AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG012723


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG012723 MtrunA17_Chr3g0087771 91.484 411 14 2 1 395 1 406 0.0 768
MsaG012723 MtrunA17_Chr8g0351881 48.889 405 146 10 10 385 18 390 4.21e-99 300
MsaG012723 MtrunA17_Chr1g0174271 35.610 410 184 16 14 383 1 370 2.27e-49 171
MsaG012723 MtrunA17_Chr2g0329041 36.580 421 204 18 20 389 1 409 7.22e-49 170
MsaG012723 MtrunA17_Chr4g0032951 33.102 432 195 15 30 390 25 433 4.66e-46 163
MsaG012723 MtrunA17_Chr7g0258181 39.583 240 107 5 166 383 92 315 6.01e-42 149
MsaG012723 MtrunA17_Chr4g0014771 68.235 85 27 0 303 387 110 194 3.04e-34 125
MsaG012723 MtrunA17_Chr1g0213791 60.577 104 40 1 281 384 236 338 2.97e-31 121
MsaG012723 MtrunA17_Chr4g0074161 54.545 66 29 1 310 375 205 269 4.82e-15 76.3
MsaG012723 MtrunA17_Chr3g0131771 53.846 65 30 0 311 375 147 211 3.43e-14 73.2
MsaG012723 MtrunA17_Chr1g0190731 47.727 88 38 3 288 375 177 256 2.34e-13 70.9
MsaG012723 MtrunA17_Chr8g0339091 50.769 65 32 0 311 375 291 355 3.31e-13 70.9
MsaG012723 MtrunA17_Chr7g0234761 50.769 65 32 0 311 375 317 381 3.34e-13 70.9
MsaG012723 MtrunA17_Chr1g0152131 47.761 67 35 0 309 375 258 324 4.66e-13 70.5
MsaG012723 MtrunA17_Chr8g0365941 50.769 65 32 0 311 375 305 369 5.21e-13 70.5
MsaG012723 MtrunA17_Chr3g0144641 50.769 65 32 0 311 375 191 255 5.23e-13 70.1
MsaG012723 MtrunA17_Chr5g0421111 43.011 93 48 1 288 375 337 429 1.99e-12 68.6
MsaG012723 MtrunA17_Chr4g0035101 49.231 65 33 0 311 375 143 207 2.51e-12 67.4
MsaG012723 MtrunA17_Chr8g0385911 49.231 65 33 0 311 375 145 209 3.02e-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
MsaG012723 AT2G42280.1 36.031 383 176 13 34 389 17 357 4.89e-47 164
MsaG012723 AT1G51140.1 32.741 394 212 12 19 385 11 378 2.30e-44 158
MsaG012723 AT2G42280.3 35.150 367 169 13 34 373 17 341 3.58e-40 146
MsaG012723 AT2G43140.1 50.714 140 56 3 259 389 77 212 2.05e-38 137
MsaG012723 AT1G05805.1 34.465 383 182 17 32 388 21 360 9.70e-38 140
MsaG012723 AT2G43140.2 50.714 140 56 3 259 389 174 309 1.69e-37 138
MsaG012723 AT1G35460.1 67.857 84 27 0 306 389 176 259 1.27e-33 126
MsaG012723 AT4G09180.1 53.782 119 51 2 273 389 146 262 6.98e-32 122
MsaG012723 AT1G35460.2 72.000 50 14 0 303 352 173 222 5.64e-17 80.1
MsaG012723 AT2G42280.2 29.907 321 158 12 34 328 17 296 1.67e-16 80.1
MsaG012723 AT2G24260.2 56.061 66 28 1 310 375 34 98 1.64e-15 76.3
MsaG012723 AT2G24260.1 56.061 66 28 1 310 375 137 201 5.41e-15 76.3
MsaG012723 AT5G58010.1 48.235 85 33 3 301 375 79 162 5.99e-15 75.5
MsaG012723 AT4G30980.1 54.545 66 29 1 310 375 129 193 1.16e-14 74.7
MsaG012723 AT4G30980.2 54.545 66 29 1 310 375 177 241 1.32e-14 75.1
MsaG012723 AT4G34530.1 52.308 65 31 0 311 375 172 236 9.33e-14 72.4
MsaG012723 AT5G50915.1 50.769 65 32 0 311 375 136 200 2.63e-13 70.5
MsaG012723 AT5G50915.2 50.769 65 32 0 311 375 136 200 2.63e-13 70.5
MsaG012723 AT5G50915.3 50.769 65 32 0 311 375 136 200 3.34e-13 69.7
MsaG012723 AT5G50915.4 50.769 65 32 0 311 375 136 200 3.34e-13 69.7
MsaG012723 AT1G25330.1 47.692 65 34 0 311 375 104 168 4.98e-13 68.6
MsaG012723 AT1G68920.3 50.769 65 32 0 311 375 302 366 7.35e-13 70.5
MsaG012723 AT1G68920.1 50.769 65 32 0 311 375 303 367 7.71e-13 70.1
MsaG012723 AT1G68920.4 50.769 65 32 0 311 375 303 367 7.71e-13 70.1
MsaG012723 AT1G68920.2 50.769 65 32 0 311 375 303 367 7.71e-13 70.1
MsaG012723 AT3G07340.1 50.769 65 32 0 311 375 258 322 1.15e-12 69.7
MsaG012723 AT3G07340.2 50.769 65 32 0 311 375 258 322 1.25e-12 69.3
MsaG012723 AT1G26260.4 50.769 65 32 0 311 375 223 287 1.59e-12 68.9
MsaG012723 AT1G26260.1 50.769 65 32 0 311 375 223 287 1.59e-12 68.9
MsaG012723 AT1G26260.6 50.769 65 32 0 311 375 223 287 1.59e-12 68.9
MsaG012723 AT1G26260.2 50.769 65 32 0 311 375 223 287 1.59e-12 68.9
MsaG012723 AT1G26260.5 50.769 65 32 0 311 375 201 265 1.60e-12 68.9
MsaG012723 AT1G26260.3 50.769 65 32 0 311 375 172 236 1.82e-12 68.6
MsaG012723 AT1G10120.2 41.379 87 43 1 289 375 192 270 2.69e-12 68.2
MsaG012723 AT1G10120.1 41.379 87 43 1 289 375 192 270 2.69e-12 68.2
MsaG012723 AT5G48560.1 49.231 65 33 0 311 375 301 365 3.46e-12 68.2
MsaG012723 AT5G48560.2 49.231 65 33 0 311 375 301 365 3.52e-12 68.2
MsaG012723 AT4G36540.2 41.463 82 48 0 294 375 124 205 8.19e-12 66.2
MsaG012723 AT4G36540.1 41.463 82 48 0 294 375 124 205 8.40e-12 65.9
MsaG012723 AT1G73830.1 47.692 65 34 0 311 375 147 211 1.12e-11 65.1
MsaG012723 AT1G73830.2 47.692 65 34 0 311 375 147 211 1.14e-11 65.1
MsaG012723 AT2G18300.1 38.889 108 62 1 268 375 146 249 5.16e-11 63.9
MsaG012723 AT2G18300.2 38.889 108 62 1 268 375 146 249 5.22e-11 63.9
MsaG012723 AT2G18300.3 38.889 108 62 1 268 375 146 249 5.81e-11 63.9

