-21335540 MsaT042403.1:CDS
GCAGATACTAACAGAGACTA+AGG 0.529764 8:-21334968 MsaT042403.1:intron
GCCTAGCTCTTCTTCCAAGA+TGG 0.534945 8:-21336091 MsaT042403.1:CDS
GTACCTTAAGTTGTTTCCTG+AGG 0.535536 8:+21335524 None:intergenic
TTTGCACCATTAAGAGAGGT+AGG 0.543973 8:-21337000 MsaT042403.1:CDS
TGAACGATACCGCGTTAAGC+CGG 0.550117 8:+21338682 None:intergenic
TGTATTAAAAGTAGAAACAT+GGG 0.555635 8:-21336847 MsaT042403.1:CDS
AGGCTTGTAAGTAATGAGCT+TGG 0.565645 8:+21338656 None:intergenic
TAGCTTCACCAATGACTACT+GGG 0.565945 8:-21336791 MsaT042403.1:CDS
AGATTCAGAATTGGTAAACA+TGG 0.566542 8:+21338529 None:intergenic
TTGTATTAAAAGTAGAAACA+TGG 0.569384 8:-21336848 MsaT042403.1:CDS
CAGTAGTCATTGGTGAAGCT+AGG 0.577944 8:+21336793 None:intergenic
TGGCATCTTGATAGAGCAAG+AGG 0.582833 8:+21336909 None:intergenic
CAAGCTTTCAACTACTCTGA+AGG 0.588993 8:-21338782 MsaT042403.1:CDS
TGCAATGCTTCTAGGGTGAG+TGG 0.590036 8:+21335999 None:intergenic
CAAGCTACTACATCATCTAG+TGG 0.611174 8:-21336964 MsaT042403.1:CDS
AAAACAATTCCGGCTTAACG+CGG 0.617284 8:-21338691 MsaT042403.1:CDS
GCCATCTTGGAAGAAGAGCT+AGG 0.619465 8:+21336090 None:intergenic
ATCTTGATAGAGCAAGAGGA+TGG 0.627820 8:+21336913 None:intergenic
GCTAGGCAGACTCAAATGAT+GGG 0.628666 8:+21336107 None:intergenic
GCTTTCAACTACTCTGAAGG+TGG 0.629565 8:-21338779 MsaT042403.1:CDS
ACTTTCCAAAGCATTTGACG+TGG 0.642789 8:+21336705 None:intergenic
AGCCTTGTAGACACAAACAT+AGG 0.644549 8:-21338638 MsaT042403.1:intron
ACCCTAGAAGCATTGCAGAG+AGG 0.691130 8:-21335993 MsaT042403.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr8 gene 21334942 21338822 21334942 ID=MsaG042403
Chr8 mRNA 21334942 21338822 21334942 ID=MsaT042403.1;Parent=MsaG042403
Chr8 exon 21334942 21334986 21334942 ID=MsaT042403.1.exon7;Parent=MsaT042403.1
Chr8 CDS 21334942 21334986 21334942 ID=cds.MsaT042403.1;Parent=MsaT042403.1
Chr8 exon 21335528 21335596 21335528 ID=MsaT042403.1.exon6;Parent=MsaT042403.1
Chr8 CDS 21335528 21335596 21335528 ID=cds.MsaT042403.1;Parent=MsaT042403.1
Chr8 exon 21335829 21335894 21335829 ID=MsaT042403.1.exon5;Parent=MsaT042403.1
Chr8 CDS 21335829 21335894 21335829 ID=cds.MsaT042403.1;Parent=MsaT042403.1
Chr8 exon 21335993 21336163 21335993 ID=MsaT042403.1.exon4;Parent=MsaT042403.1
Chr8 CDS 21335993 21336163 21335993 ID=cds.MsaT042403.1;Parent=MsaT042403.1
Chr8 exon 21336702 21337024 21336702 ID=MsaT042403.1.exon3;Parent=MsaT042403.1
Chr8 CDS 21336702 21337024 21336702 ID=cds.MsaT042403.1;Parent=MsaT042403.1
Chr8 exon 21338294 21338560 21338294 ID=MsaT042403.1.exon2;Parent=MsaT042403.1
Chr8 CDS 21338294 21338560 21338294 ID=cds.MsaT042403.1;Parent=MsaT042403.1
Chr8 exon 21338639 21338822 21338639 ID=MsaT042403.1.exon1;Parent=MsaT042403.1
Chr8 CDS 21338639 21338822 21338639 ID=cds.MsaT042403.1;Parent=MsaT042403.1
Gene Sequence