Find 59 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAAAATACCTTATCTGATTT+TGG 0.030579 3:+31648725 None:intergenic
CTAGCTTCACCAATGAATTT+TGG 0.135326 3:-31649152 MsaT012723.1:CDS
CTTGATTCTGTCACTAATTC+TGG 0.137372 3:+31648766 None:intergenic
ACCCTCTCTGCAATGCTTCT+TGG 0.180344 3:+31648898 None:intergenic
GACTCTCAAGAAGCAGATTT+TGG 0.193647 3:-31649057 MsaT012723.1:intron
GTACCTGAACTTGTTCTTGT+AGG 0.262088 3:+31648406 None:intergenic
CAGAATGGTAATTATTCTTA+TGG 0.267927 3:-31650320 MsaT012723.1:CDS
TACTTGAAGAATCCATTTCT+TGG 0.275479 3:+31650633 None:intergenic
GATTCCAATCAATCTAAAAT+TGG 0.297971 3:-31650206 MsaT012723.1:CDS
ATGCCACAAATAGCTGAAAA+TGG 0.316152 3:-31649252 MsaT012723.1:CDS
CATTATCAACAACAAAATTC+TGG 0.321728 3:-31650593 MsaT012723.1:CDS
TTTGTAGTTTGGTCACAATT+TGG 0.335830 3:+31649213 None:intergenic
ACAAACCTAGTAAATGAAAA+TGG 0.344072 3:-31649195 MsaT012723.1:CDS
CACAGCAGATATGTTGGATT+TGG 0.344268 3:-31648448 MsaT012723.1:CDS
GGAATTGCTCCAATCTTATT+AGG 0.352113 3:-31650178 MsaT012723.1:CDS
CATTTACTAGGTTTGTAGTT+TGG 0.361798 3:+31649202 None:intergenic
TCCATTTCTGAACTTGTTGA+TGG 0.362031 3:+31650458 None:intergenic
GAAGCTAGGTATGTGACTTT+TGG 0.365896 3:+31649167 None:intergenic
GCAGATACTCACAGATTGTA+AGG 0.393985 3:-31648278 MsaT012723.1:intron
TGTAAAATTCGAGCGAAAAG+AGG 0.401428 3:-31648934 MsaT012723.1:CDS
TCCATCAACAAGTTCAGAAA+TGG 0.409930 3:-31650459 MsaT012723.1:CDS
AAACCTGTGAAGCAAGAAAT+AGG 0.413405 3:-31650359 MsaT012723.1:CDS
TTTGAGCGTTGTTGTCGATA+AGG 0.416455 3:+31650525 None:intergenic
AGAATTGTTCCATCCATTGT+TGG 0.420159 3:+31650409 None:intergenic
AGAATTGTCCCAAAATTCAT+TGG 0.420165 3:+31649143 None:intergenic
TCACCTATTTCTTGCTTCAC+AGG 0.431403 3:+31650356 None:intergenic
CAGAACCATTTGAAAAGCCT+TGG 0.434899 3:+31650279 None:intergenic
TTCTACTAAGATGACATCTA+TGG 0.437415 3:-31648989 MsaT012723.1:CDS
GCTAAGAAGAAACCAAGAAA+TGG 0.440153 3:-31650645 MsaT012723.1:CDS
ATCAATCTAAAATTGGTGTT+AGG 0.440240 3:-31650199 MsaT012723.1:CDS
AAAGCCAATGGCATCTCAAA+TGG 0.469024 3:-31649318 MsaT012723.1:CDS
GTACACTTAACTTCTCATCT+AGG 0.475567 3:-31649296 MsaT012723.1:CDS
TCCAAGAAGCATTGCAGAGA+GGG 0.485454 3:-31648899 MsaT012723.1:intron
GGCCATCTACTAGCTTGAAA+AGG 0.500559 3:-31649275 MsaT012723.1:CDS
AGACCTACAAGAACAAGTTC+AGG 0.503261 3:-31648409 MsaT012723.1:intron
AACAAGCACAGCAGATATGT+TGG 0.521420 3:-31648454 MsaT012723.1:CDS
TGTACCATTTGAGATGCCAT+TGG 0.531059 3:+31649314 None:intergenic
TGATATCATCCAACAATGGA+TGG 0.538943 3:-31650418 MsaT012723.1:CDS
GTAAAATTCGAGCGAAAAGA+GGG 0.539222 3:-31648933 MsaT012723.1:CDS
AATGGTAATTATTCTTATGG+TGG 0.553621 3:-31650317 MsaT012723.1:CDS
CAAAATTCATTGGTGAAGCT+AGG 0.555453 3:+31649153 None:intergenic
GAATCTGTTCCTCAACAGAA+TGG 0.561869 3:-31650335 MsaT012723.1:CDS
AAAATTCTGGACTACTAATG+AGG 0.563972 3:-31650580 MsaT012723.1:CDS
GTAGAAAGCTTTAAAGCCAA+TGG 0.573198 3:-31649330 MsaT012723.1:CDS
TGATATCAACTTGGATAACA+TGG 0.587600 3:+31650433 None:intergenic
AGGTTTGTAAACAACGAGGT+TGG 0.588581 3:+31650545 None:intergenic
ATTGTTGGATGATATCAACT+TGG 0.590635 3:+31650424 None:intergenic
TTATTCTTATGGTGGATCTG+AGG 0.592108 3:-31650309 MsaT012723.1:CDS
GAATAATTACCATTCTGTTG+AGG 0.597552 3:+31650326 None:intergenic
GACAGAATCAAGAAACTGCA+AGG 0.604322 3:-31648755 MsaT012723.1:CDS
TGTAAACAACGAGGTTGGAG+TGG 0.605467 3:+31650550 None:intergenic
ACTAGGAAGACTCAGATGAC+TGG 0.616049 3:+31649014 None:intergenic
TGCAACATTGACATTGAGAG+AGG 0.616387 3:-31649352 MsaT012723.1:CDS
AAAGGATTAAATCAGCTACA+AGG 0.618131 3:+31648214 None:intergenic
GGATCTGAGGTGATTTACCA+AGG 0.635932 3:-31650296 MsaT012723.1:CDS
GTCATCTTAGTAGAAGAACT+AGG 0.642089 3:+31648997 None:intergenic
AAGTTGATATCATCCAACAA+TGG 0.670047 3:-31650422 MsaT012723.1:CDS
ATCCAAGAAGCATTGCAGAG+AGG 0.687513 3:-31648900 MsaT012723.1:CDS
GATAAGGTTTGTAAACAACG+AGG 0.789364 3:+31650541 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr3 gene 31648225 31650687 31648225 ID=MsaG012723
Chr3 mRNA 31648225 31650687 31648225 ID=MsaT012723.1;Parent=MsaG012723
Chr3 exon 31648225 31648296 31648225 ID=MsaT012723.1.exon6;Parent=MsaT012723.1
Chr3 CDS 31648225 31648296 31648225 ID=cds.MsaT012723.1;Parent=MsaT012723.1
Chr3 exon 31648410 31648478 31648410 ID=MsaT012723.1.exon5;Parent=MsaT012723.1
Chr3 CDS 31648410 31648478 31648410 ID=cds.MsaT012723.1;Parent=MsaT012723.1
Chr3 exon 31648733 31648798 31648733 ID=MsaT012723.1.exon4;Parent=MsaT012723.1
Chr3 CDS 31648733 31648798 31648733 ID=cds.MsaT012723.1;Parent=MsaT012723.1
Chr3 exon 31648900 31649069 31648900 ID=MsaT012723.1.exon3;Parent=MsaT012723.1
Chr3 CDS 31648900 31649069 31648900 ID=cds.MsaT012723.1;Parent=MsaT012723.1
Chr3 exon 31649118 31649378 31649118 ID=MsaT012723.1.exon2;Parent=MsaT012723.1
Chr3 CDS 31649118 31649378 31649118 ID=cds.MsaT012723.1;Parent=MsaT012723.1
Chr3 exon 31650138 31650687 31650138 ID=MsaT012723.1.exon1;Parent=MsaT012723.1
Chr3 CDS 31650138 31650687 31650138 ID=cds.MsaT012723.1;Parent=MsaT012723.1
Gene Sequence