>MsaT042403.1

ATGAGCATTGTGTATACTCAAGCTTTCAACTACTCTGAAGGTGGTTCAATGAAGAACACAGAAATGGATTCAAAATTTGGTTACTCACAAACACAACAACATTGTCTCCAAAACAATTCCGGCTTAACGCGGTATCGTTCAGCTCCAAGCTCATTACTTACAAGCCTTGTAGACACAAACATAGAAATGGAAACCATGTTTACCAATTCTGAATCTTTGTCAGTGAAACAAGAAGAAAAGGACCCTTTTTCACATGGAATACAATACAATGATTACTCTTATGGATCTCAAAATCAGATAAATTACCAAACTCAACATAATCAAGGATTTCCAAATGGTTCTTTAGGTGTTGAAGGCAATGTTTTTGATGGTTCTTCAAATAATTGCTCCAATCTCATTAGGCAAAAGAGTTCTCCTGCTGAGTTTTTCTCCAATTATTCGGTTGATAGTGGTTTTGCACCATTAAGAGAGGTAGGAAGTGTAAATGGACAAGCTACTACATCATCTAGTGGATATGGTACTTTGAACTTCTCATCTAGACCATCCTCTTGCTCTATCAAGATGCCACAAATTGTTGAAAATGAACCTGAAGCTCTTCAAGCAAATTGTATTAAAAGTAGAAACATGGGAAATGATAATGGTATCACAAAATGTTACATGCCTAGCTTCACCAATGACTACTGGGATAGTTCTACTTCTACATTCAGTGCTCCAAAAAATGCTACTAATAAGGGTGAATTCATGTTTTCCACGTCAAATGCTTTGGAAAGTCAGAATGTAGATTTTGGATACCAAAAACTTGGTTTGACCCATCATTTGAGTCTGCCTAGCTCTTCTTCCAAGATGGCTACTATGGAGAAGTTTTTACACGTTCAAGGATCTGTTCCATGTAAAATTCGTGCCAAAAGAGGCTTTGCCACTCACCCTAGAAGCATTGCAGAGAGGGAAAGAAGAATAAGAATTAGTGCAAGAATAAAAAAACTTCAAGACCTTTTCCCAAATGCAGATAAGCAAACTAGCACTGCTGATATGTTGGATGAAGCAGTTGAGTACATTAAAGACCTCAGGAAACAACTTAAGATACTAACAGAGACTAAGGCAAAGTGCAGTTGTACAAGTAATTAG
Protein sequence

>MsaT042403.1

MSIVYTQAFNYSEGGSMKNTEMDSKFGYSQTQQHCLQNNSGLTRYRSAPSSLLTSLVDTNIEMETMFTNSESLSVKQEEKDPFSHGIQYNDYSYGSQNQINYQTQHNQGFPNGSLGVEGNVFDGSSNNCSNLIRQKSSPAEFFSNYSVDSGFAPLREVGSVNGQATTSSSGYGTLNFSSRPSSCSIKMPQIVENEPEALQANCIKSRNMGNDNGITKCYMPSFTNDYWDSSTSTFSAPKNATNKGEFMFSTSNALESQNVDFGYQKLGLTHHLSLPSSSSKMATMEKFLHVQGSVPCKIRAKRGFATHPRSIAERERRIRISARIKKLQDLFPNADKQTSTADMLDEAVEYIKDLRKQLKILTETKAKCSCTSN*