>MsaT012723.1

ATGGGTGCTATGTATGAAGAGCTAAGAAGAAACCAAGAAATGGATTCTTCAAGTATTATTCATTCAAAACAACATTATCAACAACAAAATTCTGGACTACTAATGAGGTATAATTCCACTCCAACCTCGTTGTTTACAAACCTTATCGACAACAACGCTCAAAACTTTATCAACAACGAAGAATCGTTTACAAACGAGAGTTATATTCCATCAACAAGTTCAGAAATGGATACCATGTTATCCAAGTTGATATCATCCAACAATGGATGGAACAATTCTGAAGAAAATTTGCAAGAGTTTGATGTGAAACCTGTGAAGCAAGAAATAGGTGAATCTGTTCCTCAACAGAATGGTAATTATTCTTATGGTGGATCTGAGGTGATTTACCAAGGCTTTTCAAATGGTTCTGGTAATGGATTTTATGGCTCTTTTGGTGGAGTAAACACTATGGAGTCAGATGATTCCAATCAATCTAAAATTGGTGTTAGGAATTGCTCCAATCTTATTAGGCAAAAGAGTTCACCTGCTGAGTTTTTCTCTAATGAAAATGGTCTTGCAACATTGACATTGAGAGAGGTAGAAAGCTTTAAAGCCAATGGCATCTCAAATGGTACACTTAACTTCTCATCTAGGCCATCTACTAGCTTGAAAAGGATGCCACAAATAGCTGAAAATGGAATTCAAAGCTTAGAACCAAATTGTGACCAAACTACAAACCTAGTAAATGAAAATGGTAGCTCCAAAAGTCACATACCTAGCTTCACCAATGAATTTTGGGACAATTCTGCATTCAATGCACACAAAACAGAGAAAGCAGATTTTGGCTATCAAAATCTTGGTTTGACCAGTCATCTGAGTCTTCCTAGTTCTTCTACTAAGATGACATCTATGGAGAATTTTCTTCAAATTCAAGGTTCTGTTCCTTGTAAAATTCGAGCGAAAAGAGGGTTTGCAACTCATCCAAGAAGCATTGCAGAGAGGGTCAGAAGAACCAGAATTAGTGACAGAATCAAGAAACTGCAAGGTCTTTTCCCAAAATCAGATAAGCAAACAAGCACAGCAGATATGTTGGATTTGGCAGTTGAGTACATTAAAGACCTACAAGAACAAGTTCAGATACTCACAGATTGTAAGGAAAAATGCAAATGTGCAAGTCATGAGAAGAAACACTGTGAACCTTGTAGCTGA

Protein sequence

>MsaT012723.1

MGAMYEELRRNQEMDSSSIIHSKQHYQQQNSGLLMRYNSTPTSLFTNLIDNNAQNFINNEESFTNESYIPSTSSEMDTMLSKLISSNNGWNNSEENLQEFDVKPVKQEIGESVPQQNGNYSYGGSEVIYQGFSNGSGNGFYGSFGGVNTMESDDSNQSKIGVRNCSNLIRQKSSPAEFFSNENGLATLTLREVESFKANGISNGTLNFSSRPSTSLKRMPQIAENGIQSLEPNCDQTTNLVNENGSSKSHIPSFTNEFWDNSAFNAHKTEKADFGYQNLGLTSHLSLPSSSTKMTSMENFLQIQGSVPCKIRAKRGFATHPRSIAERVRRTRISDRIKKLQGLFPKSDKQTSTADMLDLAVEYIKDLQEQVQILTDCKEKCKCASHEKKHCEPCS*